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Survey of molecular profiling during human colon cancer development and progression by immunohistochemical staining on tissue microarray
AIM: To explore the molecular events taking place during human colon cancer development and progression through high-throughput tissue microarray analysis. METHODS: We constructed two separate tissue microarrays containing 1.0 mm or 1.5 mm cylindrical samples acquired from 112 formalin-fixed and paraffin-embedded blocks, including carcinomas (n = 85), adenomatous polyps (n = 18), as well as normal para-cancerous colon tissues (n = 9). Immunohistochemical staining was applied to the analysis of the consecutive tissue microarray sections with antibodies for 11 different proteins, including p53, p21, bcl-2, bax, cyclin D1, PTEN, p-Akt1, ?-catenin, c-myc, nm23-h1 and Cox-2. RESULTS: The protein expressions of p53, bcl-2, bax, cyclin D1, ?-catenin, c-myc, Cox-2 and nm23-h1 varied significantly among tissues from cancer, adenomatous polyps and normal colon mucosa (P = 0.003, P = 0.001, P = 0.000, P = 0.000, P = 0.034, P = 0.003, P = 0.002, and P = 0.007, respectively). Chi-square analysis showed that the statistically significant variables were p53, p21, bax, ?-catenin, c-myc, PTEN, p-Akt1, Cox-2 and nm23-h1 for histological grade (P = 0.005, P = 0.013, P = 0.044, P = 0.000, P = 0.000, P = 0.029, P = 0.000, P = 0.008, and P = 0.000, respectively), ?-catenin, c-myc and p-Akt1 for lymph node metastasis (P = 0.011, P = 0.005, and P = 0.032, respectively), ?-catenin, c-myc, Cox-2 and nm23-h1 for distance metastasis (P = 0.020, P = 0.000, P = 0.026, and P = 0.008, respectively), and cyclin D1, ?-catenin, c-myc, Cox-2 and nm23h1 for clinical stages (P = 0.038, P = 0.008, P = 0.000, P = 0.016, and P = 0.014, respectively). CONCLUSION: Tissue microarray immunohistochemical staining enables high-throughput analysis of genetic alterations contributing to human colon cancer development and progression. Our results implicate the potential roles of p53, cyclin D1, bcl-2, bax, Cox-2, ?-catenin and c-myc in development of human colon cancer and that of bcl-2, nm23-h1, PTEN and p-Akt1 in progression of human colon cancer.
Chen, Wei-Chang; Lin, Mao-Song; Zhang, Bao-Feng; Fang, Jing; Zhou, Qiong; Hu, Ying; Gao, Heng-Jun
Multicomponent Analysis of the Pancreatic Adenocarcinoma Progression Model Using a Pancreatic Intraepithelial Neoplasia Tissue Microarray
A multistep model for pancreatic adenocarcinoma has been proposed recently. In this model, well-defined, noninvasive ductal lesions are recognized as precursors of invasive cancer and have been classified under the nomenclature of pancreatic intraepithelial neoplasia, or PanIN. Increasing evidence suggests that PanINs represent true neoplasms of the pancreatic ductal epithelium, accumulating histologic and genetic abnormalities in their progression toward invasive
Anirban Maitra; N Volkan Adsay; Pedram Argani; Christine Iacobuzio-Donahue; Angelo De Marzo; John L Cameron; Charles J Yeo; Ralph H Hruban
Role of the mTOR Pathway in the Progression and Recurrence of Bladder Cancer: An Immunohistochemical Tissue Microarray Study
Purpose Numerous trials have been conducted to develop new treatment regimens for superficial and invasive bladder cancer, because there is an urgent need to identify novel agents to prevent the recurrence and progression of these cancers. We evaluated the prognostic and biological significance of mTOR pathway-related markers in patients with bladder cancer who had undergone transurethral resection of their bladder tumors and radical cystectomy. Materials and Methods We retrieved 208 bladder cancer specimens collected from patients between 1989 and 2007 and constructed a tissue microarray comprising 208 tumor samples and 25 benign urothelium samples. Immunohistochemical staining was performed for mTOR, phosphorylated (phos) S6, and phos4E-BP1. The pattern, percentage, and intensity of staining for all three markers were evaluated. Results The median age at diagnosis of the patient cohort was 67 years (range: 29-87 years), and the median follow-up was 72 months (range: 1-257 months). The expression of phos4E-BP1 was higher in the bladder cancer cohort than in the benign cohort, whereas phosS6 expression was lower in the bladder cancer cohort than in the benign cohort. The expression of phosS6 was significantly higher in high-grade bladder cancer (p<0.01). There was a significant positive correlation between the H-scores of mTOR and phos4E-BP1 (coefficient of correlation, r=0.37, p<0.01) as well as between the H-scores of mTOR and phosS6 (r=0.17, p<0.05). In the multivariate analysis, strong phosS6 expression predicted shorter progression (p<0.01; hazard ratio [HR], 2.516) and disease-specific survival (p<0.01; HR, 2.396) but not overall survival (p=0.112), whereas strong phos4E-BP1 expression was a predictor of disease-specific survival (p<0.05; HR, 2.105). Moreover, strong phosS6 expression predicted shorter recurrence-free (p<0.05) and progression-free (p<0.05) survival in the superficial bladder cancer cohort. Conclusions Our results demonstrate that mTOR pathway activation, as assessed by phos4E-BP1 phosphorylation, is related to bladder cancer tumorigenesis and that S6 protein phosphorylation is associated with a high level of disease recurrence and progression and poor cancer-specific survival.
Park, Se Jun; Lee, Tae Jin
Tissue microarrays: construction and use.
Tissue microarrays (TMAs) enable high-throughput tissue analysis by selecting a large number of -paraffin-embedded donor tissue block cores and transferring these tissue cores into a positionally encoded array in the recipient TMA block. Once TMAs are constructed, a variety of analysis may be performed on the arrays including histochemical, immunohistochemical, or immunofluorescent staining, and in situ hybridization for DNA or RNA. TMAs offer a cost-effective method for performing parallel analysis of a large number of tissue samples. In this chapter we outline the method of TMA construction with an emphasis on providing useful information in the analysis of a variety of pancreatic neoplasms, including pancreatic adenocarcinomas and pre-invasive lesions. The technique of TMA construction in this chapter is restricted to the use of formalin-fixed paraffin-embedded tissue. PMID:23359147
Remotti, Helen
Quantification of Subcellular Molecules in Tissue Microarray
Quantifying expression levels of proteins with sub cellular resolution is critical to many applications ranging from biomarker discovery to treatment planning. In this paper, we present a fully automated method and a new metric that quantifies the expression of target proteins in immunohisto-chemically stained tissue microarray (TMA) samples. The proposed metric is superior to existing intensity or ratio-based methods. We
Ali Can; Musodiq O. Bello; Michael J. Gerdes
Segmentation of prostate cancer tissue microarray images
NASA Astrophysics Data System (ADS)
Prostate cancer is diagnosed by histopathology interpretation of hematoxylin and eosin (H and E)-stained tissue sections. Gland and nuclei distributions vary with the disease grade. The morphological features vary with the advance of cancer where the epithelial regions grow into the stroma. An efficient pathology slide image analysis method involved using a tissue microarray with known disease stages. Digital 24-bit RGB images were acquired for each tissue element on the slide with both 10X and 40X objectives. Initial segmentation at low magnification was accomplished using prior spectral characteristics from a training tissue set composed of four tissue clusters; namely, glands, epithelia, stroma and nuclei. The segmentation method was automated by using the training RGB values as an initial guess and iterating the averaging process 10 times to find the four cluster centers. Labels were assigned to the nearest cluster center in red-blue spectral feature space. An automatic threshold algorithm separated the glands from the tissue. A visual pseudo color representation of 60 segmented tissue microarray image was generated where white, pink, red, blue colors represent glands, epithelia, stroma and nuclei, respectively. The higher magnification images provided refined nuclei morphology. The nuclei were detected with a RGB color space principle component analysis that resulted in a grey scale image. The shape metrics such as compactness, elongation, minimum and maximum diameters were calculated based on the eigenvalues of the best-fitting ellipses to the nuclei.
Cline, Harvey E.; Can, Ali; Padfield, Dirk
Automated evaluation and normalization of immunohistochemistry on tissue microarrays with a DNA microarray scanner.
Hundreds of tissue samples may be assembled in a tissue microarray format for simultaneous immunostaining assessment of protein expression profiling. A DNA microarray two-color laser scanner was used for automated analysis of tissue microarray indirect immunofluorescence. On sections from both a human lung adenocarcinoma and a squamous cell carcinoma tissue microarray, fluorescence intensity for two epidermal growth factor receptors (EGFR and c-erbB2) correlates with diagnostic pathologic assessment, indicating that immunohistochemistry quantitation can be achieved. Importantly, double-label indirect immunofluorescence detection with the cDNA scanner demonstrates that one reference antigen can normalize tumor marker immunosignal for the cellular content of tissue microarray tissue cores. Therefore, DNA microarray scanners and associated image analysis software provide general and efficient analysis of tissue microarray immunostaining, including estimation of specific protein expression levels. PMID:12866417
Haedicke, Wolfgang; Popper, Helmut H; Buck, Charles R; Zatloukal, Kurt
Tissue Microarray: A rapidly evolving diagnostic and research tool
Tissue microarray is a recent innovation in the field of pathology. A microarray contains many small representative tissue samples from hundreds of different cases assembled on a single histologic slide, and therefore allows high throughput analysis of multiple specimens at the same time. Tissue microarrays are paraffin blocks produced by extracting cylindrical tissue cores from different paraffin donor blocks and re-embedding these into a single recipient (microarray) block at defined array coordinates. Using this technique, up to 1000 or more tissue samples can be arrayed into a single paraffin block. It can permit simultaneous analysis of molecular targets at the DNA, mRNA, and protein levels under identical, standardized conditions on a single glass slide, and also provide maximal preservation and use of limited and irreplaceable archival tissue samples. This versatile technique, in which data analysis is automated facilitates retrospective and prospective human tissue studies. It is a practical and effective tool for high-throughput molecular analysis of tissues that is helping to identify new diagnostic and prognostic markers and targets in human cancers, and has a range of potential applications in basic research, prognostic oncology and drug discovery. This article summarizes the technical aspects of tissue microarray construction and sectioning, advantages, application, and limitations.
Jawhar, Nazar M.T.
Fast quantification of immunohistochemistry tissue microarrays in lung carcinoma
Tissue microarrays (TMAs) are an effective tool for high-throughput molecular analysis of tissues to help identify new diagnostic and prognostic markers and targets in human cancers. We have developed a fully automated method for rapid, continuous and quantitative analysis of TMAs based on immunohistochemistry. The method deals with complex and varying tissue architectures, segments tumour cells from normal cells, conducts
Ching-Wei Wang
TmaDB: a repository for tissue microarray data
Background: Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations (at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can
Archana Sharma-oates; Philip Quirke; David R. Westhead
Assessing the Application of Tissue Microarray Technology to Kidney Research
Tissue microarray (TMA) is a new high-throughput method that enables simultaneous analysis of the profiles of protein expression in multiple tissue samples. TMA technology has not previously been adapted for physiological and pathophysiological studies of rodent kidneys. We have evaluated the validity and reliability of using TMA to assess protein expression in mouse and rat kidneys. A representative TMA block
Ming-Zhi Zhang; Yinghao Su; Bing Yao; Wei Zheng; Mark deCaestecker; Raymond C. Harris
Classification of breast tissue-microarray spots using texton histograms
Breast-tissue microarrays facilitate the survey of very large numbers of tumours but their scoring by pathologists is time consuming, typically highly quantised and not without error. Automated segmentation of cells and intra-cellular compartments in such data can be problematic for reasons that include cell overlapping, complex tissue structure, debris, and variable appearance. This paper proposes a computationally efficient approach that
Telmo Amaral; Stephen McKenna; Katherine Robertson; Alastair Thompson
Tissue microarray analysis of interleukin-20 expression
Knowledge about the biological functions and clinical implications of interleukin (IL)-20, a recently discovered cytokine in the IL-10 family, is still incomplete. Our aim was to determine the distribution of IL-20 expression and to delineate the cell types that express IL-20 in healthy and neoplastic tissue, because this information will significantly affect the exploration of its pathophysiological roles. We used
Chung-Hsi Hsing; Chung-Liang Ho; Lih-Yun Chang; Yi-Lin Lee; Shih-Sung Chuang; Ming-Shi Chang
Application of tissue microarray for atherectomized tissues from peripheral arterial disease
It is not easy to apply tissue microarray (TMA) to atherectomized tissues from peripheral arterial disease because of their physical properties. We introduce a new TMA application technique for atherectomized tissues. Using a pre-made plastic TMA cassette and TMA punch device, we successfully made the TMA block containing 40 vertically oriented atherectomized tissue samples from 10 patients. The histogram of
Se Hoon Kim; Dong-Min Kim; Hyosup Shim; Junjeong Choi; Seong Hwan Park; Seung Min Song; Young Ho Shin; Donghoon Choi
Lithographically defined two- and three-dimensional tissue microarrays.
Traditional methods to study normal and pathological development of tissues have been limited by -difficulties in controlling experimental conditions and quantifying biological processes of interest. Here we describe methods to create microarrays of engineered tissues that enable controlled and quantitative investigations. Using soft lithography-based techniques, extracellular matrix proteins can be microcontact printed or micromolded to make two- and three-dimensional micropatterned scaffolds. The ultimate form and resulting properties of the tissue construct are dictated by the geometry of the patterned extracellular matrix components. This chapter describes elastomeric stamp fabrication, microcontact printing and micromolding of extracellular matrix proteins, cell culture in micropatterned substrata, and quantitative immunofluorescence analysis of micropatterned tissues. PMID:20967625
Gomez, Esther W; Nelson, Celeste M
TMA-Combiner, a simple software tool to permit analysis of replicate cores on tissue microarrays
We have previously published a suite of software tools that facilitates the reformulation of tissue microarray (TMA) data so that it may be analyzed using techniques originally devised for analysis of cDNA microarray data. However, current microarray data often feature multiple scores for a given tissue sample and antibody combination. Furthermore, an efficient and systematic method for combining scores that
Chih Long Liu; Kelli D Montgomery; Yasodha Natkunam; Robert B West; Torsten O Nielsen; Maggie C U Cheang; Dmitry A Turbin; Robert J Marinelli; Matt van de Rijn; John P T Higgins
Web-based tissue microarray image data analysis: Initial validation testing through prostate cancer Gleason grading
Tissue microarray technology promises to enhance tissue-based molecular research by allowing improved conservation of tissue resources and experimental reagents, improved internal experimental control, and increased sample numbers per experiment. Organized, well-validated collection and analysis of the voluminous image data produced by tissue microarray technology is critical to maximize its value. Web-based technology for visual analysis and searchable storage of microarray
G. Steven Bova; Giovanni Parmigiani; Jonathan I Epstein; Thomas Wheeler; Neil R Mucci; Mark A Rubin
TAMEE: data management and analysis for tissue microarrays
Background With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. Results TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator. Conclusion We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from .
Thallinger, Gerhard G; Baumgartner, Kerstin; Pirklbauer, Martin; Uray, Martina; Pauritsch, Elke; Mehes, Gabor; Buck, Charles R; Zatloukal, Kurt; Trajanoski, Zlatko
Image quantification of high-throughput tissue microarray
NASA Astrophysics Data System (ADS)
Tissue microarray (TMA) technology allows rapid visualization of molecular targets in thousands of tissue specimens at a time and provides valuable information on expression of proteins within tissues at a cellular and sub-cellular level. TMA technology overcomes the bottleneck of traditional tissue analysis and allows it to catch up with the rapid advances in lead discovery. Studies using TMA on immunohistochemistry (IHC) can produce a large amount of images for interpretation within a very short time. Manual interpretation does not allow accurate quantitative analysis of staining to be undertaken. Automatic image capture and analysis has been shown to be superior to manual interpretation. The aims of this work is to develop a truly high-throughput and fully automated image capture and analysis system. We develop a robust colour segmentation algorithm using hue-saturation-intensity (HSI) colour space to provide quantification of signal intensity and partitioning of staining on high-throughput TMA. Initial segmentation results and quantification data have been achieved on 16,000 TMA colour images over 23 different tissue types.
Wu, Jiahua; Dong, Junyu; Zhou, Huiyu
Tissue microarrays: one size does not fit all
Background Although tissue microarrays (TMAs) are commonly employed in clinical and basic-science research, there are no guidelines for evaluating the appropriateness of a TMA for a given biomarker and tumor type. Furthermore, TMA performance across multiple biomarkers has not been systematically explored. Methods A simulated TMA with between 1 and 10 cores was designed to study tumor expression of 6 biomarkers with varied expression patterns (B7-H1, B7-H3, survivin, Ki-67, CAIX, and IMP3) using 100 patients with clear cell renal cell carcinoma (RCC). We evaluated agreement between whole tissue section and TMA immunohistochemical biomarker quantification to assess how many TMA cores are necessary to adequately represent RCC whole tissue section expression. Additionally, we evaluated associations of whole tissue section and TMA expression with RCC-specific death. Results The number of simulated TMA cores necessary to adequately represent whole tissue section quantification is biomarker specific. Although 2-3 cores appeared adequate for B7-H3, Ki-67, CAIX, and IMP3, even as many as 10 cores resulted in poor agreement for B7-H1 and survivin compared to RCC whole tissue sections. While whole tissue section B7-H1 was significantly associated with RCC-specific death, no significant associations were detected using as many as 10 TMA cores, suggesting that TMAs can result in false-negative findings if the TMA is not optimally designed. Conclusions Prior to TMA analysis, the number of TMA cores necessary to accurately represent biomarker expression on whole tissue sections should be established as there is not a one-size-fits-all TMA. We illustrate the use of a simulated TMA as a cost-effective tool for this purpose.
Application of tissue microarray for atherectomized tissues from peripheral arterial disease.
It is not easy to apply tissue microarray (TMA) to atherectomized tissues from peripheral arterial disease because of their physical properties. We introduce a new TMA application technique for atherectomized tissues. Using a pre-made plastic TMA cassette and TMA punch device, we successfully made the TMA block containing 40 vertically oriented atherectomized tissue samples from 10 patients. The histogram of surface areas of tissue cores in the TMA showed a bell-shaped distribution, whereas that of conventionally embedded tissues showed wide distribution. This finding suggests that the TMA method might be a better way of vertical embedding than the conventional method. A TMA block prepared by our method enabled a simultaneous evaluation of the histopathology of vertically oriented atherectomized tissues and the correlation between them with intravascular ultrasound image. In addition, this new method might be applied to various tissues in different ways. PMID:21788106
Kim, Se Hoon; Kim, Dong-Min; Shim, Hyosup; Choi, Junjeong; Park, Seong Hwan; Song, Seung Min; Shin, Young Ho; Choi, Donghoon
Classification and immunohistochemical scoring of breast tissue microarray spots.
Tissue microarrays (TMAs) facilitate the survey of very large numbers of tumors. However, the manual assessment of stained TMA sections constitutes a bottleneck in the pathologist's work flow. This paper presents a computational pipeline for automatically classifying and scoring breast cancer TMA spots that have been subjected to nuclear immunostaining. Spots are classified based on a bag of visual words approach. Immunohistochemical scoring is performed by computing spot features reflecting the proportion of epithelial nuclei that are stained and the strength of that staining. These are then mapped onto an ordinal scale used by pathologists. Multilayer perceptron classifiers are compared with latent topic models and support vector machines for spot classification, and with Gaussian process ordinal regression and linear models for scoring. Intraobserver variation is also reported. The use of posterior entropy to identify uncertain cases is demonstrated. Evaluation is performed using TMA images stained for progesterone receptor. PMID:23715601
Amaral, Telmo; McKenna, Stephen J; Robertson, Katherine; Thompson, Alastair
An adapted tissue microarray for the development of a matrix arrangement of tissue samples.
The arrangement of tissue samples in a matrix, known as the tissue microarray (TMA) method, is a well-recognized method worldwide. This technique makes it possible to assess the expression of molecular markers on a large scale with high yields in terms of time, costs, and archived material. Some researchers are trying to adapt the technique to expand the research possibilities. This study proposes an adaptive simplification of low-cost instruments for obtaining samples that will be used in the construction of the TMA. The use of a manual leather puncher, which has a very low cost and a long expected life and eliminates the need to use a press machine, is a simple and effective alternative to building blocks of tissue microarrays. PMID:22285223
Gurgel, Daniel C; Dornelas, Concei��o A; Lima-J�nior, Roberto C P; Ribeiro, Ronaldo A; Almeida, Paulo R C
Assessing the application of tissue microarray technology to kidney research.
Tissue microarray (TMA) is a new high-throughput method that enables simultaneous analysis of the profiles of protein expression in multiple tissue samples. TMA technology has not previously been adapted for physiological and pathophysiological studies of rodent kidneys. We have evaluated the validity and reliability of using TMA to assess protein expression in mouse and rat kidneys. A representative TMA block that we have produced included: (1) mouse and rat kidney cortex, outer medulla, and inner medulla fixed with different fixatives; (2) rat kidneys at different stages of development fixed with different fixatives; (3) mouse and rat kidneys with different physiological or pathophysiological treatments; and (4) built-in controls. As examples of the utility, immunostaining for cyclooxygenase-2, renin, Tamm Horsfall protein, aquaporin-2, connective tissue growth factor, and synaptopodin was carried out with kidney TMA slides. Quantitative analysis of cyclooxygense-2 expression in kidneys confirms that individual cores provide meaningful representations comparable to whole-kidney sections. These studies show that kidney TMA technique is a promising and useful tool for investigating the expression profiles of proteins of interest in rodent kidneys under different physiological and pathophysiological conditions. PMID:20086233
Zhang, Ming-Zhi; Su, Yinghao; Yao, Bing; Zheng, Wei; Decaestecker, Mark; Harris, Raymond C
The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource
Background Tissue Microarrays (TMAs) have emerged as a powerful tool for examining the distribution of marker molecules in hundreds of different tissues displayed on a single slide. TMAs have been used successfully to validate candidate molecules discovered in gene array experiments. Like gene expression studies, TMA experiments are data intensive, requiring substantial information to interpret, replicate or validate. Recently, an open access Tissue Microarray Data Exchange Specification has been released that allows TMA data to be organized in a self-describing XML document annotated with well-defined common data elements. While this specification provides sufficient information for the reproduction of the experiment by outside research groups, its initial description did not contain instructions or examples of actual implementations, and no implementation studies have been published. The purpose of this paper is to demonstrate how the TMA Data Exchange Specification is implemented in a prostate cancer TMA. Results The Cooperative Prostate Cancer Tissue Resource (CPCTR) is funded by the National Cancer Institute to provide researchers with samples of prostate cancer annotated with demographic and clinical data. The CPCTR now offers prostate cancer TMAs and has implemented a TMA database conforming to the new open access Tissue Microarray Data Exchange Specification. The bulk of the TMA database consists of clinical and demographic data elements for 299 patient samples. These data elements were extracted from an Excel database using a transformative Perl script. The Perl script and the TMA database are open access documents distributed with this manuscript. Conclusions TMA databases conforming to the Tissue Microarray Data Exchange Specification can be merged with other TMA files, expanded through the addition of data elements, or linked to data contained in external biological databases. This article describes an open access implementation of the TMA Data Exchange Specification and provides detailed guidance to researchers who wish to use the Specification.
Berman, Jules J; Datta, Milton; Kajdacsy-Balla, Andre; Melamed, Jonathan; Orenstein, Jan; Dobbin, Kevin; Patel, Ashok; Dhir, Rajiv; Becich, Michael J
The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data
Background Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone using the data exchange specification can validate their TMA files using a software implementation written in Perl and distributed as a supplemental file with this publication. Conclusion The TMA data exchange specification is now available in a draft form with community-approved Common Data Elements and a community-approved general file format and data structure. The specification can be freely used by the scientific community. Efforts sponsored by the Association for Pathology Informatics to refine the draft TMA data exchange specification are expected to continue for at least two more years. The interested public is invited to participate in these open efforts. Information on future workshops will be posted at (API we site).
Berman, Jules J; Edgerton, Mary E; Friedman, Bruce A
Evaluation of prognostic indicators using validated canine insulinoma tissue microarrays.
Tissue microarray (TMA) technology allows analysis of multiple tumour samples simultaneously on a single slide. The aim of the present study was to develop and assess a TMA containing 32 primary canine insulinomas and 13 insulinoma metastases. The results of histopathological and immunohistochemical analyses of triplicate core biopsies were compared with those of individual tissue sections using weighted ? statistics. Inter-observer agreement of TMA immunohistochemistry scores were assessed for chromogranin A (CgA), insulin, growth hormone (GH), growth hormone receptor (GHR) and Ki67 index, as well as the prognostic utility of clinicopathological, histopathological and immunohistochemical criteria. There was substantial agreement of scores for histopathological parameters (??=?0.64-0.70) and a substantial to near-perfect agreement for homogenous immunohistochemical parameters (??=?0.69-1.00). Except for GH, which demonstrated heterogeneous staining, there was good to excellent inter-observer agreement for all other immunohistochemical staining scores (intra-class correlation coefficients: 0.70-1.00). On univariate analysis, the presence of nuclear atypia was significantly predictive of disease-free intervals (DFIs) for canine insulinoma, while tumour size, TNM stage, necrosis and Ki67 index were significant in terms of prognosis, with respect to both DFI and survival time. On multivariate analysis, tumour size and Ki67 index retained predictive power for survival time, as did tumour size for DFI. This study confirms the applicability of TMA technology for evaluation of canine insulinoma. PMID:24878267
Buishand, Floryne O; Visser, Judith; Kik, Marja; Gr�ne, Andrea; Keesler, Rebekah I; Briaire-de Bruijn, Inge H; Kirpensteijn, Jolle
Tissue microarrays for miniaturized high-throughput molecular profiling of tumors
New high-throughput screening technologies such as complementary (cDNA) microarrays allow identification of hundreds of candidate genes in one experiment. To prioritize the leads obtained in such studies, it is necessary to analyze a large number of tissues for candidate gene expression. Tissue microarray (TMA) technology greatly facilitates such analyses. In this method, hundreds of minute tissue samples (0.6-mm diameter) can
Ronald Simon; Guido Sauter
Gene discovery in bladder cancer progression using cDNA microarrays.
To identify gene expression changes along progression of bladder cancer, we compared the expression profiles of early-stage and advanced bladder tumors using cDNA microarrays containing 17,842 known genes and expressed sequence tags. The application of bootstrapping techniques to hierarchical clustering segregated early-stage and invasive transitional carcinomas into two main clusters. Multidimensional analysis confirmed these clusters and more importantly, it separated carcinoma in situ from papillary superficial lesions and subgroups within early-stage and invasive tumors displaying different overall survival. Additionally, it recognized early-stage tumors showing gene profiles similar to invasive disease. Different techniques including standard t-test, single-gene logistic regression, and support vector machine algorithms were applied to identify relevant genes involved in bladder cancer progression. Cytokeratin 20, neuropilin-2, p21, and p33ING1 were selected among the top ranked molecular targets differentially expressed and validated by immunohistochemistry using tissue microarrays (n = 173). Their expression patterns were significantly associated with pathological stage, tumor grade, and altered retinoblastoma (RB) expression. Moreover, p33ING1 expression levels were significantly associated with overall survival. Analysis of the annotation of the most significant genes revealed the relevance of critical genes and pathways during bladder cancer progression, including the overexpression of oncogenic genes such as DEK in superficial tumors or immune response genes such as Cd86 antigen in invasive disease. Gene profiling successfully classified bladder tumors based on their progression and clinical outcome. The present study has identified molecular biomarkers of potential clinical significance and critical molecular targets associated with bladder cancer progression. PMID:12875971
Sanchez-Carbayo, Marta; Socci, Nicholas D; Lozano, Juan Jose; Li, Wentian; Charytonowicz, Elizabeth; Belbin, Thomas J; Prystowsky, Michael B; Ortiz, Angel R; Childs, Geoffrey; Cordon-Cardo, Carlos
Expression analysis of URI/RMP gene in endometrioid adenocarcinoma by tissue microarray immunohistochemistry
Multiple studies have recently demonstrated the oncogenic property of URI (or RMP, a member of the prefoldin family of molecular chaperones) during progression of hepatocellular carcinoma, ovarian cancer, and possibly prostate cancer. Most recently, we have shown that URI/RMP is up-regulated in cervical cancer, another reproductive system tumor beside ovarian and prostate cancers. To investigate if URI/RMP also plays a role in other reproductive system tumors, especially in endometrioid adenocarcinoma, we analyzed URI/RMP expression in a TMA (tissue microarray) containing tissues from 30 cases of endometrioid adenocarcinoma (which covers tumor tissues from Grade I through Grade III) and adjacent endometrium by immunohistochemistry (IHC) and densitometry analysis using image-pro plus 6.0 software. Our results showed that the mean density of URI/RMP expression in cancerous tissue is slightly higher than that of the adjacent endometrial tissue, though not statistically significant (p>0.05). There is no significant difference either between the mean density of Grade III cancerous tissue and that of Grade I and II cancers. Notably, we detected significantly higher signal intensity in cancerous tissue of all 7 Grade III cases than that of their adjacent endometrial tissue (p<0.05), suggesting a correlation of URI/RMP expression with the differentiation and pathological classification of endometrioid adenocarcinoma. Together, our results demonstrate the heterogeneous expression of URI/RMP in endometrioid adenocarcinoma. The higher level of URI/RMP expression in high-grade endometrioid adenocarcinomas compared to tissues of adjacent endometrium or gland suggests a diagnostic and possibly, a prognostic value of URI/RMP in endometrioid adenocarcinoma.
Gu, Junxia; Liang, Yuting; Qiao, Longwei; Li, Xiaoyun; Li, Xingang; Lu, Yaojuan; Zheng, Qiping
Tissue microarray - a valuable method in diagnosis and prognosis of hematological malignances
BACKGROUND: The novel technology of tissue microarray (TMA) allows rapid and cost-effective analy- sis of hundreds of markers on the same set of specimens. Limited amount of tissue that could be ana- lyzed and problem of tissue heterogeneity, are the major drawbacks of TMA technique for immunohis- tochemical characterization of lymphomas. METHODS: In this paper 65 cases of lymphomas were
Goran Marjanovi�
A Prototype for Unsupervised Analysis of Tissue Microarrays for Cancer Research and Diagnostics
The tissue microarray (TMA) technique enables researchers to extract small cylinders of tissue from histological sections and arrange them in a matrix configuration on a recipient paraffin block such that hundreds can be analyzed simultaneously. TMA offers several advantages over traditional specimen preparation by maximizing limited tissue resources and providing a highly efficient means for visualizing molecular targets. By enabling
Wenjin Chen; Michael Reiss; David J. Foran
[Research progress of probe design software of oligonucleotide microarrays].
DNA microarray has become an essential medical genetic diagnostic tool for its high-throughput, miniaturization and automation. The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality. Several sets of probe design software have been developed and are available to perform this work now. Every set of the software aims to different target sequences and shows different advantages and limitations. In this article, the research and development of these sets of software are reviewed in line with three main criteria, including specificity, sensitivity and melting temperature (Tm). In addition, based on the experimental results from literatures, these sets of software are classified according to their applications. This review will be helpful for users to choose an appropriate probe-design software. It will also reduce the costs of microarrays, improve the application efficiency of microarrays, and promote both the research and development (R&D) and commercialization of high-performance probe design software. PMID:24804514
Chen, Xi; Wu, Zaoquan; Liu, Zhengchun
Systematic Validation of Breast Cancer Biomarkers Using Tissue Microarrays: From Construction to Image Analysis
Fundamental changes are occurring in our approach to breast cancer research, including diagnosis and treatment. Omic-based\\u000a discovery approaches, such as DNA-microarray gene expression profiling, are in part responsible for this shift (Brennan et al., 2005; McGee et al., 2006). These high-throughput technologies represent powerful tools capable of identifying breast cancer biomarkers. Promising\\u000a biomarkers can then be studied using tissue microarrays
Catherine M. A. Kelly; Denise N. Ryan; Sarah A. Penny; William M. Gallagher
Epidermal Growth Factor Receptor Expression in Pancreatic Carcinoma Using Tissue Microarray Technique
Background: The effect of overexpression of epidermal growth factor receptor (EGFR) in pancreatic carcinoma is not clear. Utilizing tissue microarrays, we evaluated EGFR expression in pancreatic cancer to determine the association of EGFR expression with histopathologic characteristics and patient outcome. Methods: 71 cases of pancreatic adenocarcinoma and 18 cases of chronic pancreatitis were retrieved from archival files. Tissue cores from
Mark Bloomston; Atul Bhardwaj; E. Christopher Ellison; Wendy L. Frankel
Validation of tissue microarray technology in squamous cell carcinoma of the esophagus
Tissue microarray (TMA) technology has been developed to facilitate high-throughput immunohistochemical and in situ hybridization\\u000a analysis of tissues by inserting small tissue biopsy cores into a single paraffin block. Several studies have revealed novel\\u000a prognostic biomarkers in esophageal squamous cell carcinoma (ESCC) by means of TMA technology, although this technique has\\u000a not yet been validated for these tumors. Because representativeness
Judith Boone; Richard van Hillegersberg; Paul J. van Diest; G. Johan A. Offerhaus; Inne H. M. Borel Rinkes; Fiebo J. W. Ten Kate
Advances in cancer tissue microarray technology: Towards improved understanding and diagnostics
Over the past few years, tissue microarray (TMA) technology has been established as a standard method for assessing the expression of proteins or genes across large sets of tissue specimens. It is being adopted increasingly among leading research institutions around the world and utilized in cancer research in parallel with the cDNA microarray technology. This article summarizes various aspects of cancer understanding and diagnostics in which TMA has had great impact. Although tremendous advances continue to be made to facilitate imaging and archiving of TMA specimens, automatic evaluation and quantitative analysis of TMA still remains an important challenge for modern investigators.
Chen, Wenjin; Foran, David J.
Microarray Evidences the Role of Pathologic Adipose Tissue in Insulin Resistance and Their Clinical Implications
Clustering of insulin resistance and dysmetabolism with obesity is attributed to pathologic adipose tissue. The morphologic hallmarks of this pathology are adipocye hypertrophy and heightened inflammation. However, it's underlying molecular mechanisms remains unknown. Study of gene function in metabolically active tissues like adipose tissue, skeletal muscle and liver is a promising strategy. Microarray is a powerful technique of assessment of gene function by measuring transcription of large number of genes in an array. This technique has several potential applications in understanding pathologic adipose tissue. They are: (1) transcriptomic differences between various depots of adipose tissue, adipose tissue from obese versus lean individuals, high insulin resistant versus low insulin resistance, brown versus white adipose tissue, (2) transcriptomic profiles of various stages of adipogenesis, (3) effect of diet, cytokines, adipokines, hormones, environmental toxins and drugs on transcriptomic profiles, (4) influence of adipokines on transcriptomic profiles in skeletal muscle, hepatocyte, adipose tissue etc., and (5) genetics of gene expression. The microarray evidences of molecular basis of obesity and insulin resistance are presented here. Despite the limitations, microarray has potential clinical applications in finding new molecular targets for treatment of insulin resistance and classification of adipose tissue based on future risk of insulin resistance syndrome.
Mathur, Sandeep Kumar; Jain, Priyanka; Mathur, Prashant
Limitations of tissue microarrays compared with whole tissue sections in survival analysis.
Tissue microarray (TMA) is a promising technique in the evaluation of immunohistochemical markers in tumors and may be used as an alternative for whole sections. However, only a few studies have correlated a clinical outcome with both TMA and results obtained from whole sections. This study compared immunostaining for Ki-67 and p16 in TMA (3 cores from each specimen) and whole sections of 171 cases of stage III epithelial ovarian cancer with clinical data. A high expression of Ki-67 was identified in 85.0, 85.5, 85.8, 90.5 and 84% of cores 1, 2 and 3, TMAs and whole tissue sections, respectively. A high p16 expression was found in 36.5, 31.4, 30.3, 46.3 and 31.0% of cores 1, 2 and 3, TMAs and whole tissue sections, respectively. The high expression of Ki-67 and p16 in whole tissue sections significantly correlated with that of Ki-67 and p16 in core 1 (P<0.0001 and P<0.0001, respectively), core 2 (P<0.0001 and P<0.0001, respectively), core 3 (P<0.0001 and P<0.0001, respectively), and TMAs (P<0.0001 and P<0.0001, respectively). In univariate analysis, a high expression of Ki-67 and p16 in two of the cores; TMA and the whole tissue sections were significantly correlated to disease-related survival (Ki-67: P=0.008, 0.012, 0.012 and 0.0001, respectively, and p16: P=0.0007, 0.0005, 0.0008 and 0.005, respectively). However, in the multivariate analysis only Ki-67 on whole tissue sections retained an independent prognostic significance (P=0.025). We concluded that more studies, with a higher number of cores, are necessary to determine the efficacy of TMA in reflecting the prognostic value of different antibodies. Morever, evaluation of this method is crucial for each type of tumor and each separate antigen. It is also essential to confirm the clinical correlations on the whole sections before investigating the same parameters on TMA. PMID:22966388
Khouja, M Haysam; Baekelandt, Mark; Sarab, Agkha; Nesland, Jahn M; Holm, Ruth
Tape transfer sectioning of tissue microarrays introduces nonspecific immunohistochemical staining artifacts.
Tissue microarrays place tens to hundreds of formalin fixed, paraffin embedded tissue cores into a paraffin block in a systematic grid pattern that permits their simultaneous evaluation in a single section. The fragmented nature of the tissue cores often makes sectioning of tissue microarrays difficult so that the resulting disks of tissue lose their shape, fracture or fall out of the paraffin section altogether. We have evaluated an alternative sectioning protocol for stabilizing the tissue microarray surface by placing an adhesive tape "window" over the face of the paraffin block prior to sectioning. Once sectioned, the tape/sections are transferred directly onto coated microscope slides, thereby avoiding routine floating of sections on a water bath. After sectioning with either the tape transfer or standard protocols, slides were stained either using hematoxylin and eosin or immunohistochemistry using antibodies to S-100 protein and the tissue specific antigens, keratin (AE1/3) and the leukocyte common antigen CD45. We found that the tape method produced thicker sections that were darker and more densely packed with loss of tissue definition compared to sections prepared using water bath flotation. Quantitative image analysis of immunohistochemical staining demonstrated that the tape method produced a higher incidence of nonspecific staining, which raised the potential for false positive staining. PMID:21091080
Catchpoole, D; Mackie, N; McIver, S; Chetcuti, A; Henwood, A; Graf, N; Arbuckle, S
Tissue MicroArray: a Distributed Grid Approach for Image Analysis
The Tissue MicroArray (TMA) technique is assuming even more importance. Digital images acquisition becomes fundamental to provide an automatic system for subsequent analysis. The accuracy of the results depends on the image resolution, which has to be very high in order to provide as many details as possible. Lossless formats are more suitable to bring information, but data file size
Federica VITI; Ivan MERELLI; Antonella GALIZIA
Reliability of cyclin A assessment on tissue microarrays in breast cancer compared to conventional histological slides
Cyclin A has in some studies been associated with poor breast cancer survival, although all studies have not confirmed this. Its prognostic significance in breast cancer needs evaluation in larger studies. Tissue microarray (TMA) technique allows a simultaneous analysis of large amount of tumours on a single microscopic slide. This makes a rapid screening of molecular markers in large amount
K Aaltonen; C Ahlin; R-M Amini; L Salonen; M-L Fj�llskog; P Heikkil�; H Nevanlinna; C Blomqvist
Immunoexpression of pRb and EGFR using tissue microarray (TMA) technique - a preliminary study
Purpose: To assess the expression of pRb and EGFR in oral epithelial lesions using TMA technique. Methods: Paraffin embedded specimens were selected from the archives of the Diagnostic Laboratories at the Faculty of Dentistry, University of Malaya and Universiti Kebangsaan Malaysia. Selected epithelial areas were cored and developed into tissue microarray blocks. A total of 32 samples for pRb and
N. P. Kipli; C. S. Cheong; R. B. Zain; S. Hamid; K. P. Lim; T. Abraham; M. S. Ismail; H. M. Hussaini
Hierarchical Normalized Cuts: Unsupervised Segmentation of Vascular Biomarkers from Ovarian Cancer Tissue Microarrays
Research has shown that tumor vascular markers (TVMs) may serve as potential OCa biomarkers for prognosis prediction. One such TVM is ESM-1, which can be visualized by staining ovarian Tissue Microarrays (TMA) with an antibody to ESM-1. The ability to quickly and quantitatively estimate vascular stained regions may yield an im- age based metric linked to disease survival and outcome.
Andrew Janowczyk; Sharat Chandran; Rajendra Singh; Dimitra Sasaroli; George Coukos; Michael D. Feldman; Anant Madabhushi
Image microarrays derived from tissue microarrays (IMA-TMA): New resource for computer-aided diagnostic algorithm development
Background: Conventional tissue microarrays (TMAs) consist of cores of tissue inserted into a recipient paraffin block such that a tissue section on a single glass slide can contain numerous patient samples in a spatially structured pattern. Scanning TMAs into digital slides for subsequent analysis by computer-aided diagnostic (CAD) algorithms all offers the possibility of evaluating candidate algorithms against a near-complete repertoire of variable disease morphologies. This parallel interrogation approach simplifies the evaluation, validation, and comparison of such candidate algorithms. A recently developed digital tool, digital core (dCORE), and image microarray maker (iMAM) enables the capture of uniformly sized and resolution-matched images, with these representing key morphologic features and fields of view, aggregated into a single monolithic digital image file in an array format, which we define as an image microarray (IMA). We further define the TMA-IMA construct as IMA-based images derived from whole slide images of TMAs themselves. Methods: Here we describe the first combined use of the previously described dCORE and iMAM tools, toward the goal of generating a higher-order image construct, with multiple TMA cores from multiple distinct conventional TMAs assembled as a single digital image montage. This image construct served as the basis of the carrying out of a massively parallel image analysis exercise, based on the use of the previously described spatially invariant vector quantization (SIVQ) algorithm. Results: Multicase, multifield TMA-IMAs of follicular lymphoma and follicular hyperplasia were separately rendered, using the aforementioned tools. Each of these two IMAs contained a distinct spectrum of morphologic heterogeneity with respect to both tingible body macrophage (TBM) appearance and apoptotic body morphology. SIVQ-based pattern matching, with ring vectors selected to screen for either tingible body macrophages or apoptotic bodies, was subsequently carried out on the differing TMA-IMAs, with attainment of excellent discriminant classification between the two diagnostic classes. Conclusion: The TMA-IMA construct enables and accelerates high-throughput multicase, multifield based image feature discovery and classification, thus simplifying the development, validation, and comparison of CAD algorithms in settings where the heterogeneity of diagnostic feature morphologic is a significant factor.
Hipp, Jennifer A.; Hipp, Jason D.; Lim, Megan; Sharma, Gaurav; Smith, Lauren B.; Hewitt, Stephen M.; Balis, Ulysses G. J.
Distribution of AQP2 and AQP3 water channels in human tissue microarrays
SummaryThe objective of this investigation was to use semi-quantitative immunohistochemistry to determine the distribution and expression levels of AQP2 and AQP3 proteins in normal human Tissue MicroArrays. Expression of the vasopressin regulated AQP2 was observed in a limited number of tissues. AQP2 was prominent in the apical and subapical plasma membranes of cortical and medullary renal collecting ducts. Surprisingly, weak
A. Mobasheri; S. Wray; D. Marples
A DNA microarray survey of gene expression in normal human tissues
Background Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states. Comparatively little is known about the genes expressed across the gamut of normal human tissues. Systematic studies of global gene-expression patterns, by linking variation in the expression of specific genes to phenotypic variation in the cells or tissues in which they are expressed, provide clues to the molecular organization of diverse cells and to the potential roles of the genes. Results Here we describe a systematic survey of gene expression in 115 human tissue samples representing 35 different tissue types, using cDNA microarrays representing approximately 26,000 different human genes. Unsupervised hierarchical cluster analysis of the gene-expression patterns in these tissues identified clusters of genes with related biological functions and grouped the tissue specimens in a pattern that reflected their anatomic locations, cellular compositions or physiologic functions. In unsupervised and supervised analyses, tissue-specific patterns of gene expression were readily discernable. By comparative hybridization to normal genomic DNA, we were also able to estimate transcript abundances for expressed genes. Conclusions Our dataset provides a baseline for comparison to diseased tissues, and will aid in the identification of tissue-specific functions. In addition, our analysis identifies potential molecular markers for detection of injury to specific organs and tissues, and provides a foundation for selection of potential targets for selective anticancer therapy.
Shyamsundar, Radha; Kim, Young H; Higgins, John P; Montgomery, Kelli; Jorden, Michelle; Sethuraman, Anand; van de Rijn, Matt; Botstein, David; Brown, Patrick O; Pollack, Jonathan R
Cell and Tissue Microarray Technologies for Protein and Nucleic Acid Expression Profiling
Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform.
Cardano, Marina; Diaferia, Giuseppe R.; Falavigna, Maurizio; Spinelli, Chiara C.; Sessa, Fausto; DeBlasio, Pasquale
Creation, Validation, and Quantitative Analysis of Protein Expression in Vascular Tissue Microarrays
Summary Seventeen tissue microarrays (TMAs) were generated containing over 1,200 vascular tissues to create a global survey of human vasculature. We validate these TMAs by comparing the disease characteristics in these representative sections to the larger vessels and through demonstrating correlations in staining for 3 separate immunohistochemical antibodies in duplicate sections. Background Tissue microarrays (TMAs) are collections of multiple tissue cores placed in parallel in a single acceptor block and traditionally used to investigate protein expression in neoplastic tissues. We validated the use of TMAs to investigate protein expression in vascular segments. Methods Vascular tissues were collected from 100 adult subjects undergoing autopsy. A diverse set of vessels were harvested and arrayed over 17 TMAs. 1,377 unique tissues, each with a 1.5 mm feature size were analyzed using histochemical and immunohistochemical (IHC) diaminobenzidine (DAB) methods. Results Histomorphometric analysis of vascular disease demonstrated the TMA features captured the majority of the vascular alterations (intimal hyperplasia and atherosclerosis) seen in the original blood vessel section. Measurements of IHC staining intensity based on color deconvolution were used to quantify antigen abundance in defined regions of interest (ROI). Validation was performed using antibodies to connective tissue growth factor (CTGF), receptor for advanced glycation end products (AGER/RAGE) and matrix metalloproteinase 3 (MMP-3). IHC staining was highly correlated between duplicate features from the same vascular site over these three proteins. Conclusion This study validates the use of TMA technology to investigate the vascular wall utilizing staining intensity data.
Halushka, Marc K; Cornish, Toby C.; Lu, Jie; Selvin, Steve; Selvin, Elizabeth
Ultra-fast processing of gigapixel Tissue MicroArray images using High Performance Computing
Background��Tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers.\\u000a The digitised TMA slides or TMA Virtual Slides, are ultra-large digital images, and can contain several hundred samples. The\\u000a processing of such slides is time-consuming, bottlenecking a potentially high throughput platform.\\u000a \\u000a \\u000a \\u000a \\u000a Methods��A High Performance Computing (HPC) platform for the rapid analysis of
Yinhai Wang; David McCleary; Ching-Wei Wang; Paul Kelly; Jackie James; Dean A. Fennell; Peter W. Hamilton
Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray
Diffuse large B-cell lymphoma (DLBCL) can be divided into prognostically impor- tant subgroups with germinal center B- cell-like (GCB), activated B-cell-like (ABC), and type 3 gene expression pro- files using a cDNA microarray. Tissue microarray (TMA) blocks were created from 152 cases of DLBCL, 142 of which had been successfully evaluated by cDNA microarray (75 GCB, 41 ABC, and 26
Christine P. Hans; Dennis D. Weisenburger; Timothy C. Greiner; Randy D. Gascoyne; Jan Delabie; German Ott; H. Konrad Muller-Hermelink; Elias Campo; Rita M. Braziel; Elaine S. Jaffe; Zenggang Pan; Pedro Farinha; Lynette M. Smith; Brunangelo Falini; Alison H. Banham; Andreas Rosenwald; Louis M. Staudt; Joseph M. Connors; James O. Armitage; Wing C. Chan
Associations between Notch2, Akt1 and HER2\\/neu Expression in Invasive Human Breast Cancer: A Tissue Microarray Immunophenotypic Analysis on 98 Patients
Objective: We aimed to investigate the existence of associations between well-established and newly recognized biological and phenotypic features of breast cancer involved in tumor progression and prognosis. Methods: Ninety-eight cases of invasive breast cancer were assessed for the immunohistochemical expression of estrogen and progesterone receptors, Ki-67, HER2, Akt-1, and Notch-2, using the tissue microarray technique. Data regarding tumor histotype, histological
Ada Maria Florena; Claudio Tripodo; Carla Guarnotta; Sabrina Ingrao; Rossana Porcasi; Anna Martorana; Giosu� Lo Bosco; Daniela Cabibi; Vito Franco
Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization.
The identification of differential gene expressionbetween cells is a frequent goal in modern biological research. Here we demonstrate the coupling of representational difference analysis (RDA) of cDNA with microarray analysis of the output for high throughput screening. Two primary Ewing's sarcoma tissue samples with different biological behavior in vivo were compared by RDA: one which was metastatic and progressed rapidly; the other localized and successfully treated. A modified RDA protocol that minimizes the necessary starting material was employed. After a reduced number of subtractive rounds, the output of RDA was shotgun cloned into a plasmid vector. Inserts from individual colonies from the subtracted library were amplified with vector-specific primers and arrayed at high density on glass slides. The arrays were then hybridized with differentially fluorescently labeled starting amplicons from the two tissues and fluorescent signals were measured at each DNA spot. We show that the relative amounts of fluorescent signal correlate well with the abundance of fragments in the RDA amplicon and in the starting mRNA. In our system, we analyzed 192 products and 173 (90%) were appropriately detected as being >2-fold differentially expressed. Fifty unique, differentially expressed clones were identified. Therefore, the use of RDA essentially provides an enriched library of differentially expressed genes, while analysis of this library with microarrays allows rapid and reproducible screening of thousands of DNA molecules simultaneously. The coupling of these two techniques in this system resulted in a large pool of differentially expressed genes.
Welford, S M; Gregg, J; Chen, E; Garrison, D; Sorensen, P H; Denny, C T; Nelson, S F
Evaluation of HER2\\/ neu oncogene status in breast tumors on tissue microarrays
The amplification and\\/or overexpression of the HER-2\\/neu oncogene and its encoded receptor protein are increasingly used for prognostication and prediction of therapeutic response to Herceptin in breast cancer. However, large-scale examination of archival tumor blocks by immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH) is prohibitively laborious and technically challenging. The tissue microarray (TMA) technique enables hundreds of tumors to
Daohai Zhang; Manuel Salto-Tellez; Elaine Do; Thomas Choudary Putti; Evelyn S. C. Koay
Tissue microarray construction from gross specimens: development of a novel simple technique
BackgroundThe tissue microarray (TMA) technique is becoming a useful tool for research and quality control methods in surgical pathology. However, the widespread use of this technique in routine surgical pathology practice, especially in developing nations, is hampered by the high cost of commercially available instruments. The authors describe a novel, inexpensive technique of construction of TMA from gross specimen.MethodsThe authors
Santosh Kumar Sharma; Lopamudra Deka; Ruchika Gupta; Shilpa Gupta; Deepak Kumar Singh; Sompal Singh
A Bayesian Learning Application to Automated Tumour Segmentation for Tissue Microarray Analysis
\\u000a Tissue microarray (TMA) is a high throughput analysis tool to identify new diagnostic and prognostic markers in human cancers.\\u000a However, standard automated method in tumour detection on routine histochemical images for TMA construction is under developed.\\u000a This paper presents a MRF based Bayesian learning system for automated tumour cell detection in routine histochemical virtual\\u000a slides to assist TMA construction. The
Ching-Wei Wang
Expression of SATB1 protein in the ductal breast carcinoma tissue microarrays - preliminary study.
Special AT-rich sequence-binding protein 1 (SATB1) is a nuclear matrix protein which interacts with specific regions of DNA, ensuring its proper organization and function in the cell. The expression of SATB1 was primarily found in thymocytes, but its increased levels were observed in various types of cancers. However, the knowledge of the function and application possibilities of this protein is still limited. The aim of this study was to investigate the expression of SATB1 protein using immunohistochemistry and tissue microarray (TMA) technique and determine its possible relationship with the proliferative marker Ki-67, estrogen a (ER) and progesterone (PR) receptors as well as grade of histological malignancy (G). The study was performed on material of 48 archival invasive ductal breast cancers (IDC). The TMAs were prepared with the use of 0.6 mm diameter punches. Immunohistochemical reactions were carried out using antibodies against Ki-67, ER, PR and SATB1 proteins. The intensity of the nuclear reaction was evaluated using a light microscope and computer-assisted image analysis. Expression of Ki-67 and SATB1 protein was observed in 89.58% and 31.25% of cancer cases, respectively. 62.5% of tumors were classified as ER-positive, and 47.92% as PR-positive. Statistical analysis showed a moderate positive correlation between Ki-67 and SATB1 expression (r = 0.291, p = 0.045 independently on the receptor status, and r = 0.392, p = 0.032 in ER-negative tumors). The expression of the Ki-67 antigen increased with higher grade of histological malignancy (G). The results suggest that SATB1 protein may play an indirect role in the cell proliferation and should be evaluated in relation to the other markers. Further studies concerning determination of its role in cancer progression and metastasis, in terms of application as therapeutic target and prognostic marker, are recommended. PMID:24497139
Kobierzycki, Christopher; Wojnar, Andrzej; Dziegiel, Piotr
Identification of Annexin A1 protein expression in human gastric adenocarcinoma using proteomics and tissue microarray
AIM: To study the differential expression of Annexin A1 (ANXA1) protein in human gastric adenocarcinoma. This study was also designed to analyze the relationship between ANXA1 expression and the clinicopathological parameters of gastric carcinoma. METHODS: Purified gastric adenocarcinoma cells (GAC) and normal gastric epithelial cells (NGEC) were obtained from 15 patients with gastric cancer by laser capture microdissection. All of the peptide specimens were labeled as 18O/16O after trypsin digestion. Differential protein expressions were quantitatively identified between GAC and NGEC by nanoliter-reverse-phase liquid chromatography-mass/mass spectrometry (nano-RPLC-MS/MS). The expressions of ANXA1 in GAC and NGEC were verified by western blot analysis. The tissue microarray containing the expressed ANXA1 in 75 pairs of gastric carcinoma and paracarcinoma specimens was detected by immunohistochemistry (IHC). The relationship between ANXA1 expression and clinicopathological parametes of gastric carcinoma was analyzed. RESULTS: A total of 78 differential proteins were identified. Western blotting revealed that ANXA1 expression was significantly upregulated in GAC (2.17/1, P < 0.01). IHC results showed the correlations between ANXA1 protein expression and the clinicopathological parameters, including invasive depth (T stage), lymph node metastasis (N stage), distant metastasis (M stage) and tumour-lymph node metastasis stage (P < 0.01). However, the correlations between ANXA1 protein expression and the remaining clinicopathological parameters, including sex, age, histological differentiation and the size of tumour were not found (P > 0.05). CONCLUSION: The upregulated ANXA1 expression may be associated with carcinogenesis, progression, invasion and metastasis of GAC. This protein could be considered as a biomarker of clinical prognostic prediction and targeted therapy of GAC.
Zhang, Zhi-Qiang; Li, Xiu-Juan; Liu, Gui-Tao; Xia, Yu; Zhang, Xiang-Yang; Wen, Hao
Progress of science from microscopy to microarrays (part 1): diagnosis of parasitic diseases.
Even though description of the magnifying glass goes back to 1021 by an Arabic physicist in his book, Antony van Leeuwenhoek was the first man to improve the then simple microscope for viewing biological specimens in 1674. This suggests that every discovery has scope for improvement, be it physics or be it biology. In the field of biology, scientists have long studied gene expression as a hallmark of gene activities reflecting the current cell conditions and response to host immune defense systems. These studies have been cumbersome, technically demanding and time-consuming. Application of microarrays has revolutionized this field and help understand the simultaneous expression of thousands of genes in a single sample put onto a single solid support. It is also now possible to compare gene expression in two different cell types, different stages of life cycle or two tissue samples, such as in healthy and diseased ones. Thus microarrays are beginning to dominate other conventional and molecular diagnostic technologies. The microarrays consist of solid supports onto which the nucleic acid sequences from thousands of different genes are immobilized, or attached at fixed locations. These solid supports themselves are usually glass slides, silicon chips or nylon membranes. The nucleic acids are spotted or synthesized directly onto the support. Application of microarrays is new for parasites. Most of these applications are done for monitoring parasite gene expression, to predict the functions of uncharacterized genes, probe the physiologic adaptations made under various environmental conditions, identify virulence-associated genes and test the effects of drug targets. The best examples are vector-borne parasites, such as Plasmodium, Trypanosoma and Leishmania, in which genes expressed, during mammalian and insect host stages, have been elucidated. Microarrays have also been successfully applied to understand the factors responsible to induce transformation from tachyzoite-to-bradyzoite and vice versa in Toxoplasma gondii. Thus microarrays provide a novel tool for diagnosis, prognosis and clinical management of infectious disease. PMID:21938240
Dey, Ayan; Singh, Sarman
Expression of serine protease matriptase in renal cell carcinoma: correlation of tissue microarray immunohistochemical expression analysis results with clinicopathological parameters.
Serine protease matriptase (matriptase) cleaves and activates proteins implicated in the progression of cancer and represents a potential therapeutic target. Immunohistochemical analysis of matriptase was performed in tissue microarrays of 168 renal cell carcinomas (RCCs). All subtypes of RCC showed significant immunohistochemical expression of matriptase. In contrast, no expression occurred in areas of RCC with sarcomatous differentiation (SRCC) and in normal collecting tubules. The matriptase scores were significantly higher in papillary RCC (341+/-28) and clear cell RCC with granular cell differentiation (GRCC; 324+/-27) than in other histologic subtypes of RCC. In GRCC, matriptase scores were correlated with TNM staging and nuclear grading. Matriptase was overexpressed in all subtypes of RCC, and matriptase scores could distinguish between conventional clear cell RCC, GRCC, and SRCC. PMID:16501837
Jin, Jong-Shiaw; Chen, Ann; Hsieh, Dar-Shih; Yao, Chen-Wen; Cheng, Ming-Fang; Lin, Yeh-Feng
Decentralized Data Sharing of Tissue Microarrays for Investigative Research in Oncology
Tissue microarray technology (TMA) is a relatively new approach for efficiently and economically assessing protein and gene expression across large ensembles of tissue specimens. Tissue microarray technology holds great potential for reducing the time and cost associated with conducting research in tissue banking, proteomics, and outcome studies. However, the sheer volume of images and other data generated from even limited studies involving tissue microarrays quickly approach the processing capacity and resources of a division or department. This challenge is compounded by the fact that large-scale projects in several areas of modern research rely upon multi-institutional efforts in which investigators and resources are spread out over multiple campuses, cities, and states. To address some of the data management issues several leading institutions have begun to develop their own �in-house� systems, independently, but such data will be only minimally useful if it isn�t accessible to others in the scientific community. Investigators at different institutions studying the same or related disorders might benefit from the synergy of sharing results. To facilitate sharing of TMA data across different database implementations, the Technical Standards Committee of the Association for Pathology Informatics organized workshops in efforts to establish a standardized TMA data exchange specification. The focus of our research does not relate to the establishment of standards for exchange, but rather builds on these efforts and concentrates on the design, development and deployment of a decentralized collaboratory for the unsupervised characterization, and seamless and secure discovery and sharing of TMA data. Specifically, we present a self-organizing, peer-to-peer indexing and discovery infrastructure for quantitatively assessing digitized TMA�s. The system utilizes a novel, optimized decentralized search engine that supports flexible querying, while guaranteeing that once information has been stored in the system, it will be found with bounded costs.
Chen, Wenjin; Schmidt, Cristina; Parashar, Manish; Reiss, Michael; Foran, David J.
Microarray analysis of the AHR system: Tissue-specific flexibility in signal and target genes
Data mining published microarray experiments require that expression profiles are directly comparable. We performed linear global normalization on the data of 1967 Affymetrix U74av2 microarrays, i.e. the transcriptomes of > 100 murine tissues or cell types. The mathematical transformation effectively nullifies inter-experimental or inter-laboratory differences between microarrays. The correctness of expression values was validated by quantitative RT-PCR. Using the database we analyze components of the aryl hydrocarbon receptor (AHR) signaling pathway in various tissues. We identified lineage and differentiation specific variant expression of AHR, ARNT, and HIF1{alpha} in the T-cell lineage and high expression of CYP1A1 in immature B cells and dendritic cells. Performing co-expression analysis we found unorthodox expression of the AHR in the absence of ARNT, particularly in stem cell populations, and can reject the hypothesis that ARNT2 takes over and is highly expressed when ARNT expression is low or absent. Furthermore the AHR shows no co-expression with any other transcript present on the chip. Analysis of differential gene expression under 308 conditions revealed 53 conditions under which the AHR is regulated, numerous conditions under which an intrinsic AHR action is modified as well as conditions activating the AHR even in the absence of known AHR ligands. Thus meta-analysis of published expression profiles is a powerful tool to gain novel insights into known and unknown systems.
Frericks, Markus [Institut fuer Umweltmedizinische Forschung (IUF) at the Heinrich Heine-University of Duesseldorf, Auf'm Hennekamp 50, 40225 Duesseldorf (Germany); Meissner, Marc [Institut fuer Umweltmedizinische Forschung (IUF) at the Heinrich Heine-University of Duesseldorf, Auf'm Hennekamp 50, 40225 Duesseldorf (Germany); Esser, Charlotte [Institut fuer Umweltmedizinische Forschung (IUF) at the Heinrich Heine-University of Duesseldorf, Auf'm Hennekamp 50, 40225 Duesseldorf (Germany)]. E-mail: firstname.lastname@example.com
Datamining Approach for Automation of Diagnosis of Breast Cancer in Immunohistochemically Stained Tissue Microarray Images
Cancer of the breast is the second most common human neoplasm, accounting for approximately one quarter of all cancers in females after cervical carcinoma. Estrogen receptor (ER), Progesteron receptor and human epidermal growth factor receptor (HER-2/neu) expressions play an important role in diagnosis and prognosis of breast carcinoma. Tissue microarray (TMA) technique is a high throughput technique which provides a standardized set of images which are uniformly stained, facilitating effective automation of the evaluation of the specimen images. TMA technique is widely used to evaluate hormone expression for diagnosis of breast cancer. If one considers the time taken for each of the steps in the tissue microarray process workflow, it can be observed that the maximum amount of time is taken by the analysis step. Hence, automated analysis will significantly reduce the overall time required to complete the study. Many tools are available for automated digital acquisition of images of the spots from the microarray slide. Each of these images needs to be evaluated by a pathologist to assign a score based on the staining intensity to represent the hormone expression, to classify them into negative or positive cases. Our work aims to develop a system for automated evaluation of sets of images generated through tissue microarray technique, representing the ER expression images and HER-2/neu expression images. Our study is based on the Tissue Microarray Database portal of Stanford university at http://tma.stanford.edu/cgi-bin/cx?n=her1, which has made huge number of images available to researchers. We used 171 images corresponding to ER expression and 214 images corresponding to HER-2/neu expression of breast carcinoma. Out of the 171 images corresponding to ER expression, 104 were negative and 67 were representing positive cases. Out of the 214 images corresponding to HER-2/neu expression, 112 were negative and 102 were representing positive cases. Our method has 92.31% sensitivity and 93.18% specificity for ER expression image classification and 96.67% sensitivity and 88.24% specificity for HER-2/neu expression image classification.
Prasad, Keerthana; Zimmermann, Bernhard; Prabhu, Gopalakrishna; Pai, Muktha
Datamining approach for automation of diagnosis of breast cancer in immunohistochemically stained tissue microarray images.
Cancer of the breast is the second most common human neoplasm, accounting for approximately one quarter of all cancers in females after cervical carcinoma. Estrogen receptor (ER), Progesteron receptor and human epidermal growth factor receptor (HER-2/neu) expressions play an important role in diagnosis and prognosis of breast carcinoma. Tissue microarray (TMA) technique is a high throughput technique which provides a standardized set of images which are uniformly stained, facilitating effective automation of the evaluation of the specimen images. TMA technique is widely used to evaluate hormone expression for diagnosis of breast cancer. If one considers the time taken for each of the steps in the tissue microarray process workflow, it can be observed that the maximum amount of time is taken by the analysis step. Hence, automated analysis will significantly reduce the overall time required to complete the study. Many tools are available for automated digital acquisition of images of the spots from the microarray slide. Each of these images needs to be evaluated by a pathologist to assign a score based on the staining intensity to represent the hormone expression, to classify them into negative or positive cases. Our work aims to develop a system for automated evaluation of sets of images generated through tissue microarray technique, representing the ER expression images and HER-2/neu expression images. Our study is based on the Tissue Microarray Database portal of Stanford university at http://tma.stanford.edu/cgi-bin/cx?n=her1, which has made huge number of images available to researchers. We used 171 images corresponding to ER expression and 214 images corresponding to HER-2/neu expression of breast carcinoma. Out of the 171 images corresponding to ER expression, 104 were negative and 67 were representing positive cases. Out of the 214 images corresponding to HER-2/neu expression, 112 were negative and 102 were representing positive cases. Our method has 92.31% sensitivity and 93.18% specificity for ER expression image classification and 96.67% sensitivity and 88.24% specificity for HER-2/neu expression image classification. PMID:21589855
Prasad, Keerthana; Zimmermann, Bernhard; Prabhu, Gopalakrishna; Pai, Muktha
Automatic handling of tissue microarray cores in high-dimensional microscopy images.
This paper describes a specific tool for automatically segmenting and archiving of tissue microarray (TMA) cores in microscopy images at different magnifications. TMA enables researchers to extract the small cylinders of a single tissue (core sections) from histological sections and arrange them in an array on a paraffin block such that hundreds can be analyzed simultaneously. A crucial step to improve the speed and quality of this process is the correct localization of each tissue core in the array. However, usually the tissue cores are not aligned in the microarray, the TMA cores are incomplete and the images are noisy and with distorted colors. We develop a robust framework to handle core sections under these conditions. The algorithms are able to detect, stitch, and archive the TMA cores at different magnifications. Once the TMA cores are segmented they are stored in a relational database allowing their processing for further studies of benign-malignant classification. The method was shown to be reliable for handling the TMA cores and therefore enabling further large-scale molecular pathology research. PMID:24107985
Del Milagro Fernandez-Carrobles, M; Bueno, Gloria; Deniz, Oscar; Salido, Jesus; Garcia-Rojo, Marcial
Multiplex quantitative measurement of mRNAs from fixed tissue microarray sections.
The development of prognostic and diagnostic biomarkers, such as those from gene expression studies, requires independent validation in clinical specimens. Immunohistochemical analysis on tissue microarrays (TMAs) of formalin-fixed paraffin-embedded tissue is often used to increase the statistical power, and it is used more often than in situ hybridization, which can be technically limiting. Herein, we introduce a method for performing quantitative gene expression analysis across a TMA using an adaptation of 2D-RT-qPCR, a recently developed technology for measuring transcript levels in a histologic section while maintaining 2-dimensional positional information of the tissue sample. As a demonstration of utility, a TMA with tumor and normal human prostate samples was used to validate expression profiles from previous array-based gene discovery studies of prostate cancer. The results show that 2D-RT-qPCR expands the utility of TMAs to include sensitive and accurate gene expression measurements. PMID:24809843
Armani, Michael; Tangrea, Michael; Yang, Brian; Rosenberg, Alex; Ylaya, Kris; Morris, Jennifer; Rodriguez-Canales, Jaime; Hanson, Jeffrey; Shapiro, Benjamin; Emmert-Buck, Michael R; Smela, Elisabeth; Hewitt, Stephen M
Tissue Specific Profiling of Females of Schistosoma japonicum by Integrated Laser Microdissection Microscopy and Microarray Analysis
Background The functions of many schistosome gene products remain to be characterized. A major step towards elucidating function of these genes would be in defining their sites of expression. This goal is rendered difficult to achieve by the generally small size of the parasites and the lack of a body cavity, which precludes analysis of transcriptional profiles of the tissues in isolation. Methodology/Principal Findings Here, we describe a combined laser microdissection microscopy (LMM) and microarray analysis approach to expedite tissue specific profiling and gene atlasing for tissues of adult female Schistosoma japonicum. This approach helps to solve the gene characterization �bottle-neck� brought about by acoelomy and the size of these parasites. Complementary RNA obtained after isolation from gastrodermis (parasite gut mucosa), vitelline glands and ovary by LMM were subjected to microarray analyses, resulting in identification of 147 genes upregulated in the gastrodermis, 4,149 genes in the ovary and 2,553 in the vitellaria. Conclusions This work will help to shed light on the molecular pathobiology of this debilitating human parasite and aid in the discovery of new targets for the development of anti-schistosome vaccines and drugs.
Gobert, Geoffrey N.; McManus, Donald P.; Nawaratna, Sujeevi; Moertel, Luke; Mulvenna, Jason; Jones, Malcolm K.
Tissue microarrays are an effective quality assurance tool for diagnostic immunohistochemistry.
There has been considerable variability in the reported results of immunohistochemical staining for some diagnostically relevant antigens. Our objectives in this study were to (1) use a multitumor tissue microarray with tissue from 351 cases received in our department, representing 16 normal tissues and 47 different tumor types, to compare immunohistochemical staining results in our laboratory with published data, using a panel of 22 antibodies; (2) assess interlaboratory variability of immunohistochemical staining for S-100 using this microarray; and (3) test the ability of hierarchical clustering analysis to group tumors by primary site, based on their immunostaining profile. Tissue microarrays consisting of duplicate 0.6-mm cores from blocks identified in the hospital archives were constructed and stained according to our usual protocols. Antibodies directed against the following antigens were used: B72.3, bcl-2, carcinoembryonic antigen, c-kit, pankeratin, CD 68, CD 99, CK 5/6, CK 7, CK 8/18, CK19, CK 20, CK 22, epithelial membrane antigen, estrogen receptor, melan-A, p53, placental alkaline phosphatase, S-100, synaptophysin, thyroid transcription factor-1, and vimentin. Staining results on the array cases were compared with published results, and hierarchical clustering analysis was performed based on the immunohistochemical staining results. Unstained slides of the multitumor tissue microarray were sent to five other diagnostic immunohistochemistry laboratories and stained for S-100 protein. The staining results from the different laboratories were compared. Staining results using our current methods and samples from our laboratory were compatible with those described in the literature for most antigens. Placental alkaline phosphatase staining was not specific with our protocol, showing staining of a broad spectrum of different tumors; this finding initiated a review of our recent requests for placental alkaline phosphatase immunostaining and revealed two instances in which placental alkaline phosphatase positivity was incorrectly interpreted as evidence of a germ cell tumor. S-100 staining was less sensitive but more specific for the diagnosis of melanoma or neural tumor in our laboratory, compared to some published reports. Assessment of interlaboratory variability of S-100 immunostaining showed that there was more frequent staining of carcinomas in some laboratories, resulting in decreased specificity of S-100 staining in distinguishing melanoma from carcinoma. Hierarchical clustering analysis showed a strong trend for tumors to cluster by tissue of origin, but there were significant exceptions. We conclude that multiple-tumor microarrays are an efficient method for assessing the sensitivity and specificity of staining with any antibody used diagnostically. As a tool for quality assurance, they offer the advantage of taking into account local differences in tissue fixation, processing, and staining. They also allow cost-effective assessment of interlaboratory variability in immunohistochemical staining. Results of hierarchical clustering analysis show the potential for panels of immunohistochemical stains to identify the primary site of metastatic carcinomas but also confirm the limitations of currently available antibodies in giving unequivocal tissue-specific staining patterns. PMID:12481020
Hsu, Forrest D; Nielsen, Torsten O; Alkushi, Abdulmohsen; Dupuis, Bev; Huntsman, David; Liu, Chih Long; van de Rijn, Matt; Gilks, C Blake
Molecular and clinico-pathological markers in rectal cancer: a tissue micro-array study
Aims��The aims of the study were to study the effect of pre-operative treatment on the expression of tumour-related proteins and\\u000a to correlate the expression of these proteins with response and survival of patients with advanced rectal cancer.\\u000a \\u000a \\u000a \\u000a Materials and methods��Tissue micro-arrays from pre- and post-treatment biopsies of 99 patients with rectal cancer treated with pre-operative (chemo)radiotherapy\\u000a were stained for epidermal
Annelies Debucquoy; Laurence Goethals; Louis Libbrecht; Christiaan Perneel; Karel Geboes; Nadine Ectors; William H. McBride; Karin Haustermans
Tissue microarray-determined expression profiles of cyclooxygenase-2 in colorectal adenocarcinoma: association with clinicopathological parameters.
Accumulated evidence reveals that increased cyclooxygenase-2 (COX-2) is involved in the development of colorectal cancer. Our purpose was to quantitate COX-2 expression in colorectal cancers using tissue microarray analysis and look for an association with clinicopathological stage. Immunohistochemical analysis of COX-2 was performed in tissue microarray slides containing 90 specimens including 32 well-differentiated, 35 moderately differentiated, and 23 poorly differentiated colorectal adenocarcinomas. All colorectal adenocarcinomas showed significant immunohistochemical expression of COX-2 when compared to normal colon epithelia. However, there was no significant difference in immunostaining scores between poorly, moderately, and well-differentiated tumors (195 +/- 28, 214 +/- 26 and 200 +/- 24, respectively). The COX-2 immunostaining score correlated significantly with T stage (P < 0.05) but not with N or M stage. The positive expression rates of CK20 were 97% for well-differentiated, 94% for moderately differentiated, and 65% for poorly differentiated colorectal adenocarcinomas, suggesting that CK20 may not be an effective discriminator between poorly differentiated colorectal adenocarcinoma and metastatic adenocarcinoma. PMID:17357536
Wu, Chi-Ying; Lee, Wei-Hwa; Wang, Jia-Yi; Chiang, Hung; Chang, Junn-Liang; Tsai, Wen-Chiuan; Sheu, Lai-Fa; Jin, Jong-Shiaw
Production of tissue microarrays, immunohistochemistry staining and digitalization within the human protein atlas.
The tissue microarray (TMA) technology provides the means for high-throughput analysis of multiple tissues and cells. The technique is used within the Human Protein Atlas project for global analysis of protein expression patterns in normal human tissues, cancer and cell lines. Here we present the assembly of 1 mm cores, retrieved from microscopically selected representative tissues, into a single recipient TMA block. The number and size of cores in a TMA block can be varied from approximately forty 2 mm cores to hundreds of 0.6 mm cores. The advantage of using TMA technology is that large amount of data can rapidly be obtained using a single immunostaining protocol to avoid experimental variability. Importantly, only limited amount of scarce tissue is needed, which allows for the analysis of large patient cohorts (1 2). Approximately 250 consecutive sections (4 ?m thick) can be cut from a TMA block and used for immunohistochemical staining to determine specific protein expression patterns for 250 different antibodies. In the Human Protein Atlas project, antibodies are generated towards all human proteins and used to acquire corresponding protein profiles in both normal human tissues from 144 individuals and cancer tissues from 216 different patients, representing the 20 most common forms of human cancer. Immunohistochemically stained TMA sections on glass slides are scanned to create high-resolution images from which pathologists can interpret and annotate the outcome of immunohistochemistry. Images together with corresponding pathology-based annotation data are made publically available for the research community through the Human Protein Atlas portal (www.proteinatlas.org) (Figure 1) (3 4). The Human Protein Atlas provides a map showing the distribution and relative abundance of proteins in the human body. The current version contains over 11 million images with protein expression data for 12.238 unique proteins, corresponding to more than 61% of all proteins encoded by the human genome. PMID:22688270
Kampf, Caroline; Olsson, Ingmarie; Ryberg, Urban; Sj�stedt, Evelina; Pont�n, Fredrik
Imaging mass spectrometry of gastric carcinoma in formalin-fixed paraffin-embedded tissue microarray.
The popularity of imaging mass spectrometry (IMS) of tissue samples, which enables the direct scanning of tissue sections within a short time-period, has been considerably increasing in cancer proteomics. Most pathological specimens stored in medical institutes are formalin-fixed; thus, they had been regarded to be unsuitable for proteomic analyses, including IMS, until recently. Here, we report an easy-to-use screening method that enables the analysis of multiple samples in one experiment without extractions and purifications of proteins. We scanned, with an IMS technique, a tissue microarray (TMA) of formalin-fixed paraffin-embedded (FFPE) specimens. We detected a large amount of signals from trypsin-treated FFPE-TMA samples of gastric carcinoma tissues of different histological types. Of the signals detected, 54 were classified as signals specific to cancer with statistically significant differences between adenocarcinomas and normal tissues. We detected a total of 14 of the 54 signals as histological type-specific with the support of statistical analyses. Tandem MS revealed that a signal specific to poorly differentiated cancer tissue corresponded to histone H4. Finally, we verified the IMS-based finding by immunohistochemical analysis of more than 300 specimens spotted on TMAs; the immunoreactivity of histone H4 was remarkably strong in poorly differentiated cancer tissues. Thus, the application of IMS to FFPE-TMA can enable high-throughput analysis in cancer proteomics to aid in the understanding of molecular mechanisms underlying carcinogenesis, invasiveness, metastasis, and prognosis. Further, results obtained from the IMS of FFPE-TMA can be readily confirmed by commonly used immunohistochemical analyses. PMID:19961487
Morita, Yoshifumi; Ikegami, Koji; Goto-Inoue, Naoko; Hayasaka, Takahiro; Zaima, Nobuhiro; Tanaka, Hiroki; Uehara, Takashi; Setoguchi, Tomohiko; Sakaguchi, Takanori; Igarashi, Hisashi; Sugimura, Haruhiko; Setou, Mitsutoshi; Konno, Hiroyuki
Sampling Strategies for Tissue Microarrays to evaluate biomarkers in Ovarian Cancer
Introduction Tissue microarrays (TMA) enable rapid analysis of biomarkers in large-scale studies involving archival tumor specimens, however their utility in heterogeneous tumors such as ovarian cancer is limited. Methods In this study, immunohistochemical (IHC) analysis was performed on TMAs comprised of epithelial ovarian cancer (EOC) to estimate the prevalence of loss of expression of three mismatch repair (MMR) proteins. TMAs were initially created using cores sampled from the center of donor tissue blocks from 59 EOC cases. Full sections were subsequently created and levels of expression were compared between tissues sampled from the central portion versus the periphery. Follow-up analyses were performed by obtaining cores from the periphery of up to 5 additional donor blocks per case. A linear mixed model for each protein was used to investigate differences between results from the initial and follow-up blocks. Results In the original TMAs created using centrally sampled cores, loss of MMR expression from was noted in 17 (29%) of the 59 cases. By comparison, analyses from peripherally sampled cores revealed loss of expression in only 6 of these 17 cases. For each protein, significant differences (p<0.05) were detected between results from the initial donor block and the majority of the follow-up blocks. Conclusions Our investigations, based on EOC, suggest that sampling variability in protein expression may result when TMAs are used. Thus, at least for EOC, it is important to preferentially sample from the periphery of tumor blocks where exposure to tissue fixatives is optimal.
Permuth-Wey, Jenny; Boulware, David; Valkov, Nikola; Livingston, Sandra; Nicosia, Santo; Lee, Ji-Hyun; Sutphen, Rebecca; Schildkraut, Joellen; Narod, Steven; Parker, Alex; Coppola, Domenico; Sellers, Thomas
Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays
Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5? splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families.
Sugnet, Charles W; Srinivasan, Karpagam; Clark, Tyson A; O'Brien, Georgeann; Cline, Melissa S; Wang, Hui; Williams, Alan; Kulp, David; Blume, John E; Haussler, David; Ares, Manuel
Immunoexpression of DIABLO, AIF and cytochrome C in gastric adenocarcinoma assessed by tissue Microarray.
The aim of this study was to analyze the immunoexpression of (Smac) DIABLO, AIF, cytochrome c, Ki-67 and cleaved caspase-3 in gastric cancer. A tissue microarray (TMA) paraffin block was constructed using gastric adenocarcinoma tissue and adjacent normal adjacent mucosa from 87 patients who had not previously undergone radiotherapy or chemotherapy. Immunohistochemistry was used to evaluate the protein levels. Samples were positive for (Smac) DIABLO in 37 (45.6%) and 37 (46.8%), for AIF in 31 (36.9%) and 36 (45.6%), for cytochrome c in 60 (68.9%) and 44 (54.4%), for Ki-67 in 63 (72.4%) and 52 (61.9%) and for cleaved caspase-3 in 21 (24.1%) and 3 (3.4%) cases of tumor and adjacent normal tissues, respectively. Our results suggest that increased expression of Ki-67 and cleaved caspase-3 could contribute to carcinogenesis. The expression of these proteins indicates an attempt of cells to maintain tissue homeostasis. PMID:23393362
DA Silva, Larissa Comparini; Forones, Nora Manoukian; Ribeiro, Daniel Araki; Ihara, Silvia Sauli Miki; Gomes, Thiago Sim�o; Neto, Ricardo Artigiani; Oshima, Celina Tizuko Fujiyama
Role of ?-catenin expression in paediatric mesenchymal lesions: a tissue microarray-based immunohistochemical study
Beta-catenin is a major protein in the Wnt signalling pathway. Although it has been studied in various types of carcinoma, little is known about its expression in mesenchymal tumours. In this study 41 specimens of a variety of mesenchymal childhood tumours were compared to 24 samples of the corresponding adult tumours to assess the diagnostic value of nuclear ?-catenin expression using tissue microarray-based immunohistochemistry. Similar to adult sarcoma and fibromatosis, ?-catenin was not expressed in the majority of childhood sarcomas, and its nuclear translocation was detected in paediatric fibromatosis; non-negligible levels of nuclear staining in other tumour types demonstrate Wnt pathway activation in mesenchymal neoplasms of childhood and adolescence.
Santoro, A.; Pannone, G.; Errico, M.E.; Bifano, D.; Lastilla, G.; Bufo, P.; Loreto, C.; Donofrio, V.
Apoptotic signal molecules in skin biopsies of cutaneous lupus erythematosus: analysis using tissue microarray.
Cutaneous lupus erythematosus (CLE) is a heterogeneous autoimmune disease. Different pathogenetic mechanisms, including the accumulation of apoptotic keratinocytes in CLE, have been reported. Therefore, we investigated whether CLE and other inflammatory skin diseases differ with regard to the epidermal expression of molecules that are crucial for the initiation and regulation of apoptosis. In this study, 241 skin biopsies from patients with CLE, psoriasis (PSO), lichen planus (LP) and healthy controls (HCs) were analysed immunohistochemically using the tissue microarray (TMA) technique. The TUNEL assay and anti-activated caspase-3 antibodies revealed a significant increase of apoptotic keratinocytes in CLE lesions compared with HCs. Furthermore, we detected a significant increase in the epidermal expression of CD95 in CLE specimens compared with PSO, LP and HCs. These data suggest that the accumulation of apoptotic keratinocytes in CLE might be due to the increased epidermal expression of CD95, resulting in increased activity of the extrinsic apoptotic pathway in the disease. PMID:24079735
Toberer, Ferdinand; Sykora, Jaromir; G�ttel, Daniel; Hartschuh, Wolfgang; Werchau, Siegfried; Enk, Alexander; Joos, Stefan; Krammer, Peter H; Kuhn, Annegret
A Bayesian Learning Application to Automated Tumour Segmentation for Tissue Microarray Analysis
NASA Astrophysics Data System (ADS)
Tissue microarray (TMA) is a high throughput analysis tool to identify new diagnostic and prognostic markers in human cancers. However, standard automated method in tumour detection on routine histochemical images for TMA construction is under developed. This paper presents a MRF based Bayesian learning system for automated tumour cell detection in routine histochemical virtual slides to assist TMA construction. The experimental results show that the proposed method is able to achieve 80% accuracy on average by pixel-based quantitative performance evaluation that compares the automated segmentation outputs with the manually marked ground truth data. The presented technique greatly reduces labor-intensive workloads for pathologists, highly speeds up the process of TMA construction and allows further exploration of fully automated TMA analysis.
Wang, Ching-Wei
High-throughput biomarker segmentation on ovarian cancer tissue microarrays via hierarchical normalized cuts.
We present a system for accurately quantifying the presence and extent of stain on account of a vascular biomarker on tissue microarrays. We demonstrate our flexible, robust, accurate, and high-throughput minimally supervised segmentation algorithm, termed hierarchical normalized cuts (HNCuts) for the specific problem of quantifying extent of vascular staining on ovarian cancer tissue microarrays. The high-throughput aspect of HNCut is driven by the use of a hierarchically represented data structure that allows us to merge two powerful image segmentation algorithms-a frequency weighted mean shift and the normalized cuts algorithm. HNCuts rapidly traverses a hierarchical pyramid, generated from the input image at various color resolutions, enabling the rapid analysis of large images (e.g., a 1500 � 1500 sized image under 6 s on a standard 2.8-GHz desktop PC). HNCut is easily generalizable to other problem domains and only requires specification of a few representative pixels (swatch) from the object of interest in order to segment the target class. Across ten runs, the HNCut algorithm was found to have average true positive, false positive, and false negative rates (on a per pixel basis) of 82%, 34%, and 18%, in terms of overlap, when evaluated with respect to a pathologist annotated ground truth of the target region of interest. By comparison, a popular supervised classifier (probabilistic boosting trees) was only able to marginally improve on the true positive and false negative rates (84% and 14%) at the expense of a higher false positive rate (73%), with an additional computation time of 62% compared to HNCut. We also compared our scheme against a k-means clustering approach, which both the HNCut and PBT schemes were able to outperform. Our success in accurately quantifying the extent of vascular stain on ovarian cancer TMAs suggests that HNCut could be a very powerful tool in digital pathology and bioinformatics applications where it could be used to facilitate computer-assisted prognostic predictions of disease outcome. PMID:22180503
Janowczyk, Andrew; Chandran, Sharat; Singh, Rajendra; Sasaroli, Dimitra; Coukos, George; Feldman, Michael D; Madabhushi, Anant
Variable levels of tissue mosaicism can confound the interpretation of chromosomal microarray results from peripheral blood.
Chromosomal microarray analysis (CMA) has significantly increased the ability to diagnose medical conditions caused by copy-number variation in the human genome. Given that the regions involved in copy-number abnormalities often encompass multiple genes, it has been common practice in recent years to compare the phenotypes of individuals with specific copy-number alterations identified by CMA, with the goal of identifying the critical regions for particular elements of a disease phenotype. It is rarely mentioned that this practice relies heavily on the assumption that the absence of mosaicism on CMA from a peripheral blood sample (the most common source of DNA in current clinical practice) reflects the absence of mosaicism in other tissues. We report here a case that violates that assumption. A 28-year-old male with Charcot-Marie-Tooth disease was found by CMA to have a duplication of 17p12 along with two other abnormalities: A duplication of 12p13.33 translocated to the long arm of chromosome 3 and an interstitial duplication of 12p11.23. The patient did not have any clinical features suggestive of 12p duplication syndrome. Chromosomal microarray analysis on skin fibroblasts revealed the duplications at 17p12 and 12p11.23, but not the terminal duplication of 12p13.33. FISH analysis on skin fibroblasts confirmed the presence of very low levels of mosaicism for the terminal 12p duplication. The case illustrates how the absence of mosaicism in blood is not always indicative of the absence of mosaicism in other tissues. Even in an era of high-throughput, highly accurate DNA-based tests, it is important to remember the limitations of testing before drawing conclusions about the relationship between a test results and a clinical phenotype. PMID:24636861
Pal, Chandni V; Eble, Tanya N; Burnside, Rachel D; Bi, Weimin; Patel, Ankita; Franco, Luis M
Effects of Tissue Handling on RNA Integrity and Microarray Measurements From Resected Breast Cancers
Background Reliable stability and yield of RNA from breast cancer tissues are important for biobanking, clinical trials, and diagnostic testing. Methods Aliquots of fresh primary tumor tissue from 17 surgically resected invasive breast cancers were placed into RNAlater at room temperature after tumor removal (baseline) and up to 3 hours thereafter or were snap frozen at baseline and 40 minutes thereafter. Samples were stored at ?80�C until gene expression profiling with Affymetrix Human Gene U133A microarrays. We evaluated the effects of cold ischemic time (the time from tumor specimen removal to sample preservation) and sample preservation method on RNA yield, Bioanalyzer-based RNA integrity number, microarray-based 3?/5? expression ratios for assessing transcript integrity, and microarray-based measurement of single-gene and multigene expression signatures. The statistical significance of the effects was assessed using linear mixed effects regression models. All statistical tests were two-sided. Results Sample preservation in RNAlater statistically significantly improved RNA integrity compared with snap freezing as assessed by the RNA integrity number, which increased from 7.31 to 8.13 units (difference = 0.82 units, 95% confidence interval [CI] = 0.53 to 1.11 units, P < .001), and RNA yield, which increased threefold from 8.9 to 28.6 ?g (difference = 19.7 ?g, 95% CI = 14.1 to 25.3 ?g, P < .001). Prolonged cold ischemic delay at room temperature before sample stabilization decreased the RNA integrity number by 0.12 units/h (95% CI = 0.02 to 0.23 units/h) compared with a projected average RNA integrity number of 7.39 if no delays were present (P = .008) and decreased the RNA yield by 1.5 ?g/h (95% CI = 0 to 4 ?g/h) from a baseline mean RNA yield of 33.5 ?g if no delays were present (P = .019). Prolonged cold ischemia statistically significantly increased the 3?/5? ratio of control gene transcripts, particularly of STAT1 (P < .001). Snap freezing statistically significantly increased the 3?/5? ratio of three control transcripts (ACTB, GAPDH, and 18S rRNA). Expression levels of single genes and multigene signatures for breast cancer were largely unaffected by sample preservation method or cold ischemia. Conclusions Sample preservation in RNAlater improves RNA yield and quality, whereas cold ischemia increases RNA fragmentation as measured by the 3?/5? expression ratio of control genes. However, expression levels of single genes and multigene signatures that are of diagnostic relevance in breast cancer were mostly unaffected by sample preservation method or prolonged cold ischemic duration.
Hatzis, Christos; Sun, Hongxia; Yao, Hui; Hubbard, Rebekah E.; Meric-Bernstam, Funda; Babiera, Gildy V.; Wu, Yun; Pusztai, Lajos
Immunoprofiles of 11 Biomarkers Using Tissue Microarrays Identify Prognostic Subgroups in Colorectal Cancer1
Abstract BACKGROUND AND AIMS: Genomewide expression profiling has identified a number of genes expressed at higher levels in colorectal cancer (CRC) than in normal tissues. Our objectives in this study were: 1) to test whether genes were also distinct on the protein level; 2) to evaluate these biomarkers in a series of well-characterized CRCs; and 3) to apply hierarchical cluster analysis to the immunohistochemical data. METHODS: Tissue microarrays (TMAs) comprising 351 CRC specimens from 270 patients were constructed to evaluate the genes Adam10, CyclinD1, AnnexinII, NFKB, Casein-kinase-2-beta (CK2B), YB-1, P32, Rad51, c-fos, IGFBP4, and Connexin26 (Cx26). In total, 3,797 samples were analyzed. RESULTS: Unsupervised hierarchical clustering discovered subgroups of CRC that differed by tumor stage and survival. Kaplan-Meier analysis showed that reduced Cx26 expression was significantly associated with shorter patient survival and higher tumor grade (G1/G2 vs G3, P = .02), and Adam10 expression with a higher tumor stage (pT1/2 vs pT3/4, P = .04). CONCLUSIONS: Our study highlights the potential of TMAs for a higher-dimensional analysis by evaluating serial sections of the same tissue core (three-dimensional TMA analysis). In addition, it endorses the use of immunohistochemistry supplemented by hierarchical clustering for the identification of tumor subgroups with diagnostic and prognostic signatures.
Knosel, Thomas; Emde, Anna; Schluns, Karsten; Chen, Yuan; Jurchott, Karsten; Krause, Matthias; Dietel, Manfred; Petersen, Iver
Evaluation of monospecific antibodies: a comparison study with commercial analogs using immunohistochemistry on tissue microarrays.
Generation of monospecific antibodies (msAbs) (multiepitope) through affinity purification of polyclonal antisera is a plausible strategy for high-throughput production of affinity reagents toward large sets of proteins. These antibodies are generated using readily accessible gene sequence information from publicly available databases. The resulting antibodies have the potential to be used in a variety of assays, probing differentially presented and altered proteins with high sensitivity and specificity. In the present study, 48 msAbs were compared with corresponding commercial analogs. Immunohistochemical staining properties were evaluated on tissue microarrays, representing various normal human tissues from 144 different individuals. MsAbs showed similar immunostaining patterns as compared with corresponding commercial analogs in 44 out of totally 48 (92%) antibody pairs analyzed. Although only few antibody pairs showed major discrepancies, minor dissimilarities were frequently seen. Our results suggest that msAbs are reliable and valuable tools in antibody-based proteomics, enabling analysis of protein expression patterns in cells and tissues. High-throughput strategies employing such antibodies provide a consistent approach in the exploration of the human proteome. PMID:18685494
Paavilainen, Linda; Wern�rus, Henrik; Nilsson, Peter; Uhl�n, Mathias; Hober, Sophia; Wester, Kenneth; Pont�n, Fredrik
A metadata-aware application for remote scoring and exchange of tissue microarray images
Background The use of tissue microarrays (TMA) and advances in digital scanning microscopy has enabled the collection of thousands of tissue images. There is a need for software tools to annotate, query and share this data amongst researchers in different physical locations. Results We have developed an open source web-based application for remote scoring of TMA images, which exploits the value of Microsoft Silverlight Deep Zoom to provide a intuitive interface for zooming and panning around digital images. We use and extend existing XML-based standards to ensure that the data collected can be archived and that our system is interoperable with other standards-compliant systems. Conclusion The application has been used for multi-centre scoring of TMA slides composed of tissues from several Phase III breast cancer trials and ten different studies participating in the International Breast Cancer Association Consortium (BCAC). The system has enabled researchers to simultaneously score large collections of TMA and export the standardised data to integrate with pathological and clinical outcome data, thereby facilitating biomarker discovery.
Identification of Novel Tissue-Specific Genes by Analysis of Microarray Databases: A Human and Mouse Model
Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI?s Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved.
Suh, Yeunsu; Davis, Michael E.; Lee, Kichoon
Identification of novel tissue-specific genes by analysis of microarray databases: a human and mouse model.
Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI's Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved. PMID:23741331
Song, Yan; Ahn, Jinsoo; Suh, Yeunsu; Davis, Michael E; Lee, Kichoon
Until recently, diagnostic and prognostic assessment of diseased tissues in a Pathology laboratory relied on histological and immunohistological studies. DNA microarray technology now allows the simultaneous analysis of up to thousands of different genes in histological or cytological specimens. Thus, the microarray techniques offer opportunities for the pathologist to obtain �molecular signatures� of the state of activity of diseased cells
Paul Hofman
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression
Background Type 2 diabetes mellitus (T2DM) is a complex systemic disease, with significant disorders of metabolism. The liver, a central energy metabolic organ, plays a critical role in the development of diabetes. Although gene expression levels are able to be measured via microarray since 1996, it is difficult to evaluate the contributions of one altered gene expression to a specific disease. One of the reasons is that a whole network picture responsible for a specific phase of diabetes is missing, while a single gene has to be put into a network picture to evaluate its importance. In the aim of identifying significant transcriptional regulatory networks in the liver contributing to diabetes, we have performed comprehensive active regulatory network survey by network screening in 4 weeks (w), 8-12 w, and 18-20 w Goto-Kakizaki (GK) rat liver microarray data. Results We identify active regulatory networks in GK rat by network screening in the following procedure. First, the regulatory networks are compiled by using the known binary relationships between the transcriptional factors and their regulated genes and the biological classification scheme, and second, the consistency of each regulatory network with the microarray data measured in GK rat is estimated to detect the active networks under the corresponding conditions. The comprehensive survey of the consistency between the networks and the measured data by the network screening approach in the case of non-insulin dependent diabetes in the GK rat reveals: 1. More pathways are active during inter-middle stage diabetes; 2. Inflammation, hypoxia, increased apoptosis, decreased proliferation, and altered metabolism are characteristics and display as early as 4weeks in GK strain; 3. Diabetes progression accompanies insults and compensations; 4. Nuclear receptors work in concert to maintain normal glycemic robustness system. Conclusion Notably this is the first comprehensive network screening study of non-insulin dependent diabetes in the GK rat based on high throughput data of the liver. Several important pathways have been revealed playing critical roles in the diabetes progression. Our findings also implicate that network screening is able to help us understand complex disease such as diabetes, and demonstrate the power of network systems biology approach to elucidate the essential mechanisms which would escape conventional single gene-based analysis.
Combined Use of Oligonucleotide and Tissue Microarrays Identifies Cancer\\/Testis Antigens as Biomarkers in Lung Carcinoma1
High density oligonucleotide microarrays (OMAs) have been used re- cently to profile gene expression in lung carcinoma tissue homogenates. The length of the lists of potentially interesting genes generated by these studies is daunting, and biological and clinical relevance of these lists remains to be validated. Moreover, specific identification of individual biomarkers that might be used for early detection and
Michio Sugita; Mark Geraci; Bifeng Gao; Roger L. Powell; Fred R. Hirsch; Gary Johnson; Razvan Lapadat; Edward Gabrielson; Roy Bremnes; Paul A. Bunn; Wilbur A. Franklin
Association of adipocyte genes with ASP expression: a microarray analysis of subcutaneous and omental adipose tissue in morbidly obese subjects
BACKGROUND: Prevalence of obesity is increasing to pandemic proportions. However, obese subjects differ in insulin resistance, adipokine production and co-morbidities. Based on fasting plasma analysis, obese subjects were grouped as Low Acylation Stimulating protein (ASP) and Triglyceride (TG) (LAT) vs High ASP and TG (HAT). Subcutaneous (SC) and omental (OM) adipose tissues (n = 21) were analysed by microarray, and
Robin E MacLaren; Wei Cui; HuiLing Lu; Serge Simard; Katherine Cianflone
Microarray Analysis of Lymphatic Tissue Reveals Stage-Specific, Gene Expression Signatures in HIV-1 Infection1
Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. Although each of the three stages has well-known clinical, virologic, and immunologic characteristics, much less is known of the molecular mechanisms underlying each stage. In this study, we report lymphatic tissue microarray analyses, revealing for the first time stage-specific patterns of gene expression during HIV-1 infection. We show that although there is a common set of key genes with altered expression throughout all stages, each stage has a unique gene expression signature. The acute stage is most notably characterized by increased expression of hundreds of genes involved in immune activation, innate immune defenses (e.g., RIG-1, MDA-5, TLR7 and TLR8, PKR, APOBEC3B, 3F, 3G), adaptive immunity, and in the proapoptotic Fas-Fas ligand pathway. Yet, quite strikingly, the expression of nearly all acute stage genes return to baseline levels in the asymptomatic stage, accompanying partial control of infection. This transition from acute to asymptomatic stage is tied to increased expression of a diverse array of immunosuppressive genes (e.g., CLEC12B, ILT4, galectin-3, CD160, BCMA, FGL2, LAG3, GPNMB). In the AIDS stage, decreased expression of numerous genes involved in T cell signaling identifies genes contributing to T cell dysfunction. These common and stage-specific gene expression signatures identify potential molecular mechanisms underlying the host response and the slow, natural course of HIV-1 infection.
Li, Qingsheng; Smith, Anthony J.; Schacker, Timothy W.; Carlis, John V.; Duan, Lijie; Reilly, Cavan S.; Haase, Ashley T.
Recent progress in tissue optical clearing
Tissue optical clearing technique provides a prospective solution for the application of advanced optical methods in life sciences. This paper gives a review of recent developments in tissue optical clearing techniques. The physical, molecular and physiological mechanisms of tissue optical clearing are overviewed and discussed. Various methods for enhancing penetration of optical-clearing agents into tissue, such as physical methods, chemical-penetration enhancers and combination of physical and chemical methods are introduced. Combining the tissue optical clearing technique with advanced microscopy image or labeling technique, applications for 3D microstructure of whole tissues such as brain and central nervous system with unprecedented resolution are demonstrated. Moreover, the difference in diffusion and/or clearing ability of selected agents in healthy versus pathological tissues can provide a highly sensitive indicator of the tissue health/pathology condition. Finally, recent advances in optical clearing of soft or hard tissue for in vivo imaging and phototherapy are introduced.
Zhu, Dan; Larin, Kirill V; Luo, Qingming; Tuchin, Valery V
Identification of tumor epithelium and stroma in tissue microarrays using texture analysis
Background The aim of the study was to assess whether texture analysis is feasible for automated identification of epithelium and stroma in digitized tumor tissue microarrays (TMAs). Texture analysis based on local binary patterns (LBP) has previously been used successfully in applications such as face recognition and industrial machine vision. TMAs with tissue samples from 643 patients with colorectal cancer were digitized using a whole slide scanner and areas representing epithelium and stroma were annotated in the images. Well-defined images of epithelium (n = 41) and stroma (n = 39) were used for training a support vector machine (SVM) classifier with LBP texture features and a contrast measure C (LBP/C) as input. We optimized the classifier on a validation set (n = 576) and then assessed its performance on an independent test set of images (n = 720). Finally, the performance of the LBP/C classifier was evaluated against classifiers based on Haralick texture features and Gabor filtered images. Results The proposed approach using LPB/C texture features was able to correctly differentiate epithelium from stroma according to texture: the agreement between the classifier and the human observer was 97 per cent (kappa value = 0.934, P < 0.0001) and the accuracy (area under the ROC curve) of the LBP/C classifier was 0.995 (CI95% 0.991-0.998). The accuracy of the corresponding classifiers based on Haralick features and Gabor-filter images were 0.976 and 0.981 respectively. Conclusions The method illustrates the capability of automated segmentation of epithelial and stromal tissue in TMAs based on texture features and an SVM classifier. Applications include tissue specific assessment of gene and protein expression, as well as computerized analysis of the tumor microenvironment. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/4123422336534537
Microvessel density is not increased in prostate cancer: digital imaging of routine sections and tissue microarrays.
Angiogenesis is considered a prognostic factor and therapy target in many tumors but remains controversial in prostate cancer. This study compares the microvessel density of normal prostate and prostate cancer of different grades using an automated approach to determine its clinical utility. Neoplastic and normal prostatic tissues from 60 prostatectomies were examined by routine histological sections (group I); 136 prostatectomies were used to create tissue microarrays (group II). Microvessel density was calculated using CD31 immunostaining. Automated Cellular Image System (ChromaVision, San Juan Capistrano, CA) and Aperio automated systems were used to digitally analyze microvessel density in Groups I and II respectively. Microvessel density was not significantly increased in tumor versus normal prostate in Group I (P = .303). Both the mean vessel count and vessel area were significantly higher in normal tissue than in tumor either by Automated Cellular Image System or Aperio analysis (P < .05). Aperio analysis in group II additionally showed significantly higher values in normal tissue for vessel lumen (P < .001), whereas vessel perimeter, wall thickness, vessel compactness, and shape were not significantly different (P > .05). Aperio comparison of low- versus high-grade prostate cancer demonstrated that only mean vessel count was increased in high-grade tumors (P = .047); no other automated parameter in either group showed significant association with Gleason scores. Irrespective of methodology, microvessel density was not increased in prostate cancer compared to normal prostate. The bias of using vascular hot spots that possibly contributed to previous contradictory results has been mitigated by automated microvessel density quantitation here. Similar microvessel density of low- and high-grade tumors indicate that microvessel density is neither an important nor reliable prognostic marker for prostate cancer. PMID:23069258
Tretiakova, Maria; Antic, Tatjana; Binder, David; Kocherginsky, Masha; Liao, Chuanhong; Taxy, Jerome B; Oto, Aytekin
Progression to islet destruction in a cyclophosphamide-induced transgenic model: a microarray overview.
Type 1 diabetes appears to progress not as an uncontrolled autoimmune attack on the pancreatic islet beta-cells, but rather in a highly regulated manner. Leukocytic infiltration of the pancreatic islets by autoimmune cells, or insulitis, can persist for long periods of time before the terminal destruction of beta-cells. To gain insight on the final stage of diabetogenesis, we have studied progression to diabetes in a CD4(+) T-cell receptor transgenic variant of the NOD mouse model, in which diabetes can be synchronously induced within days by a single injection of cyclophosphamide. A time-course analysis of the gene expression profiles of purified islets was performed using microarrays. Contrary to expectations, changes in transcripts subsequent to drug treatment did not reflect a perturbation of gene expression in CD4(+) T-cells or a reduction in the expression of genes characteristic of regulatory T-cell populations. Instead, there was a marked decrease in transcripts of genes specific to B-cells, followed by an increase in transcripts of chemokine genes (cxcl1, cxcl5, and ccl7) and of other genes typical of the myelo-monocytic lineages. Interferon-gamma dominated the changes in gene expression to a striking degree, because close to one-half of the induced transcripts issued from interferon-gamma-regulated genes. PMID:15331540
Matos, Michael; Park, Richard; Mathis, Diane; Benoist, Christophe
Tissue microarray analysis of X-linked inhibitor of apoptosis (XIAP) expression in breast cancer patients.
The goal of this study was to determine the diagnostic and prognostic potential of X-linked inhibitor of apoptosis (XIAP) expression in breast cancer. We analyzed a tissue microarray comprised of 100 breast cancer cases and 70 matched normal samples. Analysis of an online database, which included 2,977 patients, was also performed. There was a significant difference in cytoplasmic expression of XIAP (XIAP-C) between breast cancer tissue and matched normal (p<0.001). Staining of XIAP-C was defined as negative (breast cancer 8.42% vs. normal 30.91%), slight (40.0 vs. 45.45%), moderate (43.16 vs. 23.64%), or high (8.42 vs. 0%). High XIAP-C protein expression correlated with human epidermal growth factor receptor 2 (HER-2) status (p=0.010) and with human p53 mutant-type (P53) status (p=0.039). We found that XIAP expression did not correlate with disease-free survival (p=0.706) and overall survival (p=0.496) of breast cancer patients. An Internet-based system analysis confirmed our results. In the subgroup analysis, basal-like breast cancer patients with high XIAP levels in the tumor had a significantly increased risk of relapse; thus, the up-regulation of XIAP appeared to be predictive of poor relapse-free survival (p=0.013). Kaplan-Meier curves also identified a significant correlation between distant metastasis-free survival and XIAP expression in patients with lymph-node-negative disease (p=0.030). In summary, expression of XIAP-C was significantly higher in breast cancer compared to normal tissue. XIAP-C expression correlated with HER-2 status and may be considered a prognostic biomarker for basal-like breast cancer patients. PMID:24446252
Xu, Ying-Chun; Liu, Qiang; Dai, Jia-Qi; Yin, Zhi-Qiang; Tang, Lei; Ma, Yue; Lin, Xiao-Lin; Wang, Hong-Xia
Assessment of epidermal growth factor receptor (EGFR) expression in primary colorectal carcinomas and their related metastases on tissue sections and tissue microarray
Metastatic colorectal carcinomas (CRC) resistant to chemotherapy may benefit from targeting monoclonal therapy cetuximab when\\u000a they express the epidermal growth factor receptor (EGFR). Because of its clinical implications, we studied EGFR expression\\u000a by immunohistochemistry on tissue sections of primary CRC (n=32) and their related metastases (n=53). A tissue microarray (TMA) was generated from the same paraffin blocks to determine whether
Fr�d�ric Bibeau; Florence Boissi�re-Michot; Jean-Christophe Sabourin; Sophie Gourgou-Bourgade; Mich�le Radal; Fr�d�rique Penault-Llorca; Philippe Rochaix; Laurent Arnould; Marie-Pierre Bralet; David Azria; Marc Ychou
Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues
Background Rice is one of the major crop species in the world helping to sustain approximately half of the global population�s diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray� microarray platform which is suitable for two major rice subspecies, japonica and indica. Results The rice OneArray� 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI�s Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R?=?0.95, p?0.001***). Conclusion The rice OneArray� 22�K microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in rice tissues. The rice OneArray� microarray platform revealed high specificity and sensitivity. Additional information for the rice OneArray� microarray can be found at http://www.phalanx.com.tw/index.php.
Variability in the expression of polycomb proteins in different normal and tumoral tissues. A pilot study using tissue microarrays.
In spite of the known function of polycomb group (PcG) genes in stem cell self-renewal, control of cellular proliferation and differentiation, its role in cancer pathogenesis is still poorly understood. We studied the expression by immunohistochemistry of several PcG-maintenance complex proteins (RING1, RNF2, BMI1, MEL18, HPH1 and RYBP) in nontumoral (154 samples) and tumoral (550 samples) human tissues using Tissue Microarrays. For selected genes (BMI1 and RING1) FISH analysis has been also carried out. PcG proteins had a tissue- and cell-type-specific expression pattern. Some of them were highly selectively expressed, such as HPH1, which was detected in germ cells in testis, pituitary and parathyroid glands and Langerhans islets, and RYBP, which was found in placenta, umbilical cord and thyroid gland. By contrast, RING1 was ubiquitously expressed in every normal tissue analyzed. Changes in expression associated with tumoral transformation have been found for BMI1 and RNF2, which exhibited increased expression in a large series of tumors, including gastrointestinal tumors, pituitary and parathyroid adenomas, and lymphomas, compared with their expression in normal-cell counterparts. The high level of expression of BMI1 protein observed in mantle-cell lymphomas and pituitary adenomas is associated in some cases with amplification of BMI1 locus. These findings imply that upregulation of BMI1 may constitute a malignancy marker in different types of cancer, mainly in lymphoid and endocrine tumors. RING1 was lost in a group of renal-cell carcinomas and testicular germ-cell tumors. Lastly, RYBP is anomalously expressed in Hodgkin's lymphomas and oligodendrogliomas, among others tumors. A significant finding of the study is the identification of unique PcG profiles for some tumors, such as testicular germ-cell tumors, which have high levels of HPH1 expression and loss of RING1 and/or BMI1; pituitary adenomas, which expressed every PcG protein analyzed; and clear-cell renal-cell carcinoma, which was the only tumor other than testicular germ-cell tumors that did not express RING1. PMID:16528373
S�nchez-Beato, Margarita; S�nchez, Esther; Gonz�lez-Carrer�, Joaqu�n; Morente, Manuel; D�ez, Ana; S�nchez-Verde, Lydia; Mart�n, Mar�a Carmen; Cigudosa, Juan C; Vidal, Miguel; Piris, Miguel A
Cell orientation entropy (COrE): predicting biochemical recurrence from prostate cancer tissue microarrays.
We introduce a novel feature descriptor to describe cancer cells called Cell Orientation Entropy (COrE). The main objective of this work is to employ COrE to quantitatively model disorder of cell/nuclear orientation within local neighborhoods and evaluate whether these measurements of directional disorder are correlated with biochemical recurrence (BCR) in prostate cancer (CaP) patients. COrE has a number of novel attributes that are unique to digital pathology image analysis. Firstly, it is the first rigorous attempt to quantitatively model cell/nuclear orientation. Secondly, it provides for modeling of local cell networks via construction of subgraphs. Thirdly, it allows for quantifying the disorder in local cell orientation via second order statistical features. We evaluated the ability of 39 COrE features to capture the characteristics of cell orientation in CaP tissue microarray (TMA) images in order to predict 10 year BCR in men with CaP following radical prostatectomy. Randomized 3-fold cross-validation via a random forest classifier evaluated on a combination of COrE and other nuclear features achieved an accuracy of 82.7 +/- 3.1% on a dataset of 19 BCR and 20 non-recurrence patients. Our results suggest that COrE features could be extended to characterize disease states in other histological cancer images in addition to prostate cancer. PMID:24505786
Lee, George; Ali, Sahirzeeshan; Veltri, Robert; Epstein, Jonathan I; Christudass, Christhunesa; Madabhushi, Anant
Hierarchical normalized cuts: unsupervised segmentation of vascular biomarkers from ovarian cancer tissue microarrays.
Research has shown that tumor vascular markers (TVMs) may serve as potential OCa biomarkers for prognosis prediction. One such TVM is ESM-1, which can be visualized by staining ovarian Tissue Microarrays (TMA) with an antibody to ESM-1. The ability to quickly and quantitatively estimate vascular stained regions may yield an image based metric linked to disease survival and outcome. Automated segmentation of the vascular stained regions on the TMAs, however, is hindered by the presence of spuriously stained false positive regions. In this paper, we present a general, robust and efficient unsupervised segmentation algorithm, termed Hierarchical Normalized Cuts (HNCut), and show its application in precisely quantifying the presence and extent of a TVM on OCa TMAs. The strength of HNCut is in the use of a hierarchically represented data structure that bridges the mean shift (MS) and the normalized cuts (NCut) algorithms. This allows HNCut to efficiently traverse a pyramid of the input image at various color resolutions, efficiently and accurately segmenting the object class of interest (in this case ESM-1 vascular stained regions) by simply annotating half a dozen pixels belonging to the target class. Quantitative and qualitative analysis of our results, using 100 pathologist annotated samples across multiple studies, prove the superiority of our method (sensitivity 81%, Positive predictive value (PPV), 80%) versus a popular supervised learning technique, Probabilistic Boosting Trees (sensitivity, PPV of 76% and 66%). PMID:20425992
Janowczyk, Andrew; Chandran, Sharat; Singh, Rajendra; Sasaroli, Dimitra; Coukos, George; Feldman, Michael D; Madabhushi, Anant
Tissue microarray analysis of cyclin D1 gene amplification and gain in colorectal carcinomas.
Colorectal cancer is one of the most common neoplastic diseases and one of the leading causes of cancer-related deaths. Elevated beta-catenin levels in colorectal cancer result in the binding of beta-catenin to LEF-1 and increased transcriptional activation of the CCND1 gene. Overexpression of cyclin D1 is observed in one third of colorectal tumors. CCND1 amplification is the main cause of protein overexpression in numerous human carcinomas. In colorectal cancer, however, no CCND1 amplification has been reported so far. The aim of this study was to determine the frequency of CCND1 amplifications and gains in a large number of colorectal carcinomas, arranged in a tissue microarray, in order to assess their role in colorectal cancer development. The copy number changes, detected by fluorescence in situ hybridization, were predominantly gains (7.6%) and only rarely amplifications (2.5%). In colorectal cancer, the CCND1 copy number increase was neither associated with the tumor phenotype (stage and grade) nor with the tumor localization (colon, rectum or sigmoid colon). In conclusion, even in a small number of colorectal tumors, CCND1 gene amplification is a possible mechanism for the increase in cyclin D1 oncoprotein. PMID:15557752
Toncheva, D; Petrova, D; Tzenova, V; Dimova, I; Yankova, R; Yordanov, V; Damjanov, D; Todorov, T; Zaharieva, B
Comparison of tissue microarray and full section in immunohistochemistry of gastrointestinal stromal tumors.
The aim of the present study was to compare the efficiency of tissue microarray (TMA) results using immunohistochemistry markers applied to a variety of core sizes and full sections of gastrointestinal stromal tumors (GIST) using performance measures such as core loss rate and concordance rate. Six primary antibody markers (c-Kit, CD34, smooth muscle actin (SMA), S-100, p53, and Ki-67) were used with the TMA technique to analyze 0.6 mm, 2 mm, and 3 mm punch cores of GIST samples from 67 patients. No statistical association was found between core size and loss rate (P= 0.512). TMA results for the 0.6 mm, 2 mm, and 3 mm core showed that all core sizes could statistically significantly reflect full sections with regard to c-Kit, SMA, and S-100 antibodies, but that the 3 mm core section was the most representative except for CD34. With regard to p53 and Ki-67 staining, the 0.6 mm core section was not representative, but the 2 mm and 3 mm core sections could statistically significantly represent full section results. Among them, the 3 mm core section was more accurate than the 2 mm core section. Use of a single 3 mm core size in TMA is suitable for evaluating large numbers of protein and nuclear stains with regard to immunohistochemistry for GIST. PMID:20021609
Kwon, Mi Jung; Nam, Eun Sook; Cho, Seong Jin; Park, Hye Rim; Shin, Hyung Sik; Park, Jun Ho; Park, Chan Heun; Lee, Won Jae
Tissue microarray analysis as a screening tool for neuroendocrine carcinoma of the breast.
Neuroendocrine carcinoma of the breast (NCB) is a fairly recent diagnostic entity added by WHO in 2003. Since then, studies have indicated that NCB potentially displays a worse prognosis than invasive ductal carcinoma. However, due to a lack of standard use of immunohistochemical staining for neuroendocrine markers and the fact that NCB may only show slight neuroendocrine morphology that can easily be overlooked, NCB is often underdiagnosed. Consequently, there is a need for fast and reliable detection method for NCB. Here, we take a first step toward finding an easy way of identifying NCB by investigating the usefulness of tissue microarray (TMA) analysis as a screening tool. We present our findings with regard to sensitivity and specificity compared with whole-mount sections. The material consists of 240 cases of breast cancer divided into 20 TMA blocks that were all immunohistochemically stained for the neuroendocrine markers chromogranin A and synaptophysin. Cases positive in more than 50% of the tumor cells were accepted in accordance with WHO (2003) standards of NCB. Sensitivity and specificity for TMA sections vs whole-mount sections were found to be 100% and 97.8%, respectively, suggesting that TMA analysis is a reliable method for NCB detection. PMID:24283273
Brask, Julie Benedicte; Talman, Maj-Lis M�ller; Wielenga, Vera Timmermans
A Comparison between Manual and Automated Evaluations of Tissue Microarray Patterns of Protein Expression
Tissue microarray technology enables us to evaluate the pattern of protein expression in large numbers of samples. However, manual data acquisition and analysis still represent a challenge because they are subjective and time-consuming. Automated analysis may thus increase the speed and reproducibility of evaluation. However, the reliability of automated analysis systems should be independently evaluated. Herein, the expression of phosphorylated AKT and mTOR was determined by ScanScope XT (Aperio; Vista, CA) and ACIS III (Dako; Glostrup, Denmark) and compared with the manual analysis by two observers. The percentage of labeled pixels or nuclei analysis had a good correlation between human observers and automated systems (? = 0.855 and 0.879 for ScanScope vs. observers and ? = 0.765 and 0.793 for ACIS III vs. observers). The intensity of labeling determined by ScanScope was also correlated with that found by the human observers (correlation index of 0.946 and 0.851 for pAKT and 0.851 and 0.875 for pmTOR). However, the correlation between ACIS III and human observation varied for labeling intensity and was considered poor in some cases (correlation index of 0.718 and 0.680 for pAKT and 0.223 and 0.225 for pmTOR). Thus, the percentage of positive pixels or nuclei determination was satisfactorily performed by both systems; however, labeling intensity was better identified by ScanScope XT.
Alvarenga, Arthur W.; Coutinho-Camillo, Claudia M.; Rodrigues, Bruna R.; Rocha, Rafael M.; Torres, Luiz Fernando B.; Martins, Vilma R.; da Cunha, Isabela W.
Gene-specific fluorescence in-situ hybridization analysis on tissue microarray to refine the region of chromosome 20q amplification in melanoma.
Several comparative genomic hybridization studies provide evidence for overrepresentation of the long arm of chromosome 20 in malignant melanoma. These studies also suggest that chromosome 20q contains genes that may contribute to melanoma pathogenesis. To refine the region of 20q amplification and to identify potential candidate genes involved in melanoma or even in melanoma progression from these regions, we combined fluorescence in-situ hybridization with MYBL2, ZNF217, CYP24 and STK6 specific probes (chromosomal region 20q13.1-q13.2) with high-throughput tissue microarray consisting of 280 primary melanomas and melanoma metastases. Low-level amplification ranging from 0.5 to 2.0% was detected for the tumor-related genes of interest. Higher frequencies of gain when compared with amplification were detected for MYBL2, ZNF217, CYP24 and STK6. Aneusomy of centromere 20 was observed in 29.9% of the analyzed tumors. A significantly higher frequency of ZNF217, CYP24 and STK6 total copy-number increase, as well as aneusomy of centromere 20, was found in the group of metastases when compared with the group of primary melanomas. Despite the technological advantage of fluorescence in-situ hybridization on tissue microarray, which allows refining regions of amplification, we were not able to recognize any of the MYBL2, ZNF217, CYP24 and STK6 genes as a particular relevant gene for melanoma tumorigenesis. PMID:17235240
Koynova, Denitsa K; Jordanova, Ekaterina S; Milev, Angel D; Dijkman, Remco; Kirov, Krassimir S; Toncheva, Draga I; Gruis, Nelleke A
Design and performance of a turbot (Scophthalmus maximus) oligo-microarray based on ESTs from immune tissues.
An expressed sequence tag database from immune tissues was used to design the first high-density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. An Agilent custom oligo-microarray 8 x 15 k (five replicates/gene; eight microarrays/slide) was constructed. The performance of the microarray and the sources of variation along microarray analysis were examined on spleen pools of controls and Aeromonas salmonicida-challenged fish at 3 days postinfection. Only 48 out of 2,716 probes did not show signal of hybridization on the 32 microarrays employed, thus demonstrating the consistency of the bioinformatic applications of our database. An asymmetric hierarchical design was employed to ascertain the noise associated with biological and technical (RNA extraction, labeling, hybridization, slide, and dye bias) factors using 1C and 2C labeling approaches. The high correlation coefficient between replicates at most factors tested demonstrated the high reproducibility of the signal. An analysis of random-effects variance revealed that technical variation was mostly negligible, and biological variation represented the main factor, even using pooled samples. One-color approach performed at least as well as 2C, suggesting their usefulness due to its higher design flexibility and lower cost. A relevant proportion of genes turn out to be differentially labeled depending on fluorophore, which alerts for the likely need of swapping replication in 2C experiments. A set of differentially expressed genes and enriched functions related to immune/defense response were detected at 3 days postchallenging. PMID:19844759
Mill�n, Adri�n; G�mez-Tato, Antonio; Fern�ndez, Carlos; Pardo, Bel�n G; Alvarez-Dios, Jos� A; Calaza, Manuel; Bouza, Carmen; V�zquez, Mar�a; Cabaleiro, Santiago; Mart�nez, Paulino
Expression of aquaporins and PAX2 compared to CD10 and cytokeratin 7 in renal neoplasms: a tissue microarray study
Diagnostic use of antibodies against aquaporin water channel proteins and PAX-2, a nuclear transcription factor in renal development, was tested in 202 renal neoplasms, using tissue microarray technique. Immunohistochemistry for aquaporin-1, aquaporin-2, PAX-2, CD10, and cytokeratin 7 was performed on 102 clear cell renal cell carcinomas, 44 papillary renal cell carcinomas (among them 34 type 1 and 10 type 2),
Peter R Mazal; Martin Stichenwirth; Anke Koller; Sabine Blach; Andrea Haitel; Martin Susani
Expression of cancer-testis antigens in endometrial carcinomas using a tissue microarray.
Cancer-testis (CT) antigens are expressed in a variety of malignant tumors, but in normal adult tissue, they are only expressed in testicular germ cells. Owing to this tumor-associated expression pattern, these antigens are of major interest as potential targets for immunotherapy and possibly for diagnostic purposes. This study was performed to analyze the expression of four CT antigens, NY-ESO-1, MAGE-A3, MAGE-A4, and CT7/MAGE-C1, in endometrial carcinoma using immunohistochemistry, and to correlate expression with histologic subtypes, grade, and expression of WT1 and p53. Formalin-fixed paraffin-embedded tissues of 130 endometrial carcinomas of the following types and grades were analyzed using a tissue microarray: 85 endometrioid carcinomas (FIGO grade 1, 39; grade 2, 11; and grade 3, 35), 18 papillary serous carcinomas, 12 clear cell carcinomas, 13 malignant mixed mullerian tumors, one mucinous adenocarcinoma, and one undifferentiated carcinoma. The following anti-CT monoclonal antibodies/antigens were studied by immunohistochemistry: monoclonal antibody ES121/NY-ESO-1, monoclonal antibody M3H67/MAGE-A3, monoclonal antibody 57B/MAGE-A4, and monoclonal antibody CT7-33/CT7. The CT expression data were compared to WT1 and p53 protein expression as analyzed in a previous study. Positive staining with anti-CT monoclonal antibodies was graded as follows: focal, <5% positive cells; 1+, 5-25% cells; 2+, 26-50% cells; 3+, 51-75%; and 4+, >75% cells. The 3+ and 4+ staining patterns were considered homogeneous patterns of potential clinical significance and were scored positive for statistical analysis. In low-grade tumors, the most immunoreactivity was seen with mAb M3H67 but little labeling was observed with the other monoclonal antibodies. In high-grade tumors, monoclonal antibodies M3H67 (25%), 57B (23%), and CT7-33 (20%) showed the highest reactivity, while ES121 showed the lowest immunoreactivity (6%). The staining pattern was mostly heterogeneous. Statistical significance was found solely for the correlation of monoclonal antibody 57B staining and p53 expression. No correlation was found for any anti-CT monoclonal antibody staining and clinical stage or for anti-CT staining and WT1 expression. CT antigens CT7, MAGE-A3 and MAGE-A4, but not NY-ESO-1, are expressed in high-grade endometrial carcinomas, and expression of MAGE-A4 is correlated with the presence of overexpressed p53. PMID:15272278
Chitale, Dhananjay A; Jungbluth, Achim A; Marshall, David S; Leitao, Mario M; Hedvat, Cyrus V; Kolb, Denise; Spagnoli, Giulio C; Iversen, Kristin; Soslow, Robert A
Insulin signaling pathways in cortical dysplasia and TSC-tubers: tissue microarray analysis.
To evaluate the possible roles of the Akt/PKB-mTOR-p70S6K-S6 and cap-dependent translation (eIF4G) pathways in the pathogenesis of tuberous sclerosis complex (TSC)-associated cortical tubers and focal cortical dysplasia (FCD), we performed qualitative and semiquantitative immunohistochemical evaluation on surgically resected corticectomy specimens to detect phosphorylated molecules as activated downstream targets of the signaling pathways. A tissue microarray paraffin block was constructed from 63 archival specimens of surgically resected TSC tubers, FCDs with balloon cells, cortical dysplasia without balloon cells, and histologically normal-appearing neocortex obtained from cases with Rasmussen encephalitis, cystic-gliotic encephalopathy, and temporal lobe epilepsy. Abnormal neuroglial cells were positive for phospho-S6 and phospho-eIF4G with various staining intensities in FCDs and TSC tubers. Both proteins were much less abundantly expressed in normal-appearing neocortex. Phospho-mTOR expression was observed in neurons in all groups. The expression of phospho-S6 and phospho-eIF4G was associated with dysplastic lesions (p < 0.05), and the cytoplasmic phospho-p70S6K expression was most specific for and abundant in TSC tubers and much less prominent in other groups (p < 0.01). These results suggest that constitutive activation of cytoplasmic p70S6K plays a pivotal role in the pathogenesis of TSC tubers and that FCDs possess a distinct mechanism for activation of S6 and eIF4G. PMID:15455398
Miyata, Hajime; Chiang, Alexander C Y; Vinters, Harry V
Comprehensive gene expression microarray analysis of Ets-1 blockade in PC3 prostate cancer cells and correlations with prostate cancer tissues: Insights into genes involved in the metastatic cascade.
Ets-1 is the prototype of the ETS family of transcription factors and is suggested to play an important role in the malignant progression of prostatic carcinomas. Therefore, in this study we investigated the effect of blocking Ets-1 in PC3 prostate cancer cells on genes involved in the metastatic cascade, and correlated these findings with prostate cancer tissues. Two stable PC3 cell cultures were established by transfection with either an Ets-1 inverse antisense expression vector or a mock control vector. The effect of blocking Ets-1 on genes involved in the metastatic cascade was assessed by a comprehensive gene expression microarray analysis of Ets-1 inverse and mock control cells. Correlating the sets of genes found in the PC3 microarray data with prostate cancer tissues was performed by verifying the genes in a comprehensive gene expression microarray analysis of RNA extracted from laser microdissected normal prostate glands and from carcinoma glands taken from prostate cancer patients. Western blot analysis confirmed the presence of Ets-1 in mock cells and its absence in Ets-1 inverse cells. In the Ets-1 blockade microarray, many differentially expressed genes were found; however, only genes with a greater than 10-fold up- or down-regulation between the Ets-1 blockade and mock control were considered significant. The genes were placed into four groups that play a role in the so-called metastatic cascade based on their known functions in proliferation, apoptosis, migration and angiogenesis. The genes found in the Ets-1 blockade microarray analysis were verified for their presence in the microarray analysis of prostate cancer tissues. Genes found in the microarray analysis of prostate cancer tissues with an >2-fold change and a p-value <0.01 were considered significant. We identified sets of genes that are involved in the metastatic cascade and are known to be implicated in prostate cancer to show changes in the expression patterns due to the Ets-1 blockade in PC3 cells. Correlating these sets of genes with the findings in prostate cancer tissues, we identified 16 genes that are up- or down-regulated in healthy compared to tumor prostate glands. Further investigation revealed that 4 out of the 16 genes have been reported to be regulated by members of the ETS family. These findings provide in�vitro and in�vivo evidence for the importance of Ets-1 in the development and progression of prostate cancer. PMID:21424114
Shaikhibrahim, Zaki; Lindstrot, Andreas; Langer, Berit; Buettner, Reinhard; Wernert, Nicolas
Fabrication of a three-dimensional tissue model microarray using laser foaming of a gas-impregnated biodegradable polymer.
A microarray containing three-dimensional (3D) tissue models is a promising substitute for the two-dimensional (2D) cell-based microarrays currently available for high throughput, tissue-based biomedical assays. A cell culture microenvironment similar to in vivo conditions could be achieved with biodegradable porous scaffolds. In this study, a laser foaming technique is developed to create an array of micro-scale 3D porous scaffolds. The effects of major process parameters and the morphology of the resulting porous structure were investigated. For comparison, cell culture studies were conducted with both foamed and unfoamed samples using T98G cells. The results show that by laser foaming gas-impregnated polylactic acid it is possible to generate an array of inverse cone shaped wells with porous walls. The size of the foamed region can be controlled with laser power and exposure time, while the pore size of the scaffold can be manipulated with the saturation pressure. T98G cells grow well in the foamed scaffolds, forming clusters that have not been observed in 2D cell cultures. Cells are more viable in the 3D scaffolds than in the 2D cell culture cases. The 3D porous microarray could be used for parallel studies of drug toxicity, guided stem cell differentiation, and DNA binding profiles. PMID:24999514
Ock, JinGyu; Li, Wei
Evaluation of Two Outlier-Detection-Based Methods for Detecting Tissue-Selective Genes from Microarray Data
Large-scale expression profiling using DNA microarrays enables identification of tissue-selective genes for which expression is considerably higher and/or lower in some tissues than in others. Among numerous possible methods, only two outlier-detection-based methods (an AIC-based method and Sprent�s non-parametric method) can treat equally various types of selective patterns, but they produce substantially different results. We investigated the performance of these two methods for different parameter settings and for a reduced number of samples. We focused on their ability to detect selective expression patterns robustly. We applied them to public microarray data collected from 36 normal human tissue samples and analyzed the effects of both changing the parameter settings and reducing the number of samples. The AIC-based method was more robust in both cases. The findings confirm that the use of the AIC-based method in the recently proposed ROKU method for detecting tissue-selective expression patterns is correct and that Sprent�s method is not suitable for ROKU.
Kadota, Koji; Konishi, Tomokazu; Shimizu, Kentaro
Simple, inexpensive, and precise paraffin tissue microarrays constructed with a conventional microcompound table and a drill grinder.
In 1998, paraffin tissue microarrays (PTMAs) as paraffin blocks containing up to 1,000 cylindrical paraffin tissue core biopsy specimens (PTCBs) for high-throughput molecular profiling of tumor specimens were introduced. PTCBs can be constructed using a manual tissue puncher/arrayer (Beecher Instruments, Sun Prairie, WI; cost, at least $7,000). Furthermore, custom-built PTMAs such as the MaxArray are created by companies such as Zymed Laboratories (South San Francisco, CA; PTMA with 96 holes, about $900). In our search for a less expensive alternative, we constructed PTMAs with up to 558 PTCBs by using a drill grinder, a drill stand, and a microcompound table (Proxxon, Niersdorf, Germany; cost, <$300). PMID:16880136
Vogel, Ulrich F; Bueltmann, Burkhard D
Cytogenetic and cDNA Microarray Expression Analysis of MCF10A Human Breast Cancer Progression Cell Lines
We used a combination of spectral karyotyping, comparative genomic hybridization and cDNA microarrays to gain insights into the structural and functional changes of the genome in the MCF10A human breast cancer progression model cell lines. SKY data showed several chromosomal aberrations and array comparative genomic hybridization analysis identified numerous genomic gains and losses that might be involved in the progression towards cancer. Analysis of the expression levels of genes located within these genomic regions revealed a lack of correlation between chromosomal gains and losses and corresponding up or down regulation for the majority of the ? 1,000 genes analyzed in this study. We conclude that other mechanisms of gene regulation that are not directly related to chromosomal gains and losses play a major role in the progression towards breast cancer.
Marella, Narasimharao V.; Malyavantham, Kishore S.; Wang, Jianmin; Matsui, Sei-ichi; Liang, Ping; Berezney, Ronald
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats
The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement meth- odology. The
Karol L. Thompson; Barry A. Rosenzweig; P. Scott Pine; Jacques Retief; Yaron Turpaz; Cynthia A. Afshari; Hisham K. Hamadeh; Michael A. Damore; Michael Boedigheimer; Eric Blomme; Rita Ciurlionis; Jeffrey F. Waring; James C. Fuscoe; Richard Paules; Charles J. Tucker; Thomas Fare; Ernest M. Coffey; Yudong He; Patrick J. Collins; Kurt Jarnagin; Susan Fujimoto; Brigitte Ganter; Gretchen Kiser; Tamma Kaysser-Kranich; Joseph Sina; Frank D. Sistare
A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs
Microarrays to examine the global expression levels of microRNAs (miRNAs) in a systematic in-parallel manner have become important tools to help unravel the functions of miRNAs and to understand their roles in RNA-based regulation and their implications in human diseases. We have established a novel miRNA-specific microarray platform that enables the simultaneous expression analysis of both known and predicted miRNAs obtained from human or mouse origin. Chemically modified 2?-O-(2-methoxyethyl)-(MOE) oligoribonucleotide probes were arrayed onto Evanescent Resonance (ER) microchips by robotic spotting. Supplementing the complementary probes against miRNAs with carefully designed mismatch controls allowed for accurate sequence-specific determination of miRNA expression profiles obtained from a panel of mouse tissues. This revealed new expression signatures of known miRNAs as well as of novel miRNAs previously predicted using bioinformatic methods. Systematic confirmation of the array data with northern blotting and, in particular, real-time PCR suggests that the described microarray platform is a powerful tool to analyze miRNA expression patterns with rapid throughput and high fidelity.
Beuvink, Iwan; Kolb, Fabrice A.; Budach, Wolfgang; Garnier, Arlette; Lange, Joerg; Natt, Francois; Dengler, Uwe; Hall, Jonathan; Weiler, Jan
Gene expression profiles of adipose tissue of high-fat diet-induced obese rats by cDNA microarrays
To better understand the molecular basis of dietary obesity, we examined adipose tissue genes differentially expressed in\\u000a a well-characterized rat model of high-fat diet (HFD)-induced obesity using cDNA microarrays. Male Sprague�Dawley rats were\\u000a fed either the HFD or the normal diet. Seven weeks later, the weights of obese models (362.92���39.65�g) were significantly\\u000a higher than those of normal control rats (315.22���42.30�g,
Jie QiuRui; Rui Cheng; Xiao-yu Zhou; Jin-gai Zhu; Chun Zhu; Da-ni Qin; Chun-zhao Kou; Xi-rong Guo
Tissue Microarray-Based Evaluation of Chromatin Assembly Factor-1 (CAF-1)/p60 as Tumour Prognostic Marker
In this study we aimed to confirm the emerging role of Chromatin Assembly Factor 1 (CAF-1 p60) as a new proliferation and prognostic marker for cancer and to test the usefulness of the tissue microarray technique (TMA) for CAF-1 p60 rapid screening in several human malignancies. CAF-1 is a histone chaperone, regulating chromatin dynamics during DNA replication and repair in eukaryotics. TMA is a powerful high-throughput methodology in the study of cancer, allowing simultaneous assessment of different biomarkers within large numbers of tissue specimens. We generated TMA taking 3 mm diameter-core biopsies from oral squamous cell carcinoma, prostate cancer, salivary gland tumours and skin melanoma specimens, which had been previously tested for CAF-1 p60 on routine tissue sections. We also analysed, for the first time, 30 larynx and 30 skin squamous cell carcinomas. CAF-1 p60 resulted over-expressed in both the tissue sections and the TMA specimens, with the highest levels of expression in tumours which were more aggressive and metastasizing. Notably, a high degree of agreement was found between the CAF-1 p60 assessment on TMAs and on routine tissue sections. Our findings confirm the prognostic role of CAF-1 p60 and indicate TMA as a really advantageous method for CAF-1 p60 immunohistochemical screening, allowing savings on both tissue quantity and operator-time.
Mascolo, Massimo; Ilardi, Gennaro; Merolla, Francesco; Russo, Daniela; Vecchione, Maria Luisa; de Rosa, Gaetano; Staibano, Stefania
Tissue Microarray-Based Evaluation of Chromatin Assembly Factor-1 (CAF-1)/p60 as Tumour Prognostic Marker.
In this study we aimed to confirm the emerging role of Chromatin Assembly Factor 1 (CAF-1 p60) as a new proliferation and prognostic marker for cancer and to test the usefulness of the tissue microarray technique (TMA) for CAF-1 p60 rapid screening in several human malignancies. CAF-1 is a histone chaperone, regulating chromatin dynamics during DNA replication and repair in eukaryotics. TMA is a powerful high-throughput methodology in the study of cancer, allowing simultaneous assessment of different biomarkers within large numbers of tissue specimens. We generated TMA taking 3 mm diameter-core biopsies from oral squamous cell carcinoma, prostate cancer, salivary gland tumours and skin melanoma specimens, which had been previously tested for CAF-1 p60 on routine tissue sections. We also analysed, for the first time, 30 larynx and 30 skin squamous cell carcinomas. CAF-1 p60 resulted over-expressed in both the tissue sections and the TMA specimens, with the highest levels of expression in tumours which were more aggressive and metastasizing. Notably, a high degree of agreement was found between the CAF-1 p60 assessment on TMAs and on routine tissue sections. Our findings confirm the prognostic role of CAF-1 p60 and indicate TMA as a really advantageous method for CAF-1 p60 immunohistochemical screening, allowing savings on both tissue quantity and operator-time. PMID:23109837
Mascolo, Massimo; Ilardi, Gennaro; Merolla, Francesco; Russo, Daniela; Vecchione, Maria Luisa; de Rosa, Gaetano; Staibano, Stefania
No-cost manual method for preparation of tissue microarrays having high quality comparable to semiautomated methods.
Manual tissue microarray (TMA) construction had been introduced to avoid the high cost of automated and semiautomated techniques. The cheapest and simplest technique for constructing manual TMA was that of using mechanical pencil tips. This study was carried out to modify this method, aiming to raise its quality to reach that of expensive ones. Some modifications were introduced to Shebl's technique. Two conventional mechanical pencil tips of different diameters were used to construct the recipient blocks. A source of mild heat was used, and blocks were incubated at 38�C overnight. With our modifications, 3 high-density TMA blocks were constructed. We successfully performed immunostaining without substantial tissue loss. Our modifications increased the number of cores per block and improved the stability of the cores within the paraffin block. This new, modified technique is a good alternative for expensive machines in many laboratories. PMID:23235346
Foda, Abd Al-Rahman Mohammad
Gene Discovery in Bladder Cancer Progression using cDNA Microarrays
To identify gene expression changes along progres- sion of bladder cancer, we compared the expression profiles of early-stage and advanced bladder tumors using cDNA microarrays containing 17,842 known genes and expressed sequence tags. The application of bootstrapping techniques to hierarchical cluster- ing segregated early-stage and invasive transitional carcinomas into two main clusters. Multidimensional analysis confirmed these clusters and more impor-
Marta Sanchez-Carbayo; Nicholas D. Socci; Juan Jose Lozano; Wentian Li; Elizabeth Charytonowicz; Thomas J. Belbin; Michael B. Prystowsky; Angel R. Ortiz; Geoffrey Childs; Carlos Cordon-Cardo
A 'Waterfall' Transfer-based Workflow for Improved Quality of Tissue Microarray Construction and Processing in Breast Cancer Research.
A major focus in cancer research is the identification of biomarkers for early diagnosis, therapy prediction and prognosis. Hereby, validation of target proteins on clinical samples is of high importance. Tissue microarrays (TMAs) represent an essential advancement for high-throughput analysis by assembling large numbers of tissue cores with high efficacy and comparability. However, limitations along TMA construction and processing exist. In our presented study, we had to overcome several obstacles in the construction and processing of high-density breast cancer TMAs to ensure good quality sections for further research. Exemplarily, 406 breast tissue cores from formalin-fixed and paraffin embedded samples of 245 patients were placed onto three recipient paraffin blocks. Sectioning was performed using a rotary microtome with a "waterfall" automated transfer system. Sections were stained by immunohistochemistry and immunofluorescence for nine proteins. The number and quality of cores after sectioning and staining was counted manually for each marker. In total, 97.1�% of all cores were available after sectioning, while further 96�% of the remaining cores were evaluable after staining. Thereby, normal tissue cores were more often lost compared to tumor tissue cores. Our workflow provides a robust method for manufacturing high-density breast cancer TMAs for subsequent IHC or IF staining without significant sample loss. PMID:24619867
Oberl�nder, M; Alkemade, H; B�nger, S; Ernst, F; Thorns, C; Braunschweig, T; Habermann, J K
Tissue Microarray Analysis of Cyclin-Dependent Kinase Inhibitors p21 and p16 in Fuchs Dystrophy
Purpose To investigate the novel application of tissue microarray (TMA) technology to corneal disease and to report altered protein expression of senescence-associated cyclin-dependent kinase inhibitors p21 and p16 in Fuchs endothelial corneal dystrophy (FECD). Methods A TMA including 208 cores was generated from paraffin-embedded tissues including corneal buttons of 50 FECD and 5 keratoconus (KC) patients retrieved post penetrating keratoplasty, 10 autopsy globes with non-pathologic corneas, and non-ocular control specimens. TMA sections were immunolabeled for p21 and p16 and analyzed using a nine-grade scoring system (0�8). Result validation was performed by immunolabeling of individual whole tissue sections. Corneal endothelial p21 and p16 expression levels in FECD specimens compared to controls served as main outcome measures. Results TMA immunohistochemical analysis disclosed increased endothelial expression levels of nuclear p21 in FECD specimens (p<0.05) and an altered endothelial p16 expression pattern. Immunolabeling of whole tissue sections showed statistically significant endothelial overexpres-sion of both proteins (p21 and p16, p<0.05). Conclusion The present study introduces TMA technology as a valuable tool for molecular high-throughput profiling of corneal tissues. It demonstrates p21 and p16 overexpression in the corneal endothelium of genetically undifferentiated FECD patients supporting a role of cellular senescence in the pathogenesis of FECD.
Matthaei, Mario; Lackner, Eva-Maria; Meng, Huan; Hicks, Jessica L; Meeker, Alan K; Eberhart, Charles G; Jun, Albert S
A Texture Based Pattern Recognition Approach to Distinguish Melanoma from Non-Melanoma Cells in Histopathological Tissue Microarray Sections
Aims Immunohistochemistry is a routine practice in clinical cancer diagnostics and also an established technology for tissue-based research regarding biomarker discovery efforts. Tedious manual assessment of immunohistochemically stained tissue needs to be fully automated to take full advantage of the potential for high throughput analyses enabled by tissue microarrays and digital pathology. Such automated tools also need to be reproducible for different experimental conditions and biomarker targets. In this study we present a novel supervised melanoma specific pattern recognition approach that is fully automated and quantitative. Methods and Results Melanoma samples were immunostained for the melanocyte specific target, Melan-A. Images representing immunostained melanoma tissue were then digitally processed to segment regions of interest, highlighting Melan-A positive and negative areas. Color deconvolution was applied to each region of interest to separate the channel containing the immunohistochemistry signal from the hematoxylin counterstaining channel. A support vector machine melanoma classification model was learned from a discovery melanoma patient cohort (n?=?264) and subsequently validated on an independent cohort of melanoma patient tissue sample images (n?=?157). Conclusion Here we propose a novel method that takes advantage of utilizing an immuhistochemical marker highlighting melanocytes to fully automate the learning of a general melanoma cell classification model. The presented method can be applied on any protein of interest and thus provides a tool for quantification of immunohistochemistry-based protein expression in melanoma.
Rexhepaj, Elton; Agnarsdottir, Margret; Bergman, Julia; Edqvist, Per-Henrik; Bergqvist, Michael; Uhlen, Mathias; Gallagher, William M.; Lundberg, Emma; Ponten, Fredrik
Analysis of gene status in cervical dysplastic lesions and squamous cell carcinoma using tissue microarrays.
Cervical displasia are classified as CIN-I, CIN-II and CIN-III. It has been observed that in at least 60% of CIN-I and CIN-II, the pathology disappears spontaneously, while around 30% persist at 24 months, 10% progress to CIN-III and 1% develops as a SCC. The factors involved in the evolution of the pathology are not defined, although infection of HPV is a necessary condition, but not the only one. For this reason, the identification of genetic changes is an essential element for understanding the carcinogenic process. It can also serve as a helpful tool for identifying patients who may be susceptible to its evolution and treatment, from patients whose lesions could regress spontaneous and for whom periodic follow-ups would be enough. Fifty three cervical biopsies from patients with dysplasia and ISCC were included in the study. These biopsies were set into nine macroarrays. Eight genes and five proteins were examined in each samples (hTERT, PIK3CA, hTERC, MYC, CCND1, BCL2, ZNF217 and p16) by fluorescence in situ hybridization (FISH) and/or immunohistochemistry (IHC). The results reflected that the genetic alterations of PIK3CA, ZNF217 and CCND1 were associated with the evolution of normal tissue to CIN I, those of hTERC and ERBB with the evolution of LSIL to HSIL, those of hTERT and MYC with the evolution of CIN-II/CIN-III to ISCC, and those of BCL-2 with the inception of ISCC. With regards to proteins, the expression of MYC and CCND1 in the initial stages of the illness would help in the acquisition of the altered cellular phenotype. PMID:19475528
Costa, Carlota; Espinet, Blanca; Molina, Miguel A; Salgado, Rocio; Salido, Marta; Bar�, Teresa; Fust�, Pere; Mancebo, Gemma; Carreras, Ram�n; Sol�, Francesc; Serrano, Sergi; Alameda, Francesc
Microarray gene expression profiling of neural tissues in bovine spastic paresis
Background Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease. Results Microarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway�s classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated. Conclusions The cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases.
Discovery of tissue-specific exons using comprehensive human exon microarrays
Background��Higher eukaryotes express a diverse population of messenger RNAs generated by alternative splicing. Large-scale methods for\\u000a monitoring gene expression must adapt in order to accurately detect the transcript variation generated by this splicing.\\u000a \\u000a \\u000a \\u000a \\u000a Results��We have designed a high-density oligonucleotide microarray with probesets for more than one million annotated and predicted\\u000a exons in the human genome. Using these arrays and a
Tyson A Clark; Anthony C Schweitzer; Tina X Chen; Michelle K Staples; Gang Lu; Hui Wang; Alan Williams; John E Blume
Gene expression profiles of adipose tissue of high-fat diet-induced obese rats by cDNA microarrays.
To better understand the molecular basis of dietary obesity, we examined adipose tissue genes differentially expressed in a well-characterized rat model of high-fat diet (HFD)-induced obesity using cDNA microarrays. Male Sprague-Dawley rats were fed either the HFD or the normal diet. Seven weeks later, the weights of obese models (362.92 � 39.65 g) were significantly higher than those of normal control rats (315.22 � 42.30 g, P < 0.01) and the wet weights of adipose tissue of rats fed with HFD (9.29 � 5.14 g) were significantly higher than those of normal control rats (4.09 � 2.69 g, P < 0.01), which confirmed the successful preparation of obese models. cDNA microarrays containing 9 216 genes/Ests were used to investigate gene expression of adipose tissue. Autoradiographic analysis showed that 532, 154, and 22 genes were differently expressed over 2-, 3-, and 5-fold, respectively. The analysis of gene expression profiles indicated that 276 genes were up-regulated and 432 genes were down-regulated in response to HFD-induced obesity. Different clusters of genes associated with lipid metabolism, extracellular matrix, signal transduction, cytoskeleton, cell apoptosis, etc., such as VLCS-H2, DGAT, ACADVL, PHYH, SCD, ACACA, ACS, MMP-2, MMP-15, CD38, CAMK2D, CACNA1F, CAPZA2, TMOD3, ARPC2, KNS2, TPM1, MAPK8, GADD45B, DAXX, TOK-1, PRKACA, STAT6, were concerned. PMID:20191385
Qiu, Jie; Cheng, Rui; Zhou, Xiao-yu; Zhu, Jin-gai; Zhu, Chun; Qin, Da-ni; Kou, Chun-zhao; Guo, Xi-rong
Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair
Rheumatoid arthritis (RA) is a heterogeneous disease. We used cDNA microarray technology to subclassify RA patients and disclose disease pathways in rheumatoid synovium. Hierarchical clustering of gene expression data identified two main groups of tissues (RA-I and RA-II). A total of 121 genes were significantly higher expressed in the RA-I tissues, whereas 39 genes were overexpressed in the RA-II tissues.
T C T M van der Pouw Kraan; F A van Gaalen; T W J Huizinga; E Pieterman; F. C. Breedveld; C. L. Verweij; CTM van der Pouw Kraan
Microarray gene expression profiles from mature gonad tissues of Atlantic bluefin tuna, Thunnus thynnus in the Gulf of Mexico
Background Bluefin tunas are highly prized pelagic fish species representing a significant economic resource to fisheries throughout the world. Atlantic bluefin tuna (Thunnus thynnus) populations have significantly declined due to overexploitation. As a consequence of their value and population decline, T. thynnus has been the focus of considerable research effort concerning many aspects of their life history. However, in-depth understanding of T. thynnus reproductive biology is still lacking. Knowledge of reproductive physiology is a very important tool for determining effective fisheries and aquaculture management. Transcriptome techniques are proving powerful and provide novel insights into physiological processes. Construction of a microarray from T. thynnus ESTs sourced from reproductive tissues has provided an ideal platform to study the reproductive physiology of bluefin tunas. The aim of this investigation was to compare transcription profiles from the ovaries and testes of mature T. thynnus to establish sex specific variations underlying their reproductive physiology. Results Male and females T. thynnus gonad tissues were collected from the wild and histologically staged. Sub-samples of sexually mature tissues were also measured for their mRNA differential expression among the sexes using the custom microarray design BFT 4X44K. A total of 7068 ESTs were assessed for differential expression of which 1273 ESTs were significantly different (p<0.05) with >2 fold change in expression according to sex. Differential expression for 13 of these ESTs was validated with quantitative PCR. These include genes involved in egg envelope formation, hydration, and lipid transport/accumulation more highly expressed in ovaries compared with testis, while genes involved in meiosis, sperm motility and lipid metabolism were more highly expressed in testis compared with ovaries. Conclusions This investigation has furthered our knowledge of bluefin tunas reproductive biology by using a contemporary transcriptome approach. Gene expression profiles in T. thynnus sexually mature testes and ovaries were characterized with reference to gametogenesis and potential alternative functions. This report is the first application of microarray technology for bluefin tunas and demonstrates the efficacy by which this technique may be used for further characterization of specific biological aspects for this valuable teleost fish.
Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data.
Soil contamination near munitions plants and testing grounds is a serious environmental concern that can result in the formation of tissue chemical residue in exposed animals. Quantitative prediction of tissue residue still represents a challenging task despite long-term interest and pursuit, as tissue residue formation is the result of many dynamic processes including uptake, transformation, and assimilation. The availability of high-dimensional microarray gene expression data presents a new opportunity for computational predictive modeling of tissue residue from changes in expression profile. Here we analyzed a 240-sample data set with measurements of transcriptomic-wide gene expression and tissue residue of two chemicals, 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), in the earthworm Eisenia fetida. We applied two different computational approaches, LASSO (Least Absolute Shrinkage and Selection Operator) and RF (Random Forest), to identify predictor genes and built predictive models. Each approach was tested alone and in combination with a prior variable selection procedure that involved the Wilcoxon rank-sum test and HOPACH (Hierarchical Ordered Partitioning And Collapsing Hybrid). Model evaluation results suggest that LASSO was the best performer of minimum complexity on the TNT data set, whereas the combined Wilcoxon-HOPACH-RF approach achieved the highest prediction accuracy on the RDX data set. Our models separately identified two small sets of ca. 30 predictor genes for RDX and TNT. We have demonstrated that both LASSO and RF are powerful tools for quantitative prediction of tissue residue. They also leave more unknown than explained, however, allowing room for improvement with other computational methods and extension to mixture contamination scenarios. PMID:21776976
Gong, Ping; Loh, Po-Ru; Barker, Natalie D; Tucker, George; Wang, Nan; Zhang, Chenhua; Escalon, B Lynn; Berger, Bonnie; Perkins, Edward J
Variability in the expression of polycomb proteins in different normal and tumoral tissues. A pilot study using tissue microarrays
In spite of the known function of polycomb group (PcG) genes in stem cell self-renewal, control of cellular proliferation and differentiation, its role in cancer pathogenesis is still poorly understood. We studied the expression by immunohistochemistry of several PcG-maintenance complex proteins (RING1, RNF2, BMI1, MEL18, HPH1 and RYBP) in nontumoral (154 samples) and tumoral (550 samples) human tissues using Tissue
Margarita S�nchez-Beato; Esther S�nchez; Joaqu�n Gonz�lez-Carrer�; Manuel Morente; Ana D�ez; Lydia S�nchez-Verde; Mar�a Carmen Mart�n; Juan C Cigudosa; Miguel Vidal; Miguel A Piris
Tissue microarray analysis reveals site-specific prevalence of oncogene amplifications in head and neck squamous cell carcinoma.
Fluorescence in situ hybridization was applied on a collection of 609 squamous cell carcinomas of the head and neck (HNSCCs),including 511 primary carcinomas of different clinical stage and anatomical localization and 98 recurrent carcinomas, second primary carcinomas, and regional metastases on a tissue microarray. The overall prevalence of amplifications of five oncogenes analyzed was 34.5% for CCND1, 12.7% for EGFR, 8.8% for MYC, 6.2% for ZNF217, and 3.6% for ERBB2. CCND1 amplifications were associated with the pharyngeal site in primary carcinomas (P < 0.001), whereas amplifications of ZNF217 were less frequent in pharyngeal carcinomas as compared with primary oral and laryngeal carcinomas (P = 0.02). The amplification pattern of these oncogenes suggests that different molecular pathways are involved in HNSCCs of different localizations. PMID:12649172
Freier, Kolja; Joos, Stefan; Flechtenmacher, Christa; Devens, Frauke; Benner, Axel; Bosch, Franz X; Lichter, Peter; Hofele, Christof
p53 and c-kit (CD117) protein expression as prognostic indicators in breast phyllodes tumors: a tissue microarray study.
Breast phyllodes tumors are fibroepithelial neoplasms whose clinical behavior is difficult to predict on histology. There is relatively scant data on the role of biological markers. In this study, we determined if p53 and CD117 (c-kit) protein expression was predictive of behavior in a series of 335 phyllodes tumors diagnosed at the Singapore General Hospital, using immunohistochemistry on tissue microarrays. Representative areas from 250 (75%) benign, 54 (16%) borderline and 31 (9%) malignant phyllodes tumors were selected for construction of tissue microarrays using the 2 mm punch. Immunohistochemistry for p53 and CD117 was carried out using the streptavidin-biotin method. Staining proportion and intensity of both epithelial and stromal elements were analyzed. p53 immunostaining was observed in the epithelium of 28 (10%) of 278 microarrays; myoepithelium of 53 (21%) of 251 microarrays; and stromal cells in 105 (36%) of 289 microarrays. CD117 immunohistochemical reactivity was noted in epithelial and stromal components of 175 (of 267, 66%) and 17 (of 273, 6%) microarrays, respectively. Stromal p53 and CD117 protein expression was associated with tumor grade (P < 0.05). Of 43 (13%) women who suffered recurrences during the follow-up period, CD117 stromal staining predicted recurrent disease (P<0.05), but p53 was not correlative. We conclude that tissue microarrays are a convenient method for evaluating immunostaining results of large numbers of phyllodes tumors. Although positive p53 stromal immunohistochemical detection may corroborate histologic malignancy, it is CD117 protein expression in phyllodes tumor stromal cells that may be of potential utility in predicting recurrent disease. PMID:16258510
Tan, Puay-Hoon; Jayabaskar, Thiyagarajan; Yip, George; Tan, Yen; Hilmy, Maryam; Selvarajan, Sathiyamoorthy; Bay, Boon-Huat
Fas, FasL, and cleaved caspases 8 and 3 in glioblastomas: A tissue microarray-based study.
This investigation analyzed the immunoexpression of FasL, Fas, cleaved caspase-8, and cleaved caspase-3 in glioblastomas. Formalin-fixed and paraffin-embedded glioblastoma tissues and control brain tissues from 97 patients were analyzed by tissue microarrays and immunohistochemistry. Patients with glioblastomas that were negative or weakly stained (<50% of cells positive) for cleaved caspase-8 had worse cancer-specific overall survival (median=8.5 months) than did patients with tumors that highly expressed cleaved caspase-8 (median=11.7 months; P=0.0325), independent of clinical variables. There was no association of other markers with survival, treatment, sex, age, tumor size, and primary site. Among the tumors, there were reasonable to good positive correlations between the expression of FasL and Fas (r=0.47) and between Fas and cleaved caspase-8 (r=0.41), and there were poor positive correlations between Fas and cleaved caspase-3 (r=0.26), FasL and cleaved caspase-8 (r=0.22), and cleaved caspase-8 and -3 (r=0.31). Our results suggest that Fas-Fas-ligand signal transduction could be inhibited, especially at the stage of caspase-8 activation, thereby establishing a major mechanism for evasion of apoptosis by these tumors. The absence or low expression of cleaved caspase-8 in the tumors was a negative prognostic indicator for patient survival. PMID:24561085
Saggioro, Fabiano P; Neder, Luciano; St�vale, Jo�o Norberto; Paix�o-Becker, Aline Nazareth P; Malheiros, Suzana M F; Soares, Fernando A; Pittella, Jos� Eymard H; Matias, Caio C�sar M S; Colli, Benedicto O; Carlotti, Carlos Gilberto; Franco, Marcello
Overexpression of steroid receptor coactivator-3 in bone cancers: an in vivo immunohistochemical study with tissue microarray.
Bone tissue is steroid-responsive and profoundly regulated by steroids and/or their receptors. Bone cancers (either primary or metastatic) belong to the most dangerous tumors. Previous studies have demonstrated overexpression of steroid receptor coactivator-3 (SRC-3) in many cancers, such as breast cancer, prostate cancer, thyroid cancer, functioning in the regulation of cancer cell proliferation, invasion, and metastasis. However, so far, the expression and function of SRC-3 in bone cancers have not yet been clarified. In this study, nickel-intensified immunohistochemistry was conducted using a commercial tissue microarray (with 94 cases of bone cancer tissue and 10 normal bone tissues), and the 4-scoring system was employed to evaluate the expression levels of SRC-3 immunoreactivity. The results showed that in normal bone tissue, levels of SRC-3 are almost negative (score=0), the total positivity (score=1-3) of SRC-3 immunoreactivities in bone cancers was 74.47%. There were no significant differences in gender, status (malignant or benign) or (mean) age (p>0.05). The percentage of positivity was 77.78% in osteogenic tumors, 58.82% in cartilage tumors, 70% in giant cell tumors, 100% in hematopoietic tumors, 77.78% in miscellaneous lesions, and 75% in miscellaneous tumors. Age related differences of SRC-3 immunoreactivities were detected in cartilage tumors and giant cell tumors (p<0.05). The above results clearly demonstrated a high frequency of overexpression of SRC-3 immunoreactivities in different bone cancers, indicating its potential roles in the prognosis and treatment of these cancers. PMID:24134957
Luo, Fei; Li, Wei; Zhang, Jiqiang; Huang, Ke; Fu, Jingshu; Xie, Zhao
Comparison of in situ hybridization methods for the assessment of HER2\\/neu gene amplification status in breast cancer using a tissue microarray
Background: This project compared HER-2\\/neu gene status in breast cancers, as demonstrated by FISH (fluorescent in situ hybridization) and CISH (Chromogenic in situ hybridization) and using a tissue microarray (TMA). The study also aimed to show whether the TMA technique could be used in clinical diagnostics, rather than remain a scientific tool.
Anna Malicka
p53 and c-kit (CD117) protein expression as prognostic indicators in breast phyllodes tumors: a tissue microarray study
Breast phyllodes tumors are fibroepithelial neoplasms whose clinical behavior is difficult to predict on histology. There is relatively scant data on the role of biological markers. In this study, we determined if p53 and CD117 (c-kit) protein expression was predictive of behavior in a series of 335 phyllodes tumors diagnosed at the Singapore General Hospital, using immunohistochemistry on tissue microarrays.
Puay-Hoon Tan; Thiyagarajan Jayabaskar; George Yip; Yen Tan; Maryam Hilmy; Sathiyamoorthy Selvarajan; Boon-Huat Bay
Proliferation centers in chronic lymphocytic leukemia: correlation with cytogenetic and clinicobiological features in consecutive patients analyzed on tissue microarrays.
To better define the significance of proliferation centers (PCs), the morphological hallmark of chronic lymphocytic leukemia (CLL), lymph node biopsies taken from 183 patients were submitted to histopathologic and fluorescence in situ hybridization (FISH) studies using a 5-probe panel on tissue microarrays. Seventy-five cases (40.9%) with confluent PCs were classified as 'PCs-rich' and 108 cases (59.1%) with scattered PCs were classified as 'typical'. Complete FISH data were obtained in 101 cases (55.1%), 79 of which (78.2%) displayed at least one chromosomal aberration. The incidence of each aberration was: 13q- 36,7%, 14q32 translocations 30.8%, 11q- 24.7%, trisomy 12 19.5% and 17p- 15.6%. Five cases showed extra copies of the 14q32 region. The 'PCs-rich' group was associated with 17p-, 14q32/IgH translocation, +12, Ki-67>30%. The median survival from the time of tissue biopsy for PCs-rich and typical groups was 11 and 64 months, respectively (P=0.00001). The PCs-rich pattern was the only predictive factor of an inferior survival at multivariate analysis (P=0.022). These findings establish an association between cytogenetic profile and the amount of PC in CLL, and show that this histopathologic characteristic is of value for risk assessment in patients with clinically significant adenopathy. PMID:21941366
Ciccone, M; Agostinelli, C; Rigolin, G M; Piccaluga, P P; Cavazzini, F; Righi, S; Sista, M T; Sofritti, O; Rizzotto, L; Sabattini, E; Fioritoni, G; Falorio, S; Stelitano, C; Olivieri, A; Attolico, I; Brugiatelli, M; Zinzani, P L; Saccenti, E; Capello, D; Negrini, M; Cuneo, A; Pileri, S
Relational Database Structure to Manage High-Density Tissue Microarray Data and Images for Pathology Studies Focusing on Clinical Outcome
With the completion of the Human Genome Project and high-throughput screening methods using cDNA array and tissue microarray (TMA) technology, there is a pressing need to manage the voluminous data sets generated from these types of investigations. Herein is described a database model to handle 1) clinical and pathology data, 2) TMA location information, and 3) web-based histology results. The model is useful for managing clinical, pathology, and molecular data on >1300 prostate cancer patients dating back to 1995 from the University of Michigan Specialized Program of Research Excellence for prostate cancer. The key components in this multidatabase model are 1) the TMA database, 2) the TMA-image database (TMA-I DB), and 3) the prostate pathology and clinical information databases. All databases were created in Microsoft Access (Microsoft, Redmond, WA). Desired patient, tissue, block, diagnosis, array location, and respective clinical and pathology information is obtained by linking the unique identifier fields among database tables. The TMA database is comprised of interrelated data from 336 prostate cancer patients transferred into 19 TMA blocks with 5451 TMA biopsy cores. Tissue samples include 1695 normal prostate, 3171 prostate cancer, 464 prostatic intraepithelial neoplasia, and 121 atrophy. All 19 TMA blocks have been analyzed over the Internet for several immunohistochemical biomarkers including E-cadherin, prostate-specific antigen, p27Kip1, and Ki-67 labeling index. This system facilitates the statistical analysis of high-density TMA data with clinical and pathology information in an efficient and cost-effective manner. Because the review is performed over the Internet, this system is ideal for collaborative multi-institutional studies.
Manley, Sargum; Mucci, Neil R.; De Marzo, Angelo M.; Rubin, Mark A.
Quantitative multiplex quantum dot in-situ hybridisation based gene expression profiling in tissue microarrays identifies prognostic genes in acute myeloid leukaemia
Highlights: Black-Right-Pointing-Pointer Development of a quantitative high throughput in situ expression profiling method. Black-Right-Pointing-Pointer Application to a tissue microarray of 242 AML bone marrow samples. Black-Right-Pointing-Pointer Identification of HOXA4, HOXA9, Meis1 and DNMT3A as prognostic markers in AML. -- Abstract: Measurement and validation of microarray gene signatures in routine clinical samples is problematic and a rate limiting step in translational research. In order to facilitate measurement of microarray identified gene signatures in routine clinical tissue a novel method combining quantum dot based oligonucleotide in situ hybridisation (QD-ISH) and post-hybridisation spectral image analysis was used for multiplex in-situ transcript detection in archival bone marrow trephine samples from patients with acute myeloid leukaemia (AML). Tissue-microarrays were prepared into which white cell pellets were spiked as a standard. Tissue microarrays were made using routinely processed bone marrow trephines from 242 patients with AML. QD-ISH was performed for six candidate prognostic genes using triplex QD-ISH for DNMT1, DNMT3A, DNMT3B, and for HOXA4, HOXA9, Meis1. Scrambled oligonucleotides were used to correct for background staining followed by normalisation of expression against the expression values for the white cell pellet standard. Survival analysis demonstrated that low expression of HOXA4 was associated with poorer overall survival (p = 0.009), whilst high expression of HOXA9 (p < 0.0001), Meis1 (p = 0.005) and DNMT3A (p = 0.04) were associated with early treatment failure. These results demonstrate application of a standardised, quantitative multiplex QD-ISH method for identification of prognostic markers in formalin-fixed paraffin-embedded clinical samples, facilitating measurement of gene expression signatures in routine clinical samples.
Tholouli, Eleni [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom)] [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); MacDermott, Sarah [The Medical School, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom)] [The Medical School, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Hoyland, Judith [School of Biomedicine, Faculty of Medical and Human Sciences, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom)] [School of Biomedicine, Faculty of Medical and Human Sciences, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Yin, John Liu [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom)] [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); Byers, Richard, E-mail: email@example.com [School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, The University of Manchester, Stopford Building, Oxford Road, M13 9PT Manchester (United Kingdom)] [School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, The University of Manchester, Stopford Building, Oxford Road, M13 9PT Manchester (United Kingdom)
Microarray gene expression analysis of fixed archival tissue permits molecular classification and identification of potential therapeutic targets in diffuse large B-cell lymphoma.
Refractory/relapsed diffuse large B-cell lymphoma (DLBCL) has a poor prognosis. Novel drugs targeting the constitutively activated NF-?B pathway characteristic of ABC-DLBCL are promising, but evaluation depends on accurate activated B cell-like (ABC)/germinal center B cell-like (GCB) molecular classification. This is traditionally performed on gene microarray expression profiles of fresh biopsies, which are not routinely collected, or by immunohistochemistry on formalin-fixed, paraffin-embedded (FFPE) tissue, which lacks reproducibility and classification accuracy. We explored the possibility of using routine archival FFPE tissue for gene microarray applications. We examined Affymetrix HG U133 Plus 2.0 gene expression profiles from paired archival FFPE and fresh-frozen tissues of 40 ABC/GCB-classified DLBCL cases to compare classification accuracy and test the potential for this approach to aid the discovery of therapeutic targets and disease classifiers in DLBCL. Unsupervised hierarchical clustering of unselected present probe sets distinguished ABC/GCB in FFPE with remarkable accuracy, and a Bayesian classifier correctly assigned 32 of 36 cases with >90% probability. Enrichment for NF-?B genes was appropriately seen in ABC-DLBCL FFPE tissues. The top discriminatory genes expressed in FFPE separated cases with high statistical significance and contained novel biology with potential therapeutic insights, warranting further investigation. These results support a growing understanding that archival FFPE tissues can be used in microarray experiments aimed at molecular classification, prognostic biomarker discovery, and molecular exploration of rare diseases. PMID:22446084
Linton, Kim; Howarth, Christopher; Wappett, Mark; Newton, Gillian; Lachel, Cynthia; Iqbal, Javeed; Pepper, Stuart; Byers, Richard; Chan, Wing John; Radford, John
Cathepsin D Expression in Colorectal Cancer: From Proteomic Discovery through Validation Using Western Blotting, Immunohistochemistry, and Tissue Microarrays
Despite recent advances in surgical techniques and therapeutic treatments, survival from colorectal cancer (CRC) remains disappointing with some 40�50% of newly diagnosed patients ultimately dying of metastatic disease. Current staging by light microscopy alone is not sufficiently predictive of prognosis and would benefit from additional support from biomarkers in order to stratify patients appropriately for adjuvant therapy. We have identified that cathepsin D expression was significantly greater in cells from invasive front (IF) area and liver metastasis (LM) than those from main tumour body (MTB). Cathepsin D expression was subsequently examined by immunohistochemistry in tissue microarrays from 119 patients with CRC. Strong expression in tumour cells at the IF did not correlate significantly with any clinico-pathological parameters examined or patient survival. However, cathepsin D expression in cells from the MTB was highly elevated in late stage CRC and showed significant correlation with subsequent distant metastasis and shorter cancer-specific survival. We also found that macrophages surrounding tumour cells stained strongly for cathepsin D but there was no significant correlation found between cathepsin D in macrophages at IF and MTB of CRC patient with the clinic-pathological parameters examined.
Kirana, Chandra; Shi, Hongjun; Laing, Emma; Hood, Kylie; Miller, Rose; Bethwaite, Peter; Keating, John; Jordan, T. William; Hayes, Mark; Stubbs, Richard
Integrative Proteomics and Tissue Microarray Profiling Indicate the Association between Overexpressed Serum Proteins and Non-Small Cell Lung Cancer
Lung cancer is the leading cause of cancer deaths worldwide. Clinically, the treatment of non-small cell lung cancer (NSCLC) can be improved by the early detection and risk screening among population. To meet this need, here we describe the application of extensive peptide level fractionation coupled with label free quantitative proteomics for the discovery of potential serum biomarkers for lung cancer, and the usage of Tissue microarray analysis (TMA) and Multiple reaction monitoring (MRM) assays for the following up validations in the verification phase. Using these state-of-art, currently available clinical proteomic approaches, in the discovery phase we confidently identified 647 serum proteins, and 101 proteins showed a statistically significant association with NSCLC in our 18 discovery samples. This serum proteomic dataset allowed us to discern the differential patterns and abnormal biological processes in the lung cancer blood. Of these proteins, Alpha-1B-glycoprotein (A1BG) and Leucine-rich alpha-2-glycoprotein (LRG1), two plasma glycoproteins with previously unknown function were selected as examples for which TMA and MRM verification were performed in a large sample set consisting about 100 patients. We revealed that A1BG and LRG1 were overexpressed in both the blood level and tumor sections, which can be referred to separate lung cancer patients from healthy cases.
Hu, Haichuan; Wang, Rui; Sun, Yihua; Zeng, Rong; Chen, Haiquan
Technical validation of cDNA based microarray as screening technique to identify candidate genes in synovial tissue biopsy specimens from patients with spondyloarthropathy
Objectives: To validate the use of cDNA based microarray on synovial biopsies by analysing the experimental variability due to amplification of RNA, reproducibility of the assay, heterogeneity of the tissue, and statistical analysis. Methods: Total RNA was extracted from three spondyloarthropathy (SpA) and three osteoarthritis (OA) synovial tissue biopsy specimens and from the peripheral blood mononuclear cells (PBMC) of four healthy donors. Exponential RNA amplification by SMART-PCR was compared with linear amplification. Reproducibility was tested by comparing different microarray systems and by performing duplicate experiments. Sample heterogeneity was assessed by comparing overall gene expression profiles, histopathology, and analysis of genes expressed in the synovium and normal PBMC. Statistical analysis using t test and Bonferroni adjustment was verified by permutation of class labels. Results: Gene expression was concordant in 12/14 (86%) cytokine/chemokine genes between both microarrays and different RNA amplification systems. When one microarray system was used, expressed genes were 78�95% concordant in duplicate experiments. Gene expression profiles had a higher degree of similarity between SpA synovium than between PBMC or OA synovium despite clear histopathological differences between synovial samples. Comparison of SpA synovium with OA synovium and with PBMC yielded 11 and 18 expressed transcripts, respectively; six were shared in both comparisons. Permutations of SpA and OA samples yielded only one expressed gene in 19 comparisons. Conclusions: These data provide evidence that microarrays can be used for analysis of synovial tissue biopsies with high reproducibility and low variability of the generated gene expression profiles.
Rihl, M; Baeten, D; Seta, N; Gu, J; De Keyser, F; Veys, E; Kuipers, J; Zeidler, H; Yu, D
Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue
Acute progressive feed restriction (APFR) represents a specific form of caloric restriction in which feed availability is increasingly curtailed over a period of a few days to a few weeks. It is often used for control animals in toxicological and pharmacological studies on compounds causing body weight loss to equalize weight changes between experimental and control groups and thereby, intuitively, to also set their metabolic states to the same phase. However, scientific justification for this procedure is lacking. In the present study, we analyzed by microarrays the impact on hepatic gene expression in rats of two APFR regimens that caused identical diminution of body weight (19%) but differed slightly in duration (4 vs. 10 days). In addition, white adipose tissue (WAT) was also subjected to the transcriptomic analysis on day-4. The data revealed that the two regimens led to distinct patterns of differentially expressed genes in liver, albeit some major pathways of energy metabolism were similarly affected (particularly fatty acid and amino acid catabolism). The reason for the divergence appeared to be entrainment by the longer APFR protocol of peripheral oscillator genes, which resulted in derailment of circadian rhythms and consequent interaction of altered diurnal fluctuations with metabolic adjustments in gene expression activities. WAT proved to be highly unresponsive to the 4-day APFR as only 17 mRNA levels were influenced by the treatment. This study demonstrates that body weight is a poor proxy of metabolic state and that the customary protocols of feed restriction can lead to rhythm entrainment.
Pohjanvirta, Raimo [Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, P.O. Box 66, FI-00014, University of Helsinki (Finland); Finnish Food Safety Authority EVIRA, Research Unit of Kuopio, P.O. Box 92, FI-70701 Kuopio (Finland); National Public Health Institute, Laboratory of Toxicology, P.O. Box 95, FI-70701 Kuopio (Finland)], E-mail: firstname.lastname@example.com; Boutros, Paul C.; Moffat, Ivy D. [Department of Pharmacology, University of Toronto, MSB, Toronto, Ontario, M5S 1A8 (Canada); Linden, Jere; Wendelin, Dominique [Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, P.O. Box 66, FI-00014, University of Helsinki (Finland); Okey, Allan B. [Department of Pharmacology, University of Toronto, MSB, Toronto, Ontario, M5S 1A8 (Canada)
Functional Protein Microarray Technology
Functional protein microarrays are emerging as a promising new tool for large-scale and high-throughput studies. In this article, we will review their applications in basic proteomics research, where various types of assays have been developed to probe binding activities to other biomolecules, such as proteins, DNA, RNA, small molecules, and glycans. We will also report recent progress of using functional protein microarrays in profiling protein posttranslational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. Finally, we will discuss potential of functional protein microarrays in biomarker identification and clinical diagnostics. We strongly believe that functional protein microarrays will soon become an indispensible and invaluable tool in proteomics research and systems biology.
Hu, Shaohui; Xie, Zhi; Qian, Jiang; Blackshaw, Seth; Zhu, Heng
Tissue microarray design and construction for scientific, industrial and diagnostic use
Context: In 2013 the high throughput technology known as Tissue Micro Array (TMA) will be fifteen years old. Its elements (design, construction and analysis) are intuitive and the core histopathology technique is unsophisticated, which may be a reason why has eluded a rigorous scientific scrutiny. The source of errors, particularly in specimen identification and how to control for it is unreported. Formal validation of the accuracy of segmenting (also known as de-arraying) hundreds of samples, pairing with the sample data is lacking. Aims: We wanted to address these issues in order to bring the technique to recognized standards of quality in TMA use for research, diagnostics and industrial purposes. Results: We systematically addressed the sources of error and used barcode-driven data input throughout the whole process including matching the design with a TMA virtual image and segmenting that image back to individual cases, together with the associated data. In addition we demonstrate on mathematical grounds that a TMA design, when superimposed onto the corresponding whole slide image, validates on each and every sample the correspondence between the image and patient's data. Conclusions: High throughput use of the TMA technology is a safe and efficient method for research, diagnosis and industrial use if all sources of errors are identified and addressed.
Pilla, Daniela; Bosisio, Francesca M.; Marotta, Roberto; Faggi, Stefano; Forlani, Paolo; Falavigna, Maurizio; Biunno, Ida; Martella, Emanuele; De Blasio, Pasquale; Borghesi, Simone; Cattoretti, Giorgio
Mechanisms of benzene-induced hematotoxicity and leukemogenicity: cDNA microarray analyses using mouse bone marrow tissue.
Although the mechanisms underlying benzene-induced toxicity and leukemogenicity are not yet fully understood, they are likely to be complicated by various pathways, including those of metabolism, growth factor regulation, oxidative stress, DNA damage, cell cycle regulation, and programmed cell death. With this as a background, we performed cDNA microarray analyses on mouse bone marrow tissue during and after a 2-week benzene exposure by inhalation. Our goal was to clarify the mechanisms underlying the hematotoxicity and leukemogenicity induced by benzene at the level of altered multigene expression. Because a few researchers have postulated that the cell cycle regulation mediated by p53 is a critical event for benzene-induced hematotoxicity, the present study was carried out using p53-knockout (KO) mice and C57BL/6 mice. On the basis of the results of large-scale gene expression studies, we conclude the following: (a) Benzene induces DNA damage in cells at any phase of the cell cycle through myeloperoxidase and in the redox cycle, resulting in p53 expression through Raf-1 and cyclin D-interacting myb-like protein 1. (b) For G1/S cell cycle arrest, the p53-mediated pathway through p21 is involved, as well as the pRb gene-mediated pathway. (c) Alteration of cyclin G1 and Wee-1 kinase genes may be related to the G2/M arrest induced by benzene exposure. (d) DNA repair genes such as Rad50 and Rad51 are markedly downregulated in p53-KO mice. (e) p53-mediated caspase 11 activation, aside from p53-mediated Bax gene induction, may be an important pathway for cellular apoptosis after benzene exposure. Our results strongly suggest that the dysfunction of the p53 gene, possibly caused by strong and repeated genetic and epigenetic effects of benzene on candidate leukemia cells, may induce fatal problems such as those of cell cycle checkpoint, apoptosis, and the DNA repair system, finally resulting in hemopoietic malignancies. Our cDNA microarray data provide valuable information for future investigations of the mechanisms underlying the toxicity and leukemogenicity of benzene.
Yoon, Byung-Il; Li, Guang-Xun; Kitada, Kunio; Kawasaki, Yasushi; Igarashi, Katsuhide; Kodama, Yukio; Inoue, Tomoaki; Kobayashi, Kazuko; Kanno, Jun; Kim, Dae-Yong; Inoue, Tohru; Hirabayashi, Yoko
Application of a novel and low cost technique to construct paraffin tissue microarrays out of paraffinised needle biopsy specimens from patients with breast cancer
BackgroundParaffin tissue microarrays (TMAs) are a well accepted tool in pathology for high throughput molecular profiling, quality control and clinicopathological trials. No reports on TMAs constructed from paraffinised needle biopsy specimens (PNBSs) derived from patients with breast cancer can be found in the literature. PNBSs are sometimes the only source for tumour characterisation important for treatment.AimTo develop a novel and
Ulrich Felix Vogel; Burkhard B�ltmann
Altered E-cadherin and epidermal growth factor receptor expressions are associated with patient survival in lung cancer: a study utilizing high-density tissue microarray and immunohistochemistry
E-cadherin (E-cad) and epidermal growth factor receptor (EGFR) are important cell adhesion and signaling pathway mediators. This study aimed to assess their expression in lung adenocarcinoma (AdC) and squamous cell carcinoma (SCC) and their association with clinicopathologic variables. In all, 130 resectable lung cancers (stages I�IIIA) were studied using a high-density tissue microarray. Two to three cores from each case
George Deeb; Jianmin Wang; Nithya Ramnath; Harry K Slocum; Sam Wiseman; Amy Beck; Dongfeng Tan
Simultaneous over activation of EGFR, telomerase (h TERT), and cyclin D1 correlates with advanced disease in larynx squamous cell carcinoma: a tissue microarray analysis
Overexpression of Epidermal Growth Factor Receptor (EGFR) and also of cell cycle control proteins, such as cyclin D1 is a\\u000a frequent event in squamous cell carcinoma of the larynx (LSSC). Our aim was to correlate their protein levels with telomerase\\u000a catalytic subunit (h-TERT) expression. Using tissue microarray technology, fifty-five paraffin embedded histologically confirmed\\u000a primary LSSCs and also ten dysplastic lesions
Aristeidis ChrysovergisVasilios; Vasilios G. Gorgoulis; Ioannis Giotakis; Evangelos Tsiambas; Andreas Karameris; Christos Kittas; Aspasia Kyroudi
A model for the design and construction of a resource for the validation of prognostic prostate cancer biomarkers: the Canary Prostate Cancer Tissue Microarray.
Tissue microarrays (TMAs) provide unique resources for rapid evaluation and validation of tissue biomarkers. The Canary Foundation Retrospective Prostate Tissue Microarray Resource used a rigorous statistical design, quota sampling, a variation of the case-cohort study, to select patients for inclusion in a multicenter, retrospective prostate cancer TMA cohort. The study is designed to definitively validate tissue biomarkers of prostate cancer recurrence after radical prostatectomy. Tissue samples from over 1000 participants treated for prostate cancer with radical prostatectomy between 1995 and 2004 were selected at 6 participating institutions in the United States and Canada. This design captured the heterogeneity of screening and clinical practices in the contemporary North American population. Standardized clinical data were collected in a centralized database. The project has been informative in several respects. The scale and complexity of assembling TMAs with over 200 cases at each of 6 sites involved unanticipated levels of effort and time. Our statistical design promises to provide a model for outcome-based studies where tissue localization methods are applied to high-density TMAs. PMID:23232570
Hawley, Sarah; Fazli, Ladan; McKenney, Jesse K; Simko, Jeff; Troyer, Dean; Nicolas, Marlo; Newcomb, Lisa F; Cowan, Janet E; Crouch, Luis; Ferrari, Michelle; Hernandez, Javier; Hurtado-Coll, Antonio; Kuchinsky, Kyle; Liew, Janet; Mendez-Meza, Rosario; Smith, Elizabeth; Tenggara, Imelda; Zhang, Xiaotun; Carroll, Peter R; Chan, June M; Gleave, Martin; Lance, Raymond; Lin, Daniel W; Nelson, Peter S; Thompson, Ian M; Feng, Ziding; True, Lawrence D; Brooks, James D
Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Background Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations. Results In this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster. Conclusions This study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis.
Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers.
Familial breast cancers that are associated with BRCA1 or BRCA2 germline mutations differ in both their morphological and immunohistochemical characteristics. To further characterize the molecular difference between genotypes, the authors evaluated the expression of 37 immunohistochemical markers in a tissue microarray (TMA) containing cores from 20 BRCA1, 14 BRCA2, and 59 sporadic age-matched breast carcinomas. Markers analyzed included, amog others, common markers in breast cancer, such as hormone receptors, p53 and HER2, along with 15 molecules involved in cell cycle regulation, such as cyclins, cyclin dependent kinases (CDK) and CDK inhibitors (CDKI), apoptosis markers, such as BCL2 and active caspase 3, and two basal/myoepithelial markers (CK 5/6 and P-cadherin). In addition, we analyzed the amplification of CCND1, CCNE, HER2 and MYC by FISH. Unsupervised cluster data analysis of both hereditary and sporadic cases using the complete set of immunohistochemical markers demonstrated that most BRCA1-associated carcinomas grouped in a branch of ER-, HER2-negative tumors that expressed basal cell markers and/or p53 and had higher expression of activated caspase 3. The cell cycle proteins associated with these tumors were E2F6, cyclins A, B1 and E, SKP2 and Topo IIalpha. In contrast, most BRCA2-associated carcinomas grouped in a branch composed by ER/PR/BCL2-positive tumors with a higher expression of the cell cycle proteins cyclin D1, cyclin D3, p27, p16, p21, CDK4, CDK2 and CDK1. In conclusion, our study in hereditary breast cancer tumors analyzing 37 immunohistochemical markers, define the molecular differences between BRCA1 and BRCA2 tumors with respect to hormonal receptors, cell cycle, apoptosis and basal cell markers. PMID:15770521
Palacios, Jos�; Honrado, Emiliano; Osorio, Ana; Cazorla, Alicia; Sarri�, David; Barroso, Alicia; Rodr�guez, Sandra; Cigudosa, Juan C; Diez, Orland; Alonso, Carmen; Lerma, Enrique; Dopazo, Joaqu�n; Rivas, Carmen; Ben�tez, Javier
HER2 evaluation using the novel rabbit monoclonal antibody SP3 and CISH in tissue microarrays of invasive breast carcinomas
Background Laboratory methods for HER2 assessment currently include immunohistochemical (IHC) methods (measuring protein overexpression) and fluorescence in situ hybridisation (FISH) (measuring gene amplification). The measure of HER2 protein by IHC is usually assessed by the mouse monoclonal antibody CB11, and polyclonal antibodies (Herceptest) directed against the internal portion of the receptor. Recently, chromogenic in situ hybridisation (CISH), in which HER2 is detected by a peroxidase reaction and the gene amplification can be determined by regular bright?field microscopy, has emerged as an alternative to FISH. Aims To evaluate the status of HER2 in tissue microarrays (TMAs) of invasive breast cancer using the novel rabbit monoclonal antibody SP3 directed against the external portion of HER2, and correlate the results with CB11 and CISH. Methods IHC was performed with two antibodies (CB11 and SP3) and CISH for HER2 in 10 TMA blocks with 190 formalin?fixed paraffin?embedded cases of invasive breast carcinomas. Results The correlation between SP3 and CB11 was significant (p<0.001) with an agreement rate of 86.9%. When the staining pattern of the two antibodies was compared, the majority of SP3 immunostainings were assessed more easily, with a strong complete membrane staining pattern without non?specific cytoplasmic staining. There was a good correlation between SP3 and CISH (p<0.001). 23/24 SP3 3+ cases showed gene amplification, 97.3% of the cases without gene amplification were SP3 negative, and 6/7 SP3 2+ were amplified. Conclusion The high level of agreement between SP3, a monoclonal antibody that recognises the extracellular domain of the HER2 receptor, and CB11 and CISH, shows that this novel antibody is a reliable candidate to evaluate the expression of HER2 in breast cancer.
Ricardo, Sara Alexandra Vinhas; Milanezi, Fernanda; Carvalho, Silvia Teresa; Leitao, Dina Raquel Aguilera
Characterization of gene expression profiles associated with glioma progression using oligonucleotide-based microarray analysis and real-time reverse transcription-polymerase chain reaction.
Diffuse astrocytoma of World Health Organization (WHO) grade II has an inherent tendency to spontaneously progress to anaplastic astrocytoma (WHO grade III) and/or glioblastoma (WHO grade IV). The molecular basis of astrocytoma progression is still poorly understood, in particular with respect to the progression-associated changes at the mRNA level. Therefore, we compared the transcriptional profile of approximately 6800 genes in primary WHO grade II gliomas and corresponding recurrent high-grade (WHO grade III or IV) gliomas from eight patients using oligonucleotide-based microarray analysis. We identified 66 genes whose mRNA levels differed significantly (P < 0.01, > or =2-fold change) between the primary and recurrent tumors. The microarray data were corroborated by real-time reverse transcription-polymerase chain reaction analysis of 12 selected genes, including 7 genes with increased expression and 5 genes with reduced expression on progression. In addition, the expression of these 12 genes was determined in an independent series of 43 astrocytic gliomas (9 diffuse astrocytomas, 10 anaplastic astrocytomas, 17 primary, and 7 secondary glioblastomas). These analyses confirmed that the transcript levels of nine of the selected genes (COL4A2, FOXM1, MGP, TOP2A, CENPF, IGFBP4, VEGFA, ADD3, and CAMK2G) differed significantly in WHO grade II astrocytomas as compared to anaplastic astrocytomas and/or glioblastomas. Thus, we identified and validated a set of interesting candidate genes whose differential expression likely plays a role in astrocytoma progression. PMID:12937144
van den Boom, J�rg; Wolter, Marietta; Kuick, Rork; Misek, David E; Youkilis, Andrew S; Wechsler, Daniel S; Sommer, Clemens; Reifenberger, Guido; Hanash, Samir M
Distribution of p63, cytokeratins 5/6 and cytokeratin 14 in 51 normal and 400 neoplastic human tissue samples using TARP-4 multi-tumor tissue microarray.
p63, cytokeratin (CK) 5/6 and CK 14 have been employed in diagnostic pathology as markers of basal, squamous and myoepithelial differentiation in several types of human neoplasms; however, there is scant data on the concurrent expression of these markers in large series of human neoplasms. We analyzed the distribution of these three immunohistochemical markers in 51 normal human tissue samples, 350 carcinomas, 25 malignant melanomas (MMs), and 25 glioblastomas using three serial sections of tissue array research program (TARP)-4 multi-tumor tissue microarray. Also, we performed double immunostainings to characterize the differential distribution of p63/CK 5/6 and p63/CK 14 in normal breast, salivary gland and skin. p63, CK 5/6 and CK 14 were expressed in basal cells of the prostate and respiratory epithelia and in breast and bronchial myoepithelial cells. p63 was also expressed in cytotrophoblast cells of human placenta and in scattered cells of lymph node germinal center. CK 5/6 and CK 14 also stained the cytoplasm of basal cells of esophageal stratified squamous epithelium and transitional epithelial cells of the bladder. No mesenchymal, neural, endothelial, smooth muscle or adipose cells were stained by any of the markers. p63, CK 5/6, and CK 14 were respectively expressed in 92.6%, 75.0%, and 52.9% of the squamous cell carcinomas of the lung, 10.2%, 20.0%, and 7.4% of the ductal carcinomas of the breast, 12.9%, 34.4%, and 11.8% of the serous and 25.0%, 0%, and 0% of the endometrioid carcinomas of the ovary. Lung, prostate and colonic adenocarcinomas, as well as MMs and glioblastomas were only rarely decorated by one of the markers. Only matched samples of 16 squamous cell carcinomas and two ductal carcinomas of the breast co-expressed these three markers. In double immunostainings, p63-CK 5/6, as well as p63-CK 14 were co-expressed by basal/myoepithelial cells of the salivary glands and basal cells of the epidermis. Our results demonstrate that p63, CK 5/6 and CK 14 may be used together in immunohistochemical panels to characterize squamous differentiation in poorly differentiated carcinomas or carcinomas of unknown origin. PMID:12884041
Reis-Filho, Jorge S; Simpson, Pete T; Martins, Albino; Preto, Ana; G�rtner, F�tima; Schmitt, Fernando C
Gene Expression Profiling with DNA Microarrays
DNA microarrays are small solid supports on the surface of which DNA probes for thousands of genes have been orderly arrayed.\\u000a Hybridization of labeled RNA from tissues or tumors allows evaluation of the relative amount of any specific mRNA present\\u000a in the samples, depicting its gene expression profile. During development and progression of breast cancers, specific genetic\\u000a programs are activated,
Michele Bortoli; Nicoletta Biglia
Overview of Protein Microarrays
Protein microarray is an emerging technology that provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput way. Two major classes of protein microarrays are defined to describe their applications: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. While the fabrication technology is maturing, applications of protein microarrays, especially functional protein microarrays, have flourished during the past decade. Here, we will first review recent advances in the protein microarray technologies, and then present a series of examples to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. The research areas will include detection of various binding properties of proteins, study of protein posttranslational modifications, analysis of host-microbe interactions, profiling antibody specificity, and identification of biomarkers in autoimmune diseases. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade.
Reymond Sutandy, FX; Qian, Jiang; Chen, Chien-Sheng; Zhu, Heng
Functional tissue engineering: Ten more years of progress.
"Functional tissue engineering" is a subset of the field of tissue engineering that was proposed by the United States National Committee on Biomechanics over a decade ago in order to place more emphasis on the roles of biomechanics and mechanobiology in tissue repair and regeneration. Over the past decade, there have been tremendous advances in this area, pointing out the critical role that biomechanical factors can play in the engineered repair of virtually all tissue and organ systems. In this special issue of the Journal of Biomechanics, we present a series of articles that address a broad array of the fundamental topics of functional tissue engineering, including: (1) measurement and modeling of the in vivo biomechanical environment and history in native and repair tissues; (2) further understanding of the biomechanical properties of native tissues across all geometric scales, in the context of repair or regeneration; (3) prioritization of specific biomechanical properties as design criteria; (4) development of biomaterials, scaffolds, and engineered tissues with prescribed biomechanical properties; (5) development of success criteria based on appropriate outcome measures; (6) investigation of the effects of mechanical factors on tissue repair in vivo; (7) investigation of the mechanisms by which physical factors may enhance tissue regeneration in vitro; and (8) development and validation of computational models of tissue growth and remodeling. These articles represent the tremendous expansion of this field in recent years, and emphasize the critical roles that biomechanics and mechanobiology play in controlling tissue repair and regeneration. PMID:24746021
Guilak, Farshid; Baaijens, Frank P T
Validation of 2-mm Tissue Microarray Technology in Gastric Cancer. Agreement of 2-mm TMAs and Full Sections for Glut-1 and Hif-1 Alpha.
Background/Aim: Tissue Microarray (TMA) is a widely used method to perform high-throughput immunohistochemical analyses on different tissues by arraying small sample cores from paraffin-fixed tissues into a single paraffin block. TMA-technology has been validated on numerous cancer tissues and also for gastric cancer studies, although it has not been validated for this tumor tissue so far. The objective of this study was to assess, whether the 2-mm TMA-technology is able to provide representative samples of gastric cancer tissue. Materials and Methods: TMA paraffin blocks were constructed by means of 220 formalin-fixed and paraffin-embedded gastric cancer samples with a sample diameter of 2 mm. The agreement of immunohistochemical stainings of Glut-1 and Hif-1 alpha in TMA sections and the original full sections was calculated using kappa statistics and direct adjustment. Results: The congruence was substantial for Glut-1 (kappa 0.64) and Hif-1 alpha (kappa 0.70), but with an agreement of only 71% and 52% within the marker-positive cases of the full-section slides. Conclusion: Due to tumor heterogeneity primarily, the TMA technology with a 2-mm sample core shows relevant limitations in gastric cancer tissue. Although being helpful for tissue screening purposes, the 2-mm TMA technology cannot be recommended as a method equal to full-section investigations in gastric cancer. PMID:24982335
Berlth, Felix; M�nig, Stefan P; Schl�sser, Hans A; Maus, Martin; Baltin, Christoph T H; Urbanski, Alexander; Drebber, Uta; Bollschweiler, Elfriede; H�lscher, Arnulf H; Alakus, Hakan
In-house Manual Construction of High-Density and High-Quality Tissue Microarrays by Using Homemade Recipient Agarose-Paraffin Blocks
Background Self-made tissue punches can be effectively used to punch holes in blank recipient paraffin blocks and extract tissue cores from the donor paraffin blocks for the low-cost construction of tissue microarrays (TMAs). However, variable degrees of section distortion and loss of the tissue cores can occurs during cutting of the TMAs, posing technical problems for in-house manual construction of high-density TMAs. We aimed to update the method for in-house manual TMA construction to improve the quality of high-density TMAs. Methods Blocks of agarose gel were subjected to the standard tissue processing and embedding procedure to prepare recipient agarose-paraffin blocks. The self-made tissue punches and recipient agarose-paraffin blocks were used to construct TMAs, which were completely melted and re-embedded in paraffin to make finished TMA blocks. Results The donor tissue cores were completely integrated into the surrounding paraffin of the recipient blocks. This method enabled us to construct high-density TMAs with significantly less section distortion or loss of tissue cores during microtomy. Conclusions Simple and inexpensive construction of high-density and high-quality TMAs can be warranted by using paraffinized agarose gels as recipient blocks.
Kim, Kyu Ho; Choi, Yeon Il; Kim, Lucia; Park, In Suh; Han, Jee Young; Kim, Joon Mee; Chu, Young Chae
Expression profiling of colorectal carcinomas using tissue microarrays: cell cycle regulatory proteins p21, p27, and p53 as immunohistochemical prognostic markers in univariate and multivariate analysis.
With the rapidly growing understanding of tumor biology, molecular staging of cancer is expected to improve prognostication. This would be particularly important for cancers amenable to adjuvant treatment, such as colorectal carcinomas. To generate data for this, the tissue microarray technique may prove useful. Tissue microarrays were constructed with triplicate cores (0.6 mm diameter) from the invasive margins of a consecutive single-institution series of 184 colorectal carcinomas. Immunostaining for p53, p21, p27, Ecadherin, and beta-catenin was scored. Tumor cell proliferation was assessed by mitotic indices and Ki-67 labeling, apoptosis by quantification of apoptotic bodies. Reduced nuclear immunostaining for p21 (<10%) and p27 (< or =50%) and reduced membranous expression of Ecadherin were significantly associated with a poorer clinical course by univariate analysis. beta-catenin immunostaining had no prognostic impact. Mitotic and apoptotic indices as well as Ki-67 labeling below the median were indicators of poor prognosis. Complete absence of p53 nuclear staining was a significant adverse prognostic factor. By Cox regression, p53 = 0%, p53 = 0%, in combination with p27 < or = 50%, the mitotic index and the combined mitotic and apoptotic index added prognostic information to UICC stage. The authors found that growth pattern, lymphohistiocytic response, lymphatic permeation, and venous spread, too, each was a strong prognosticator in addition to UICC stage. The results support that tissue microarrays are a useful tool for screening immunohistochemical markers for prognostic use. An immunopanel of p21, p27, and p53 could be useful for prognostication in colorectal carcinoma in addition to UICC stage. PMID:15354735
Prall, Friedrich; Ostwald, Christiane; Nizze, Horst; Barten, Malte
Pulp and dentin tissue engineering and regeneration: current progress
Dental pulp tissue is vulnerable to infection. Entire pulp amputation followed by pulp-space disinfection and filling with an artificial rubber-like material is employed to treat the infection � commonly known as root-canal therapy. Regeneration of pulp tissue has been difficult as the tissue is encased in dentin without collateral blood supply except from the root apical end. However, with the advent of the concept of modern tissue engineering and the discovery of dental stem cells, regeneration of pulp and dentin has been tested. This article will review the early attempts to regenerate pulp tissue and the current endeavor of pulp and dentin tissue engineering, and regeneration. The prospective outcome of the current advancement in this line of research will be discussed.
Huang, George TJ
Hydrogel scaffolds for tissue engineering: Progress and challenges
Designing of biologically active scaffolds with optimal characteristics is one of the key factors for successful tissue engineering. Recently, hydrogels have received a considerable interest as leading candidates for engineered tissue scaffolds due to their unique compositional and structural similarities to the natural extracellular matrix, in addition to their desirable framework for cellular proliferation and survival. More recently, the ability to control the shape, porosity, surface morphology, and size of hydrogel scaffolds has created new opportunities to overcome various challenges in tissue engineering such as vascularization, tissue architecture and simultaneous seeding of multiple cells. This review provides an overview of the different types of hydrogels, the approaches that can be used to fabricate hydrogel matrices with specific features and the recent applications of hydrogels in tissue engineering. Special attention was given to the various design considerations for an efficient hydrogel scaffold in tissue engineering. Also, the challenges associated with the use of hydrogel scaffolds were described.
El-Sherbiny, Ibrahim M.; Yacoub, Magdi H.
Oligonucleotide microarray analysis of distinct gene expression patterns in colorectal cancer tissues harboring BRAF and K-ras mutations
Various types of human cancers harbor BRAF somatic mutations, leading researchers to seek molecular targets for BRAF inhibitors. A mutually exclusive relationship has been observed between the BRAF-V600E mutation and K-ras mutations, suggesting that the BRAF-V600E mutation may differ from the other BRAF mutant types. Here, we used microarray analysis to examine differences between the BRAF and K-ras mutant colorectal
Il-Jin Kim; Hio Chung Kang; Sang-Geun Jang; Kun Kim; Sun-A Ahn; Hyun-Ju Yoon; Sang Nam Yoon; Jae-Gahb Park
Automated ERCC1 immunochemistry on hybrid cytology/tissue microarray of malignant effusions: evaluation of antibodies 8F1 and D-10
Background The excision repair cross-complementation group 1 (ERCC1) protein is the key enzyme of the nucleotide excision repair (NER) pathway. Loss of protein expression on immunohistochemistry is predictive for platinum-based chemotherapy response. Frequently, the diagnosis of malignancy is made on cytologic effusion samples. Therefore, we evaluated the staining quality of monoclonal anti-ERCC1 antibodies 8F1 and D-10 on microarrays of malignant pleural and peritoneal effusions by automated immunochemistry. Methods Cores from effusion cell blocks of 117 patients with > 40 malignant cell clusters per whole section (pleural n = 75, peritoneal n = 42) were assembled together with 30 histologic control cores from large tissue blocks (lung, breast and ovarian carcinoma, each n = 10) on hybrid cytology-tissue microarrays (C/TMA). Four immunochemistry protocols (Mab 8F1 and D-10, CC1-mono Ventana and H2-60 Bond automat) were performed. Immunoreactivity was semi-quantitatively scored for intensity and intensity multiplied by percentage staining (H-score). Results Tumors were classified into female genital tract carcinoma (n = 39), lung adenocarcinoma (n = 23), mesothelioma (n = 15), unknown primary (n = 14), breast carcinoma (n = 10), gastro-intestinal carcinoma (n = 12) and other (n = 4). On both platforms, reproducible nuclear ERCC1 immunoreactivity was achieved with both antibodies, although D-10 was slightly weaker and presented more background staining as well as more variation in the low expression range. No significant differences were found between cytologic and histologic cores. Using the 8F1 CC1-mono protocol, lung and breast carcinomas had lower ERCC1 expression in comparison to the other entities (p-value < 0.05). Conclusions Cytology microarrays (CMA) are suitable for investigation of clinical biomarkers and can be combined with conventional TMA's. Dichotomization of ERCC1 immunoreactivity scores is most suitable for patient stratification since definition of negativity is antibody-dependent.
Progress and opportunities for tissue-engineered skin
NASA Astrophysics Data System (ADS)
Tissue-engineered skin is now a reality. For patients with extensive full-thickness burns, laboratory expansion of skin cells to achieve barrier function can make the difference between life and death, and it was this acute need that drove the initiation of tissue engineering in the 1980s. A much larger group of patients have ulcers resistant to conventional healing, and treatments using cultured skin cells have been devised to restart the wound-healing process. In the laboratory, the use of tissue-engineered skin provides insight into the behaviour of skin cells in healthy skin and in diseases such as vitiligo, melanoma, psoriasis and blistering disorders.
MacNeil, Sheila
NASA Astrophysics Data System (ADS)
Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.
Nguyen, C.; Gidrol, X.
Progress and opportunities for tissue-engineered skin
Tissue-engineered skin is now a reality. For patients with extensive full-thickness burns, laboratory expansion of skin cells to achieve barrier function can make the difference between life and death, and it was this acute need that drove the initiation of tissue engineering in the 1980s. A much larger group of patients have ulcers resistant to conventional healing, and treatments using
Sheila MacNeil
Expression of SHP2 and related markers in non-small cell lung cancer: a tissue microarray study of 80 cases.
The purpose of this study was to assess the relationships between the expression of SHP2 and VEGF, VEGFR-1, VEGFR-2, MMP-2, MMP-9, TIMP-1, TIMP-2, and microvessel density (MVD), as well as the clinicopathologic parameters of these markers in non-small cell lung cancer (NSCLC). Using a tissue microarray, the expression of these 8 markers in 80 NSCLC cases was detected by immunohistochemistry. The expression of the markers was higher in cancer tissues when compared with the surrounding tissues. The MVD was lower in the CD34-positive cancer tissues than in the surrounding tissues. Significantly higher positive rates of expression for SHP2, MMP-9, and MMP-2 were observed in patients with lymph node metastases. The later the clinical stage was, the higher the expression of MMP-9 and MMP-2. The expression of VEGF in patients with lung squamous cell carcinomas was significantly higher than in patients with lung adenocarcinomas. The positive expression of SHP2 correlated significantly with that of VEGFR-2 and the MVD and a survival disadvantage was noted in the patients with SHP2-positive tumors. Therefore, our data suggest that the expression of SHP2 in NSCLC has high specificity and sensitivity and is closely related to lymph node metastasis and the expression of VEGFR-2 and the MVD in patients with NSCLC. SHP2 expression may promote the invasion and metastasis of NSCLC through angiogenesis and the lymphatic system. PMID:23343958
Tang, Chunlan; Luo, Dan; Yang, Heping; Wang, Qingliang; Zhang, Rong; Liu, Guoxiang; Zhou, Xiangdong
A striking feature of stress relaxation in biological soft tissue is that it frequently follows a power law in time with an exponent that is independent of strain even when the elastic properties of the tissue are highly nonlinear. This kind of behavior is an example of quasi-linear viscoelasticity, and is usually modeled in a purely empirical fashion. The goal of the present study was to account for quasi-linear viscoelasticity in mechanistic terms based on our previously developed hypothesis that it arises as a result of isolated micro-yield events occurring in sequence throughout the tissue, each event passing the stress it was sustaining on to other regions of the tissue until they themselves yield. We modeled stress relaxation computationally in a collection of stress-bearing elements. Each element experiences a stochastic sequence of either increases in elastic equilibrium length or decreases in stiffness according to the stress imposed upon it. This successfully predicts quasi-linear viscoelastic behavior, and in addition predicts power-law stress relaxation that proceeds at the same slow rate as observed in real biological soft tissue.
Bates, Jason H.T.; Ma, Baoshun
Molecular Profiling of Bladder Cancer Using cDNA Microarrays: Defining Histogenesis and Biological Phenotypes1
This study was designed to characterize the expression profiles of nine bladder cancer cell lines (T24, J82, 5637, HT1376, RT4, SCaBER, TCCSUP, UMUC-3, and HT1197) using cDNA microarrays (8976 genes and expressed sequence tags). Novel targets involved in bladder cancer progression of potential clinical relevance were validated by immunohis- tochemistry using tissue microarrays of primary bladder tumors (n 193 cases).
Marta Sanchez-Carbayo; Nicholas D. Socci; Elizabeth Charytonowicz; Minglan Lu; Michael Prystowsky; Geoffrey Childs; Carlos Cordon-Cardo
[Progress on research of tissue culture of Siraitia grosvenorii].
In this paper we reviewed the development of tissue culture, current situations of virus-free plantlets industrialization and the way to deal with the situations, application prospects of Siraitia grosvenorii so as to give some advice for its further study and application. PMID:15806960
Fu, Chang-Liang; Ma, Xiao-Jun; Bai, Long-Hua; Zhao, Xin
Cellular Proliferation and Regeneration Following Tissue Damage. Progress Report.
National Technical Information Service (NTIS)
Tissue cultures of rabbit retinal vasculature were studied in vivo and in vitro by scanning electron microscopy to elucidate the regnerative process from an injury. Human lens are now being compared with a goal for developing a bioassay for testing the ef...
C. V. Harding
ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology
Objective and design The design and implementation of ImageMiner, a software platform for performing comparative analysis of expression patterns in imaged microscopy specimens such as tissue microarrays (TMAs), is described. ImageMiner is a federated system of services that provides a reliable set of analytical and data management capabilities for investigative research applications in pathology. It provides a library of image processing methods, including automated registration, segmentation, feature extraction, and classification, all of which have been tailored, in these studies, to support TMA analysis. The system is designed to leverage high-performance computing machines so that investigators can rapidly analyze large ensembles of imaged TMA specimens. To support deployment in collaborative, multi-institutional projects, ImageMiner features grid-enabled, service-based components so that multiple instances of ImageMiner can be accessed remotely and federated. Results The experimental evaluation shows that: (1) ImageMiner is able to support reliable detection and feature extraction of tumor regions within imaged tissues; (2) images and analysis results managed in ImageMiner can be searched for and retrieved on the basis of image-based features, classification information, and any correlated clinical data, including any metadata that have been generated to describe the specified tissue and TMA; and (3) the system is able to reduce computation time of analyses by exploiting computing clusters, which facilitates analysis of larger sets of tissue samples.
Foran, David J; Yang, Lin; Hu, Jun; Goodell, Lauri A; Reiss, Michael; Wang, Fusheng; Kurc, Tahsin; Pan, Tony; Sharma, Ashish; Saltz, Joel H
Pathomechanisms: homeostatic chemokines in health, tissue regeneration, and progressive diseases.
Homeostatic chemokines control stem and progenitor cell migration and activation during vasculogenesis and organ development. They orchestrate hematopoietic stem cell (HSC) homing to their bone marrow niches and direct immature lymphocytes to a series of maturation sites within lymphoid organs. Along these lines, homeostatic chemokines regulate the niches of peripheral committed progenitor cell populations for tissue renewal. These biological functions support neovascularization and wound healing, including the recruitment of endothelial and other progenitor cells from the bone marrow. Here, we summarize the roles of homeostatic chemokines, their signaling receptors, and atypical decoy receptors during homeostasis and tissue regeneration in order to better understand their pathogenic roles in disease, for example, in diabetes complications, cancer, autoimmunity, epithelial hyperplasia, or hypertrophic scarring and fibrosis. PMID:24440002
Anders, Hans-Joachim; Romagnani, Paola; Mantovani, Alberto
Novel functional profiling approach combining reverse phase protein microarrays and human 3-D ex vivo tissue cultures: expression of apoptosis-related proteins in human colon cancer.
Cancer is caused by a complex pattern of molecular perturbations. To understand the biology of cancer, it is thus important to look at the activation state of key proteins and signaling networks. The limited amount of available sample material from patients and the complexity of protein expression patterns make the use of traditional protein analysis methods particularly difficult. In addition, the only approach that is currently available for performing functional studies is the use of serial biopsies, which is limited by ethical constraints and patient acceptance. The goal of this work was to establish a 3-D ex vivo culture technique in combination with reverse-phase protein microarrays (RPPM) as a novel experimental tool for use in cancer research. The RPPM platform allows the parallel profiling of large numbers of protein analytes to determine their relative abundance and activation level. Cancer tissue and the respective corresponding normal tissue controls from patients with colorectal cancer were cultured ex vivo. At various time points, the cultured samples were processed into lysates and analyzed on RPPM to assess the expression of carcinoembryonic antigen (CEA) and 24 proteins involved in the regulation of apoptosis. The methodology displayed good robustness and low system noise. As a proof of concept, CEA expression was significantly higher in tumor compared with normal tissue (p<0.0001). The caspase 9 expression signal was lower in tumor tissue than in normal tissue (p<0.001). Cleaved Caspase 8 (p=0.014), Bad (p=0.007), Bim (p=0.007), p73 (p=0.005), PARP (p<0.001), and cleaved PARP (p=0.007) were differentially expressed in normal liver and normal colon tissue. We demonstrate here the feasibility of using RPPM technology with 3-D ex vivo cultured samples. This approach is useful for investigating complex patterns of protein expression and modification over time. It should allow functional proteomics in patient samples with various applications such as pharmacodynamic analyses in drug development. PMID:19609961
Pirnia, Farzaneh; Pawlak, Michael; Thallinger, Gerhard G; Gierke, Berthold; Templin, Markus F; Kappeler, Andi; Betticher, Daniel C; Gloor, Beat; Borner, Markus M
Microarrays for Undergraduate Classes
ERIC Educational Resources Information Center
A microarray experiment is presented that, in six laboratory sessions, takes undergraduate students from the tissue sample right through to data analysis. The model chosen, the murine erythroleukemia cell line, can be easily cultured in sufficient quantities for class use. Large changes in gene expression can be induced in these cells by�
Hancock, Dale; Nguyen, Lisa L.; Denyer, Gareth S.; Johnston, Jill M.
Tissue hemoglobin monitoring of progressive central hypovolemia in humans using broadband diffuse optical spectroscopy
We demonstrate noninvasive near-infrared diffuse optical spectroscopy (DOS) measurements of tissue hemoglobin contents that can track progressive reductions in central blood volume in human volunteers. Measurements of mean arterial blood pressure (MAP), heart rate (HR), stroke volume (SV), and cardiac output (Q) are obtained in ten healthy human subjects during baseline supine rest and exposure to progressive reductions of central blood volume produced by application of lower body negative pressure (LBNP). Simultaneous quantitative noninvasive measurements of tissue oxyhemoglobin (OHb), deoxyhemoglobin (RHb), total hemoglobin concentration (THb), and tissue hemoglobin oxygen saturation (StO2) are performed throughout LBNP application using broadband DOS. As progressively increasing amounts of LBNP are applied, HR increases, and MAP, SV, and Q decrease (p<0.001). OHb, StO2, and THb decrease (p <0.001) in correlation with progressive increases in LBNP, while tissue RHb remained relatively constant (p=0.378). The average fractional changes from baseline values in DOS OHb (fOHb) correlate closely with independently measured changes in SV (r2=0.95) and Q (r2=0.98) during LBNP. Quantitative noninvasive broadband DOS measurements of tissue hemoglobin parameters of peripheral perfusion are capable of detecting progressive reductions in central blood volume, and appear to be sensitive markers of early hypoperfusion associated with hemorrhage as simulated by LBNP.
Lee, Jangwoen; Kim, Jae G.; Mahon, Sari; Tromberg, Bruce J.; Ryan, Kathy L.; Convertino, Victor A.; Rickards, Caroline A.; Osann, Kathryn; Brenner, Matthew
Numerical and Structural Genomic Aberrations Are Reliably Detectable in Tissue Microarrays of Formalin-Fixed Paraffin-Embedded Tumor Samples by Fluorescence In-Situ Hybridization
Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL) and six malignant mesothelioma (MM) samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.
Horn, Heike; Bausinger, Julia; Staiger, Annette M.; Sohn, Maximilian; Schmelter, Christopher; Gruber, Kim; Kalla, Claudia; Ott, M. Michaela; Rosenwald, Andreas; Ott, German
Microarray-Based Capture of Novel Expressed Cell Type-Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster
Faithful annotation of tissue-specific transcript isoforms is important not only to understand how genes are organized and regulated but also to identify potential novel, unannotated exons of genes, which may be additional targets of mutation in disease states or while performing mutagenic screens. We have developed a microarray enrichment methodology followed by long-read, next-generation sequencing for identification of unannotated transcript isoforms expressed in two Drosophila tissues, the ovary and the testis. Even with limited sequencing, these studies have identified a large number of novel transcription units, including 5? exons and extensions, 3? exons and extensions, internal exons and exon extensions, gene fusions, and both germline-specific splicing events and promoters. Additionally, comparing our capture dataset with tiling array and traditional RNA-seq analysis, we demonstrate that our enrichment strategy is able to capture low-abundance transcripts that cannot readily be identified by the other strategies. Finally, we show that our methodology can help identify transcriptional signatures of minority cell types within the ovary that would otherwise be difficult to reveal without the CoNECT enrichment strategy. These studies introduce an efficient methodology for cataloging tissue-specific transcriptomes in which specific classes of genes or transcripts can be targeted for capture and sequence, thus reducing the significant sequencing depth normally required for accurate annotation.
Hong, X.; Doddapaneni, H.; Comeron, J. M.; Rodesch, M. J.; Halvensleben, H. A.; Nien, C. Y.; Bolei, F.; Metpally, R.; Richmond, T. A.; Albert, T. J.; Manak, J. R.
Discovery of Colorectal Cancer Biomarker Candidates by Membrane Proteomic Analysis and Subsequent Verification using Selected Reaction Monitoring (SRM) and Tissue Microarray (TMA) Analysis.
Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851. PMID:24687888
Kume, Hideaki; Muraoka, Satoshi; Kuga, Takahisa; Adachi, Jun; Narumi, Ryohei; Watanabe, Shio; Kuwano, Masayoshi; Kodera, Yoshio; Matsushita, Kazuyuki; Fukuoka, Junya; Masuda, Takeshi; Ishihama, Yasushi; Matsubara, Hisahiro; Nomura, Fumio; Tomonaga, Takeshi
Measuring brain lesion progression with a supervised tissue classification system.
Brain lesions, especially White Matter Lesions (WMLs), are associated with cardiac and vascular disease, but also with normal aging. Quantitative analysis of WML in large clinical trials is becoming more and more important. In this paper, we present a computer-assisted WML segmentation method, based on local features extracted from conventional multi-parametric Magnetic Resonance Imaging (MRI) sequences. A framework for preprocessing the temporal data by jointly equalizing histograms reduces the spatial and temporal variance of data, thereby improving the longitudinal stability of such measurements and hence the estimate of lesion progression. A Support Vector Machine (SVM) classifier trained on expert-defined WML's is applied for lesion segmentation on each scan using the AdaBoost algorithm. Validation on a population of 23 patients from 3 different imaging sites with follow-up studies and WMLs of varying sizes, shapes and locations tests the robustness and accuracy of the proposed segmentation method, compared to the manual segmentation results from an experienced neuroradiologist. The results show that our CAD-system achieves consistent lesion segmentation in the 4D data facilitating the disease monitoring. PMID:18979798
Zacharaki, Evangelia I; Kanterakis, Stathis; Bryan, R Nick; Davatzikos, Christos
NSDL National Science Digital Library
Microarray analysis of RNA expression has been changing the way gene expression is assayed, but challenges remain in analyzing the results and interpreting the data to gain biologically meaningful mechanistic insights.
Michael B. Yaffe (American Association for the Advancement of Science;Science Signaling REV)
Matrix Metalloproteases and Tissue Inhibitors of Metalloproteinases in Medial Plica and Pannus-like Tissue Contribute to Knee Osteoarthritis Progression
Osteoarthritis (OA) is characterized by degradation of the cartilage matrix, leading to pathologic changes in the joints. However, the pathogenic effects of synovial tissue inflammation on OA knees are not clear. To investigate whether the inflammation caused by the medial plica is involved in the pathogenesis of osteoarthritis, we examined the expression of matrix metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), interleukin (IL)-1?, and tumor necrosis factor (TNF)-? in the medial plica and pannus-like tissue in the knees of patients with medial compartment OA who underwent either arthroscopic medial release (stage II; 15 knee joints from 15 patients) or total knee replacement (stage IV; 18 knee joints from 18 patients). MMP-2, MMP-3, MMP-9, IL-1?, and TNF-? mRNA and protein levels measured, respectively, by quantitative real-time PCR and Quantibody human MMP arrays, were highly expressed in extracts of medial plica and pannus-like tissue from stage IV knee joints. Immunohistochemical staining also demonstrated high expression of MMP-2, MMP-3, and MMP-9 in plica and pannus-like tissue of stage IV OA knees and not in normal cartilage. Some TIMP/MMP ratios decreased significantly in both medial plica and pannus-like tissue as disease progressed from stage II to stage IV. Furthermore, the migration of cells from the pannus-like tissue was enhanced by IL-1?, while plica cell migration was enhanced by TNF-?. The results suggest that medial plica and pannus-like tissue may be involved in the process of cartilage degradation in medial compartment OA of the knee.
Yang, Chih-Chang; Lin, Cheng-Yu; Wang, Hwai-Shi; Lyu, Shaw-Ruey
Clinico-Pathological and Prognostic Significance of p53, Bcl-2 and Her-2/neu Protein Markers in Colorectal Cancer Using Tissue Microarray.
Background: The prognostic role of her-2/neu has been established in breast cancer but remains controversial in colorectal cancer (CRC). Widespread genetic mutations in colorectal carcinogenesis exist on chromosome 17. Her- 2/neu gene and the tumor suppressor gene p53 are both located on this chromosome. Bcl-2 protein prolongs survival of a variety of cells by blocking apoptosis. The aim of this study is to evaluate the relationship between the overexpression of p53, bcl-2 and her-2/neu protein markers and the clinico-pathologic characteristics of CRC, and their influence on survival rates. Patients and Methods: One hundred and four cases of CRC had paraffin blocks with representative tissue, and sufficient follow-up data. They were arrayed and evaluated for protein marker expression using tissue microarray (TMA). Results: Ten (9.6%), 35 (33.7%) and 27 (26%) of the patients were her-2/neu, p53 and bcl-2 positive, respectively. None of the examined clinico-pathologic factors had a significant relation with her-2/neu overexpression. Patients with +ve bcl-2 had a significantly higher mean age (52.4-/+13.3years) compared to 45.4-/+14.4 years for bcl-2 negative patients, p=0.03. Positive p53 was overexpressed in 20/44 (45.5%), 6/17 (35%), 9/43 (21%) cases of the colon, recto-sigmoid, and rectal sites, respectively, p=0.05. For the whole population, p53 overexpression had a significantly lower disease-free survival (DFS). For patients with Dukes' stage B, overexpression of p53 protein had a significant reduced overall survival (OS) p=0.04, metastasis free survival (MFS) p=0.004, and DFS p=0.01 rates. Expression of bcl-2 had a significantly better MFS p=0.001, while her-2/neu overexpression worsened the OS rate significantly, p=0.04. Conclusion: This study recommends the application of TMA technique for its economic importance and reliable quick throughput. The results from this study also suggest that overexpression of p53, bcl-2, and her-2/neu protein markers appear to be useful in selecting a group of CRC patients with a worse prognosis and constitute potential candidates for adjuvant therapy. Key Words: Her-2/neu , p53 , Bcl-2 , Colorectal cancer , Tissue microarray , Prognostic factors. PMID:18839030
Ismail, Hoda M; El-Baradie, Manal; Moneer, Manar; Khorshid, Ola; Touny, Ahmed
Trans-10, cis-12 conjugated linoleic acid causes inflammation and delipidation of white adipose tissue in mice: a microarray and histological analysis.
A combined histological and microarray analysis of the white adipose tissue (WAT) of mice fed trans-10, cis-12 conjugated linoleic acid (t10c12 CLA) was performed to better define functional responses. Mice fed t10c12 CLA for 14 days lost 85% of WAT mass, 95% of adipocyte lipid droplet volume, and 15 or 47% of the number of adipocytes and total cells, respectively. Microarray profiling of replicated pools (n = 2 per day x diet) of control and treated mice (n = 140) at seven time points after 1-17 days of t10c12 CLA feeding found between 2,682 and 4,216 transcript levels changed by twofold or more. Transcript levels for genes involved in glucose and fatty acid import or biosynthesis were significantly reduced. Highly expressed transcripts for lipases were significantly reduced but still abundant. Increased levels of mRNAs for two key thermogenesis proteins, uncoupling protein 1 and carnitine palmitoyltransferase 1, may have increased energy expenditures. Significant reductions of mRNAs for major adipocyte regulatory factors, including peroxisome proliferator activated receptor-gamma, sterol regulatory binding protein 1, CAAT/enhancer binding protein-alpha, and lipin 1 were correlated with the reduced transcript levels for key metabolic pathways in the WAT. A prolific inflammation response was indicated by the 2- to 100-fold induction of many cytokine transcripts, including those for IL-6, IL-1beta, TNF ligands, and CXC family members, and an increased density of macrophages. The mRNA changes suggest that a combination of cell loss, increased energy expenditure, and residual transport of lipids out of the adipocytes may account for the cumulative mass loss observed. PMID:16868072
LaRosa, P Christopher; Miner, Jess; Xia, Yuannan; Zhou, You; Kachman, Steve; Fromm, Michael E
Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Preliminary assessment of cross-platform concordance
Next-generation sequencing is increasingly employed in biomedical investigations. Strong concordance between microarray and mRNA-seq levels has been reported in high quality specimens but information is lacking on formalin-fixed, paraffin-embedded (FFPE) tissues, and particularly for microRNA (miRNA) analysis. We conducted a preliminary examination of the concordance between miRNA-seq and cDNA-mediated annealing, selection, extension, and ligation (DASL) miRNA assays. Quantitative agreement between platforms is moderate (Spearman correlation 0.514�0.596) and there is discordance of detection calls on a subset of miRNAs. Quantitative PCR (q-RT-PCR) performed for several discordant miRNAs confirmed the presence of most sequences detected by miRNA-seq but not by DASL but also that miRNA-seq did not detect some sequences, which DASL confidently detected. Our results suggest that miRNA-seq is specific, with few false positive calls, but it may not detect certain abundant miRNAs in FFPE tissue. Further work is necessary to fully address these issues that are pertinent for translational research.
Kelly, Andrew D.; Hill, Katherine E.; Correll, Mick; Hu, Lan; Wang, Yaoyu; Rubio, Renee; Duan, Shenghua; Quackenbush, John; Spentzos, Dimitrios
Endothelial necrosis at 1h post-burn predicts progression of tissue injury
Burn injury progression has not been well characterized at the cellular level. To define burn injury progression in terms of cell death, histopathologic spatiotemporal relationships of cellular necrosis and apoptosis were investigated in a validated porcine model of vertical burn injury progression. Cell necrosis was identified by High Mobility Group Box 1 protein and apoptosis by Caspase 3a staining of tissue samples taken 1h, 24h and 7 days post-burn. Level of endothelial cell necrosis at 1h was predictive of level of apoptosis at 24h (Pearson's r=0.87) and of level of tissue necrosis at 7 days (Pearson's r=0.87). Furthermore, endothelial cell necrosis was deeper than interstitial cell necrosis at 1h (p<0.001). Endothelial cell necrosis at 1h divided the zone of injury progression (Jackson's zone of stasis) into an upper subzone with necrotic endothelial cells and initially viable adnexal and interstitial cells at 1h that progressed to necrosis by 24h, and a lower zone with initially viable endothelial cells at 1h, but necrosis and apoptosis of all cell types by 24h. Importantly, this spatiotemporal series of events and rapid progression resembles myocardial infarction and stroke, and implicates mechanisms of these injuries, ischemia, ischemia reperfusion, and programmed cell death, in burn progression.
Hirth, Douglas; McClain, Steve A.; Singer, Adam J.; Clark, Richard A.F.
From gene expression analysis to tissue microarrays: a rational approach to identify therapeutic and diagnostic targets in lymphoid malignancies.
Mantle cell lymphoma (MCL) is an aggressive lymphoid malignancy for which better treatment strategies are needed. To identify potential diagnostic and therapeutic targets, a signature consisting of MCL-associated genes was selected based on a comprehensive gene expression analysis of malignant and normal B cells. The corresponding protein epitope signature tags were identified and used to raise monospecific, polyclonal antibodies, which were subsequently analyzed on paraffin-embedded sections of malignant and normal tissue. In this study, we demonstrate that the initial selection strategy of MCL-associated genes successfully allows identification of protein antigens either uniquely expressed or overexpressed in MCL compared with normal lymphoid tissues. We propose that genome-based, affinity proteomics, using protein epitope signature tag-induced antibodies, is an efficient way to rapidly identify a number of disease-associated protein candidates of both previously known and unknown identities. PMID:16524965
Ek, Sara; Andr�asson, Ulrika; Hober, Sophia; Kampf, Caroline; Pont�n, Fredrik; Uhl�n, Mathias; Merz, Hartmut; Borrebaeck, Carl A K
Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in Drosophila melanogaster.
Faithful annotation of tissue-specific transcript isoforms is important not only to understand how genes are organized and regulated but also to identify potential novel, unannotated exons of genes, which may be additional targets of mutation in disease states or while performing mutagenic screens. We have developed a microarray enrichment methodology followed by long-read, next-generation sequencing for identification of unannotated transcript isoforms expressed in two Drosophila tissues, the ovary and the testis. Even with limited sequencing, these studies have identified a large number of novel transcription units, including 5' exons and extensions, 3' exons and extensions, internal exons and exon extensions, gene fusions, and both germline-specific splicing events and promoters. Additionally, comparing our capture dataset with tiling array and traditional RNA-seq analysis, we demonstrate that our enrichment strategy is able to capture low-abundance transcripts that cannot readily be identified by the other strategies. Finally, we show that our methodology can help identify transcriptional signatures of minority cell types within the ovary that would otherwise be difficult to reveal without the CoNECT enrichment strategy. These studies introduce an efficient methodology for cataloging tissue-specific transcriptomes in which specific classes of genes or transcripts can be targeted for capture and sequence, thus reducing the significant sequencing depth normally required for accurate annotation. Ovary and testis isotigs over 200 bp have been deposited with the GenBank Transcriptome Shotgun Assembly Sequence Database as bioproject no.PRJNA89451 (accession nos. JV208106�JV230865). PMID:22908036
Hong, X; Doddapaneni, H; Comeron, J M; Rodesch, M J; Halvensleben, H A; Nien, C Y; Bolei, F; Metpally, R; Richmond, T A; Albert, T J; Manak, J R
True cytokeratin 8/18 immunohistochemistry is of no use in distinguishing between primary endocervical and endometrial adenocarcinomas in a tissue microarray study.
The choice of appropriate therapeutic plans for primary endocervical adenocarcinomas and endometrial adenocarcinomas depends on the site of origin of the tumor. The purpose of this study was to make clear whether the immunohistochemistry of the true cytokeratin 8/18 monoclonal antibody (Leica Microsystems, Newcastle, United Kingdom), instead of CAM 5.2 (Becton Dickinson Biosciences, San Jose, CA), has potential use in distinguishing between endocervical adenocarcinomas and endometrial adenocarcinomas. A tissue microarray was constructed using paraffin-embedded, formalin-fixed tissues from 34 hysterectomy specimens, including 14 endocervical adenocarcinomas and 20 endometrial adenocarcinomas. Using the Bond-Max autostainer (Leica Microsystems) and the associated Bond Refine Polymer Detection Kit, tissue array sections were immunostained with cytokeratin 8, 18, and 8/18 commercially available antibodies. The immunohistochemical expressions of all 3 markers, cytokeratin 8, 18, and 8/18 showed nonsignificant (P>0.05) frequency differences between the immunostaining results (positive vs. negative) in tumors of both gynecologic adenocarcinomas. Although CAM 5.2 has been reported to be helpful in distinguishing between primary endocervical adenocarcinomas and endometrial adenocarcinomas, we could not verify this point of view using the true cytokeratin 8/18 monoclonal antibody (Leica Microsystems). It has often been mistakenly cited that CAM 5.2 reacts with cytokeratin 8 and 18, and the results herein confer that there is a wrong impression that cytokeratin 8/18 is differentially expressed in these 2 gynecologic malignancies. In conclusion, the true cytokeratin 8/18 monoclonal antibody is of no use in distinguishing between primary endocervical adenocarcinomas and endometrial adenocarcinomas. PMID:20407331
Hsu, Jeng-Dong; Yao, Chung-Chin; Lee, Ming-Yung; Kok, Lai-Fong; Wang, Po-Hui; Tyan, Yeu-Sheng; Han, Chin-Ping
Combined Array Comparative Genomic Hybridization and Tissue Microarray Analysis Suggest PAK1 at 11q13.5-q14 as a Critical Oncogene Target in Ovarian Carcinoma
Amplification of chromosomal regions leads to an increase of DNA copy numbers and expression of oncogenes in many human tumors. The identification of tumor-specific oncogene targets has potential diagnostic and therapeutic implications. To identify distinct spectra of oncogenic alterations in ovarian carcinoma, metaphase comparative genomic hybridization (mCGH), array CGH (aCGH), and ovarian tumor tissue microarrays were used in this study. Twenty-six primary ovarian carcinomas and three ovarian carcinoma cell lines were analyzed by mCGH. Frequent chromosomal overrepresentation was observed on 2q (31%), 3q (38%), 5p (38%), 8q (52%), 11q (21%), 12p (21%), 17q (21%), and 20q (52%). The role of oncogenes residing in gained chromosomal loci was determined by aCGH with 59 genetic loci commonly amplified in human tumors. DNA copy number gains were most frequently observed for PIK3CA on 3q (66%), PAK1 on 11q (59%), KRAS2 on 12p (55%), and STK15 on 20q (55%). The 11q13-q14 amplicon, represented by six oncogenes (CCND1, FGF4, FGF3, EMS1, GARP, and PAK1) revealed preferential gene copy number gains of PAK1, which is located at 11q13.5-q14. Amplification and protein expression status of both PAK1 and CCND1 were further examined by fluorescence in situ hybridization and immunohistochemistry using a tissue microarray consisting of 268 primary ovarian tumors. PAK1 copy number gains were observed in 30% of the ovarian carcinomas and PAK1 protein was expressed in 85% of the tumors. PAK1 gains were associated with high grade (P < 0.05). In contrast, CCND1 gene alterations and protein expression were less frequent (10.6% and 25%, respectively), suggesting that the critical oncogene target of amplicon 11q13�14 lies distal to CCND1. This study demonstrates that aCGH facilitates further characterization of oncogene candidates residing in amplicons defined by mCGH.
Schraml, Peter; Schwerdtfeger, Georg; Burkhalter, Felix; Raggi, Anna; Schmidt, Dietmar; Ruffalo, Teresa; King, Walter; Wilber, Kim; Mihatsch, Michael J.; Moch, Holger
Monitoring cardiopulmonary function and progression toward shock: oxygen micro-sensor for peripheral tissue
We are developing a robust, minimally invasive device for detecting progression toward hemorrhagic shock in trauma patients. To accomplish this, oxygen micro-sensors are being developed that contain a solution of oxygen sensitive phosphorescent probes within gas permeable tubing attached to optical fibers. These micro-sensors can be inserted into peripheral tissue to accurately measure tissue oxygenation. As the blood volume decreases (hemorrhage), physiological mechanisms progressively restrict blood flow to �non essential� peripheral tissues, redirecting that flow to the essential internal organs. It is hypothesized that the sensors will detect the shut down of peripheral blood flow well before the decreasing blood volume reaches the threshold where multi-organ failure begins. Proactive treatment with volume expanders or blood, guided by peripheral oxygen measurements, would significantly reduce multi-organ failure and other complications in trauma cases.
Wilson, David F.; Vinogradov, Sergei A.; Schears, Gregory J.; Esipova, Tatiana V.; Pastuszko, Anna
Microarray analysis of prostate cancer progression to reduced androgen dependence: studies in unique models contrasts early and late molecular events.
Three unique variants of the CWR22 human prostate cancer xenograft model (CWR22LD1, LD2, and LD3) with a decrease in dependence on androgens were selected under noncastrate conditions, i.e., by outgrowth after transplantation into male NCR (AT) nu mice without testosterone supplementation. These variants were unable to grow in castrated male mice. For comparison, a second set of variants with even less dependence on androgens (castrate-resistant) were derived following outgrowth from CWR22 (CWR22Rv1 and RC) or CWRLD1 (CWR22RS) after transplantion in castrated male mice. The androgen receptor (AR) gene in the CWR22LD variants was transcriptionally active and was neither mutated nor significantly overexpressed compared to CWR22. Oligonucleotide microarray analysis showed distinctly different profiles of dysregulated gene expression among the CWR22LD variants. Groups of only 26-41 genes were dysregulated greater than threefold with a different proportion of up versus downregulated genes in each variant. Only one of the castrate-resistant variants (CWR22Rv1) had a highly overexpressed AR gene but AR in this variant and the two other castrate-resistant variants, CWR22 RS and RC, was not mutated beyond that seen in CWR22. In contrast to the CWR22LD variants, a total of 342, 295, and 222 genes were dysregulated at least threefold in CWR22Rv1, CWR22RS, and CWR22RC, respectively, differing as well in the proportion of up versus downregulated genes. Many of the genes dysregulated in CWR22LD1, LD2, and LD3 were further dysregulated in CWR22Rv1, RC, or RS. The most downregulated gene was microseminoprotein beta (MSPB). Along with cyclin D1, the most upregulated gene by an order of magnitude compared to other upregulated genes was hepatocyte growth factor (HGF) (scatter factor). These results suggest that the onset in the loss of androgen dependence in CWR22 proceeds through multiple pathways and does not require any direct change in the status of AR. However, upregulation of other survival pathways like that involving HGF in these studies could co-activate AR signaling. The endogenous overexpression of genes regulating sterol biosynthesis also observed in castrate-resistant CWR22 variants delineated a clinically relevant, compensatory mechanism for overcoming androgen deprivation reaffirming a central role for AR signaling in this process. PMID:15390081
Sirotnak, F M; She, Yuhong; Khokhar, Nushmia Z; Hayes, Paula; Gerald, William; Scher, Howard I
Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays
CpG island arrays represent a high-throughput epigenomic discovery platform to identify global disease-specific promoter hypermethylation candidates along bladder cancer progression. DNA obtained from 10 pairs of invasive bladder tumours were profiled vs their respective normal urothelium using differential methylation hybridisation on custom-made CpG arrays (n=12?288 clones). Promoter hypermethylation of 84 clones was simultaneously shown in at least 70% of the tumours. SOX9 was selected for further validation by bisulphite genomic sequencing and methylation-specific polymerase chain reaction in bladder cancer cells (n=11) and primary bladder tumours (n=101). Hypermethylation was observed in bladder cancer cells and associated with lack of gene expression, being restored in vitro by a demethylating agent. In primary bladder tumours, SOX9 hypermethylation was present in 56.4% of the cases. Moreover, SOX9 hypermethylation was significantly associated with tumour grade and overall survival. Thus, this high-throughput epigenomic strategy has served to identify novel hypermethylated candidates in bladder cancer. In vitro analyses supported the role of methylation in silencing SOX9 gene. The association of SOX9 hypermethylation with tumour progression and clinical outcome suggests its relevant clinical implications at stratifying patients affected with bladder cancer.
Aleman, A; Adrien, L; Lopez-Serra, L; Cordon-Cardo, C; Esteller, M; Belbin, T J; Sanchez-Carbayo, M
Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays.
CpG island arrays represent a high-throughput epigenomic discovery platform to identify global disease-specific promoter hypermethylation candidates along bladder cancer progression. DNA obtained from 10 pairs of invasive bladder tumours were profiled vs their respective normal urothelium using differential methylation hybridisation on custom-made CpG arrays (n=12 288 clones). Promoter hypermethylation of 84 clones was simultaneously shown in at least 70% of the tumours. SOX9 was selected for further validation by bisulphite genomic sequencing and methylation-specific polymerase chain reaction in bladder cancer cells (n=11) and primary bladder tumours (n=101). Hypermethylation was observed in bladder cancer cells and associated with lack of gene expression, being restored in vitro by a demethylating agent. In primary bladder tumours, SOX9 hypermethylation was present in 56.4% of the cases. Moreover, SOX9 hypermethylation was significantly associated with tumour grade and overall survival. Thus, this high-throughput epigenomic strategy has served to identify novel hypermethylated candidates in bladder cancer. In vitro analyses supported the role of methylation in silencing SOX9 gene. The association of SOX9 hypermethylation with tumour progression and clinical outcome suggests its relevant clinical implications at stratifying patients affected with bladder cancer. PMID:18087279
Aleman, A; Adrien, L; Lopez-Serra, L; Cordon-Cardo, C; Esteller, M; Belbin, T J; Sanchez-Carbayo, M
Tissue microarray analysis of ezrin, KBA.62, CD166, nestin, and p-Akt in melanoma versus banal and atypical nevi, and nonmelanocytic lesions.
Multiple melanocytic markers are useful for differentiating between melanoma and nonmelanocytic lesions but generally do not distinguish melanoma from nevi and atypical melanocytic lesions. We sought to determine if several immunohistochemical markers recently described in the literature, including ezrin, KBA.62, p-Akt, CD166, and nestin, may be helpful in distinguishing these lesions. One hundred ten tissue microarray samples were scored for nestin and CD166 and 220 samples for ezrin, KBA.62, and p-Akt. We found that putative stem cell markers nestin and CD166 were both expressed in most melanomas (86% and 65% of samples, respectively), including desmoplastic melanoma, but were also expressed at similar levels in nevi (79% and 74%, respectively). In addition, these markers were not specific for melanocytic lesions. Ezrin was also expressed in both nevi and melanoma (81% each), including desmoplastic melanoma (75%), and in neural tumors. KBA.62 stained more cases of nevi versus melanoma (93% and 65%, respectively) and was positive in 53% of desmoplastic melanoma. However, it was also positive in several nonmelanocytic tumors. P-Akt expression was generally weak but was increased in nevi (75%) versus melanoma (43%), and was lost in desmoplastic melanomas (5%). Overall, only KBA.62 and p-Akt expression differed between melanoma and nevi, and none of these markers were completely specific for melanocytic tumors versus nonmelanocytic lesions. PMID:21915031
Shanesmith, Rebecca P; Smart, Chandra; Cassarino, David S
Microarrayed Materials for Stem Cells
Stem cells hold remarkable promise for applications in disease modeling, cancer therapy and regenerative medicine. Despite the significant progress made during the last decade, designing materials to control stem cell fate remains challenging. As an alternative, materials microarray technology has received great attention because it allows for high throughput materials synthesis and screening at a reasonable cost. Here, we discuss recent developments in materials microarray technology and their applications in stem cell engineering. Future opportunities in the field will also be reviewed.
Mei, Ying
RUNX2 correlates with subtype-specific breast cancer in a human tissue microarray, and ectopic expression of Runx2 perturbs differentiation in the mouse mammary gland
RUNX2, a master regulator of osteogenesis, is oncogenic in the lymphoid lineage; however, little is known about its role in epithelial cancers. Upregulation of RUNX2 in cell lines correlates with increased invasiveness and the capacity to form osteolytic disease in models of breast and prostate cancer. However, most studies have analysed the effects of this gene in a limited number of cell lines and its role in primary breast cancer has not been resolved. Using a human tumour tissue microarray, we show that high RUNX2 expression is significantly associated with oestrogen receptor (ER)/progesterone receptor (PR)/HER2-negative breast cancers and that patients with high RUNX2 expression have a poorer survival rate than those with negative or low expression. We confirm RUNX2 as a gene that has a potentially important functional role in triple-negative breast cancer. To investigate the role of this gene in breast cancer, we made a transgenic model in which Runx2 is specifically expressed in murine mammary epithelium under the control of the mouse mammary tumour virus (MMTV) promoter. We show that ectopic Runx2 perturbs normal development in pubertal and lactating animals, delaying ductal elongation and inhibiting lobular alveolar differentiation. We also show that the Runx2 transgene elicits age-related, pre-neoplastic changes in the mammary epithelium of older transgenic animals, suggesting that elevated RUNX2 expression renders such tissue more susceptible to oncogenic changes and providing further evidence that this gene might have an important, context-dependent role in breast cancer.
McDonald, Laura; Ferrari, Nicola; Terry, Anne; Bell, Margaret; Mohammed, Zahra M.; Orange, Clare; Jenkins, Alma; Muller, William J.; Gusterson, Barry A.; Neil, James C.; Edwards, Joanne; Morris, Joanna S.; Cameron, Ewan R.; Blyth, Karen
The immunohistochemical expression of BNIP3 protein in non-small-cell lung cancer: a tissue microarray study.
Drug resistance is one of the reasons for chemotherapy failure in non-small-cell lung carcinoma (NSCLC). One of the major mechanisms of drug resistance is the inhibition of chemotherapy-induced apoptosis. Therefore, the study of novel cell death pathways could possibly enable us to overcome resistance to apoptosis in NSCLC. One of the non-caspase types of cell death is autophagy. BNIP3 protein, a Bcl-2 family member, highly expressed in some tumours, plays a key role in the induction of autophagy. In the present study, we investigated the immunohistochemical expression and subcellular localization of BNIP3 in a series of early- and late-stage non-small-cell lung carcinomas and normal bronchial tissues, and correlated this expression with the occurrence of metastasis and survival. BNIP3 was strongly expressed in the nucleus of cancer cells in 16/79 (20.3%) cases. This BNIP3 positivity did not correlate with histological grade, stage, histology type, metastatic potential, or expression of BNIP3 according to median values. No significant correlation was observed between the expression of BNIP3 and the overall survival of NSCLC patients (p = 0.55). Nor did we find any significant correlation between BNIP3 expression and the occurrence of site-specific metastasis (p = 0.85). PMID:20666737
Uberall, Ivo; Kolek, V�t?zslav; Klein, Jir�; Krejc�, Veronika; Stastn�, Jitka; Radov�, Lenka; Skarda, Josef; Fridman, Eddie
[Progress and prospect of applications of silk fibroin in construction of tissue engineering scaffold].
With the development of tissue engineering, a variety of forms of silk fibroin (SF) scaffolds has been applied to research of constructing variety of organization based on cells, which has become scientific focus in recent years. In this paper we introduced the source and structure of SF and the fabrication method of the scaffold, and also address the SF application progress in several relevant fields of tissue engineering, such as bone, cartilage, skin, blood vessel and nerves. Finally, we discuss the future leading prospect of the SF in order to provide reference for subsequent research. PMID:25039161
Yin, Lihua; Wang, Lin; Yu, Zhanhai
Tissue microarray immunohistochemical expression analysis of mismatch repair (hMLH1 and hMSH2 genes) in endometrial carcinoma and atypical endometrial hyperplasia: relationship with microsatellite instability.
Alterations in the mismatch repair genes (hMLH1 and hMSH2) play an important role in the development of microsatellite instability in sporadic endometrial cancer. Tissue microarray technology allows molecular profiling of tumor samples at the DNA, RNA, and protein levels. We analyzed hMLH1 and hMSH2 expression by immunohistochemistry in a group of atypical endometrial hyperplasias (n = 10), endometrioid endometrial carcinomas (n = 58), and nonendometrioid endometrial carcinomas (n = 27) on tissue microarray. The results were correlated with microsatellite instability status as evaluated by BAT-25 and BAT-26. Overall, 29.4% of lesions showed microsatellite instability. Loss of nuclear hMLH1 and hMSH2 protein expression was seen in 22.3% and 6.5% of cases, respectively. Immunohistochemistry for hMLH1 and hMSH2 showed lack of protein expression in 64% and 16.6% of microsatellite instability-positive endometrial lesions, respectively. Taken together, hMLH1 or hMSH2 protein expression was absent in 18 of 24 microsatellite instability-positive cases (75% sensitivity). A high level of concordance was found between immunohistochemistry for hMLH1 and hMSH2 and microsatellite instability status evaluated by BAT-25 and BAT-26 (kappa value of 0.7). Of the 57 cases found to be microsatellite instability negative, 53 showed normal expression of both proteins (93% specificity). The observed predictive value of absence of expression of hMLH1 for predicting microsatellite instability-positive status was 82%. The predictive value of normal expression of both proteins for predicting microsatellite instability-negative status was 90%. These results are consistent with those previously reported in whole tissue sections. Therefore, immunohistochemical analysis of hMLH1 and hMSH2 expression on tissue microarray provides an accurate technique for screening for tumors with microsatellite instability. Tissue microarrays represent an ideal approach for comparing different diagnostic or predictive markers with one another in consecutive tissue microarray sections. PMID:14614055
Hardisson, David; Moreno-Bueno, Gema; S�nchez, Lydia; Sarri�, David; Su�rez, Asunci�n; Calero, Francisco; Palacios, Jos�
Recent Progress on Tissue-Resident Adult Stem Cell Biology and Their Therapeutic Implications
Recent progress in the field of the stem cell research has given new hopes to treat and even cure diverse degenerative disorders and incurable diseases in human. Particularly, the identification of a rare population of adult stem cells in the most tissues/organs in human has emerged as an attractive source of multipotent stem/progenitor cells for cell replacement-based therapies and tissue engineering in regenerative medicine. The tissue-resident adult stem/progenitor cells offer the possibility to stimulate their in vivo differentiation or to use their ex vivo expanded progenies for cell replacement-based therapies with multiple applications in human. Among the human diseases that could be treated by the stem cell-based therapies, there are hematopoietic and immune disorders, multiple degenerative disorders, such as Parkinson�s and Alzeimeher�s diseases, type 1 or 2 diabetes mellitus as well as eye, liver, lung, skin and cardiovascular disorders and aggressive and metastatic cancers. In addition, the genetically-modified adult stem/progenitor cells could also be used as delivery system for expressing the therapeutic molecules in specific damaged areas of different tissues. Recent advances in cancer stem/progenitor cell research also offer the possibility to targeting these undifferentiated and malignant cells that provide critical functions in cancer initiation and progression and disease relapse for treating the patients diagnosed with the advanced and metastatic cancers which remain incurable in the clinics with the current therapies.
The epidermal growth factor receptor is frequently overexpressed in penile squamous cell carcinomas: a tissue microarray and digital image analysis study of 112 cases.
Disseminated penile cancer is usually treated with chemotherapy. However, response rates are far from acceptable. Recently, anti-epidermal growth factor receptor (EGFR) monoclonal antibodies have shown to be clinically useful in penile carcinomas. Nevertheless, only a few cases of penile carcinomas have been evaluated for EGFR expression. In this study, we assessed the immunohistochemical expression of EGFR in 112 patients with penile squamous cell carcinoma. We built 4 tissue microarrays and evaluated EGFR expression using a monoclonal mouse anti-EGFR antibody. For digital image analysis, we used the open-source software ImageJ version 1.47 (NIH, Bethesda, MD) along with the immunomembrane plug-in. Membranous EGFR expression was evaluated, taking into account staining completeness (0-10 points) and staining intensity (0-10 points) for a combined score (0-20 points). We classified the cases as follows: negative EGFR expression, 0 to 3 points; low EGFR expression, 4 to 8 points; and high EGFR expression, 9 to 20 points. The distribution of EGFR immunohistochemical expression was as follows: 13 cases (12%) were EGFR negative, 49 cases (44%) had low EGFR expression, and 50 cases (44%) had high EGFR expression. EGFR expression was not associated with histologic subtype (P = .47), histologic grade (P = .77), or human papillomavirus status (P = .14). In conclusion, immunohistochemical EGFR expression appears to be a common feature of penile carcinomas, independently of histologic subtype, histologic grade, and human papillomavirus presence. Whether or not EGFR expression is associated with EGFR gene mutation or if it can be used to predict response to therapy in patients with disseminated penile cancer should be evaluated in future studies. PMID:24075601
Chaux, Alcides; Munari, Enrico; Katz, Betina; Sharma, Rajni; Lecksell, Kristen; Cubilla, Antonio L; Burnett, Arthur L; Netto, George J
Comparison of in situ hybridization methods for the assessment of HER-2/neu gene amplification status in breast cancer using a tissue microarray
Background This project compared HER-2/neu gene status in breast cancers, as demonstrated by FISH (fluorescent in situ hybridization) and CISH (chromogenic in situ hybridization) and using a tissue microarray (TMA). The study also aimed to show whether the TMA technique could be used in clinical diagnostics, rather than remain a scientific tool. Materials and methods A TMA was constructed using 121 breast cancer specimens, 6 cores from each specimen. Demonstration and assessment of HER-2/neu gene status was by FISH (Vysis Path) and CISH (DAKO Duo CISH). Results The 121 breast cancer specimens were divided into 3 groups by HER-2 status, as determined by immunohistochemistry. In the HER-2 negative group no amplification was observed in 36 out of 40 cases. 3 cases showed amplification by both methods and one by CISH alone. The equivocal HER-2 group showed no amplification in 30 out of 41 cases and amplification in 9 cases. One case was FISH negative CISH positive and one was discarded. In the HER-2 positive group, amplification was confirmed in 37 of the 40 cases by both methods. 3 cases were unsuitable for assessment. Conclusions This study indicated that CISH is a sensitive alternative to FISH in detecting HER2 gene amplification and may replace FISH in HER2 testing. Good agreement was observed between methods (98.5% � 119 out of 121 cases). Furthermore, as only 4 out of 121 cases were unsuitable for assessment (no signal or missing TMA cores) � it may be feasible to use TMA in diagnostics.
Malicka-Durczak, Anna; Korski, Konstanty; Ibbs, Matthew
Clinical Utility of Microarrays: Current Status, Existing Challenges and Future Outlook
Microarray-based clinical tests have become powerful tools in the diagnosis and treatment of diseases. In contrast to traditional DNA-based tests that largely focus on single genes associated with rare conditions, microarray-based tests are ideal for the study of diseases with underlying complex genetic causes. Several microarray based tests have been translated into clinical practice such as MammaPrint and AmpliChip CYP450. Additional cancer-related microarray-based tests are either in the process of FDA review or under active development, including Tissue of Tumor Origin and AmpliChip p53. All diagnostic microarray testing is ordered by physicians and tested by a Clinical Laboratories Improvement Amendment-certified (CLIA) reference laboratory. Recently, companies offering consumer based microarray testing have emerged. Individuals can order tests online and service providers deliver the results directly to the clients via a password-protected secure website. Navigenics, 23andMe and deCODE Genetics represent pioneering companies in this field. Although the progress of these microarray-based tests is extremely encouraging with the potential to revolutionize the recognition and treatment of common diseases, these tests are still in their infancy and face technical, clinical and marketing challenges. In this article, we review microarray-based tests which are currently approved or under review by the FDA, as well as the consumer-based testing. We also provide a summary of the challenges and strategic solutions in the development and clinical use of the microarray-based tests. Finally, we present a brief outlook for the future of microarray-based clinical applications.
Li, Xinmin; Quigg, Richard J; Zhou, Jian; Gu, Weikuan; Nagesh Rao, P; Reed, Elaine F
Microarray analysis of thioacetamide-treated type 1 diabetic rats
It is well known that diabetes imparts high sensitivity to numerous hepatotoxicants. Previously, we have shown that a normally non-lethal dose of thioacetamide (TA, 300 mg/kg) causes 90% mortality in type 1 diabetic (DB) rats due to inhibited tissue repair allowing progression of liver injury. On the other hand, DB rats exposed to 30 mg TA/kg exhibit delayed tissue repair and delayed recovery from injury. The objective of this study was to investigate the mechanism of impaired tissue repair and progression of liver injury in TA-treated DB rats by using cDNA microarray. Gene expression pattern was examined at 0, 6, and 12 h after TA challenge, and selected mechanistic leads from microarray experiments were confirmed by real-time RT-PCR and further investigated at protein level over the time course of 0 to 36 h after TA treatment. Diabetic condition itself increased gene expression of proteases and decreased gene expression of protease inhibitors. Administration of 300 mg TA/kg to DB rats further elevated gene expression of proteases and suppressed gene expression of protease inhibitors, explaining progression of liver injury in DB rats after TA treatment. Inhibited expression of genes involved in cell division cycle (cyclin D1, IGFBP-1, ras, E2F) was observed after exposure of DB rats to 300 mg TA/kg, explaining inhibited tissue repair in these rats. On the other hand, DB rats receiving 30 mg TA/kg exhibit delayed expression of genes involved in cell division cycle, explaining delayed tissue repair in these rats. In conclusion, impaired cyclin D1 signaling along with increased proteases and decreased protease inhibitors may explain impaired tissue repair that leads to progression of liver injury initiated by TA in DB rats.
Devi, Sachin S. [Department of Toxicology, College of Pharmacy, University of Louisiana at Monroe, 700 University Ave, Sugar Hall 306, Monroe, LA 71209-0470 (United States); Mehendale, Harihara M. [Department of Toxicology, College of Pharmacy, University of Louisiana at Monroe, 700 University Ave, Sugar Hall 306, Monroe, LA 71209-0470 (United States)]. E-mail: email@example.com
Hypoxia-Inducible Factors: Mediators of Cancer Progression; Prognostic and Therapeutic Targets in Soft Tissue Sarcomas
Soft-tissue sarcomas remain aggressive tumors that result in death in greater than a third of patients due to either loco-regional recurrence or distant metastasis. Surgical resection remains the main choice of treatment for soft tissue sarcomas with pre- and/or post-operational radiation and neoadjuvant chemotherapy employed in more advanced stage disease. However, in recent decades, there has been little progress in the average five-year survival for the majority of patients with high-grade soft tissue sarcomas, highlighting the need for improved targeted therapeutic agents. Clinical and preclinical studies demonstrate that tumor hypoxia and up-regulation of hypoxia-inducible factors (HIFs) is associated with decreased survival, increased metastasis, and resistance to therapy in soft tissue sarcomas. HIF-mediated gene expression regulates many critical aspects of tumor biology, including cell survival, metabolic programming, angiogenesis, metastasis, and therapy resistance. In this review, we discuss HIFs and HIF-mediated genes as potential prognostic markers and therapeutic targets in sarcomas. Many pharmacological agents targeting hypoxia-related pathways are in development that may hold therapeutic potential for treating both primary and metastatic sarcomas that demonstrate increased HIF expression.
Sadri, Navid; Zhang, Paul J.
Microarray technologies for intracellular kinome analysis.
Microarray-based kinomics, which measure the enzymatic activity or the presence of intracellular protein kinases, are now regarded as alternative tools to conventional mass spectrometry-based kinomics for examining intracellular kinomics. Here, we reviewed the principal advantages, recent progress, and remaining problems of representative microarray- based kinomics, including substrate peptide and protein microarrays, anti-protein kinase antibody microarrays, and reverse protein microarrays. Microarray-based kinomics are not as good at quantitative evaluation of kinomics as the conventional mass spectrometry-based kinomics. However, their simplicity and high throughput make the microarraybased kinomics unique tools, being especially suited for a practical analysis; monitoring drug effects on cellular kinomics as a tool for drug development, and for the diagnosis and prognosis of diseases based on kinomics. PMID:24358971
Yamamoto, T; Mori, T; Katayama, Y
Treatment of progressive supranuclear palsy with autologous adipose tissue-derived mesenchymal stem cells: a case report
Introduction Progressive supranuclear palsy is a relentlessly progressive neurodegenerative disorder and is clinically characterized by parkinsonism. Adipose tissue-derived mesenchymal stem cells have recently demonstrated the possibility of treating neurological disorders. Therefore, autologous adipose tissue-derived mesenchymal stem cells transplantation can be an alternative method for treating progressive supranuclear palsy. Case presentation This study was approved by the Korea Food and Drug Administration through the Emergency Use Investigational New Drug Application. A 71-year-old Asian man from South Korea with progressive supranuclear palsy was treated with five intravenous infusions (each time 2�108 cells) and four intrathecal infusions (each time 5�107 cells) with autologous adipose tissue-derived mesenchymal stem cells expanded under good manufacturing practice conditions. Clinical examinations were performed immediately before treatment and throughout the six months of follow-up. The tests included: 1) Progressive Supranuclear Palsy Rating Scale; 2) Berg Balance Scale; 3) Korean Mini Mental State Examination; 4) Modified Barthel Index; 5) grip strength; 6) Box and Block Test; and 7) Nine-Hole Peg Test. The Progressive Supranuclear Palsy Rating Scale results gradually decreased, and the clinical rating scale scores of the Berg Balance Scale, Korean Mini Mental State Examination, and Modified Barthel Index gradually increased. Grip strength was maintained. Performance in the Box and Block Test and Nine-Hole Peg Test improved after adipose tissue-derived mesenchymal stem cells treatment compared to baseline throughout the six months of follow-up. Except for the intermittent mild fever and transient elevated blood pressure, the treatment of our patient with progressive supranuclear palsy with autologous adipose tissue-derived mesenchymal stem cells showed no significant adverse events, and delayed the progression of neurological deficits by achieving functional improvement in the follow-up period. Conclusions These results are encouraging and hopeful for further studies in patients with progressive supranuclear palsy using autologous adipose tissue-derived mesenchymal stem cells as a safe and effective therapy. This case report is the first known study of adipose tissue-derived mesenchymal stem cells safely delaying the progression of progressive supranuclear palsy with functional improvement during the follow-up period.
NASA Astrophysics Data System (ADS)
In vitro selection can yield specific, high-affinity aptamers. We and others have devised methods for the automated selection of aptamers and have begun to use these reagents for the construction of arrays. Arrayed aptamers have proven to be almost as sensitive as their solution-phase counterparts and when ganged together can provide both specific and general diagnostic signals for proteins and other ana-lytes. We describe here technical details regarding the production and processing of aptamer microarrays, including blocking, washing, drying, and scanning. We also discuss the challenges involved in developing standardized and reproducible methods for binding and quantitating protein targets. Although signals from fluorescent analytes or sandwiches are typically captured, it has proven possible for immobilized aptamers to be uniquely coupled to amplification methods not available to protein reagents, thus allowing for protein-binding signals to be greatly amplified. Into the future, many of the biosensor methods described in this book can potentially be adapted to array formats, thus further expanding the their utility and applications for aptamer arrays.
Syrett, Heather Angel; Collett, James R.; Ellington, Andrew D.
In vitro selection can yield specific, high-affinity aptamers. We and others have devised methods for the automated selection of aptamers, and have begun to use these reagents for the construction of arrays. Arrayed aptamers have proven to be almost as sensitive as their solution phase counterparts, and when ganged together can provide both specific and general diagnostic signals for proteins and other analytes. We describe here technical details regarding the production and processing of aptamer microarrays, including blocking, washing, drying, and scanning. We will also discuss the challenges involved in developing standardized and reproducible methods for binding and quantitating protein targets. While signals from fluorescent analytes or sandwiches are typically captured, it has proven possible for immobilized aptamers to be uniquely coupled to amplification methods not available to protein reagents, thus allowing for protein-binding signals to be greatly amplified. Into the future, many of the biosensor methods described in this book can potentially be adapted to array formats, thus further expanding the utility of and applications for aptamer arrays.
Angel-Syrett, Heather; Collett, Jim; Ellington, Andrew D.
The relation of beclin 1 and bcl-2 expressions in high grade prostatic intraepithelial neoplasia and prostate adenocarcinoma: A tissue microarray study.
The aim of the present study was to evaluate the expressions of beclin 1 and bcl-2 in prostate cancer (PC) and high grade prostatic intraepithelial neoplasia (HGPIN), and to investigate their relationship with clinicopathological parameters. The study included 30 benign prostatic hyperplasia (BPH), 40 HGPIN and 106 primary PC cases. The expressions of beclin 1 and bcl-2 were assessed semiquantitatively based on both the percentage and intensity of positive staining cells. Beclin 1 was positive in 27 (90%) BPH, 37 (92.5%) HGPIN, and 90 (84.9%) PC cases (p>0.05). Bcl-2 immunostaining was detected in 99 (93.4%) PC, 37 (92.5%) HGPIN, and 9 (30%) BPH cases (p<0.0001). Regarding expression scores, beclin 1 was significantly lower in PC cases than in the HGPIN and BPH groups (p<0.0001), and it was also negatively correlated with Gleason score (p=0.004, r=-0.274). Bcl-2 expression score was significantly higher in PC than in the other groups (p<0.0001), and also positively correlated with Gleason score (p<0.0001, r=0.425). Furthermore, a negative correlation was found between bcl-2 and beclin 1 expression scores in PC cases (p=0.006, r=-0.265). Our results suggest an association between bcl-2 and beclin 1 expressions in malignant transformation of prostate tissue and also in regulating PC cell differentiation, progression and the aggressiveness of PC. PMID:24690321
Baspinar, Sirin; Bircan, Sema; Orhan, Hikmet; Kapucuoglu, Nilgun; Bozkurt, Kemal Kursat
Possible utilization of in vitro synthesized mRNAs specifically expressed in certain tissues as standards for quantitative evaluation of the results of microarray analysis
To examine the possible usefulness of in vitro synthesized RNA as standards in microarray analysis, we prepared full-length mRNAs encoded by 3 rat metabolic genes for heart\\/muscle type carnitine palmitoyltransferase I (M-CPTI), uncoupling protein (UCP1), and heart\\/muscle type fatty acid-binding protein (H-FABP). Artificial RNA samples were prepared by adding known amounts of these synthetic mRNAs to total RNA from rat
Rei Kakuhata; Masahiro Watanabe; Takenori Yamamoto; Rie Akamine; Naoshi Yamazaki; Masatoshi Kataoka; Satoshi Fukuoka; Mitsuru Ishikawa; Toshihiko Ooie; Yoshinobu Baba; Tomoshige Hori; Yasuo Shinohara
Tissue Prostate-Specific Antigen Facilitates Refractory Prostate Tumor Progression via Enhancing ARA70-Regulated Androgen Receptor Transactivation
Despite being well recognized as the best biomarker for prostate cancer, pathophysiologic roles of prostate-specific antigen (PSA) remain unclear. We report here that tissue PSA may be involved in the hormone-refractory prostate cancer progression. Histologic analyses show that the increased tissue PSA levels are correlated with lower cell apoptosis index and higher cell proliferation rate in hormone-refractory tumor specimens. By
Yuanjie Niu; Shuyuan Yeh; Hiroshi Miyamoto; Gonghui Li; Saleh Altuwaijri; Jianqun Yuan; Ruifa Han; Hann-Chorng Kuo; Chawnshang Chang
Argyrophilic nucleolar organizer regions in the evaluation of tumour progression in the oral mucosa: correlation with tissue pathology
The present study has analysed the numbers of argyrophilic nucleolar organizer regions (AgNOR) in normal tissues and in premalignant and malignant lesions of the oral mucosa in order to assess their potential as a biological marker for tumour progression. On comparison of AgNOR numbers in different lesions, carcinomas showed the highest number (4.65�0.98) compared to leukoplakias (2.38�0.47) and normal tissues
K. Raveendran Pillai; K. Sujathan; S. Kannan; Elizabeth K. Abraham; Babu Mathew; N. Sreedevi Amma; M. Krishnan Nair; Venugopal P. Menon
Effect of tobacco smoking on tissue protein citrullination and disease progression in patients with rheumatoid arthritis
The aim of the present work was to study the effect of tobacco smoking on disease progression in rheumatoid arthritis patients and its relation to anti-cyclical citrullinated peptide (anti-CCP) antibodies. The study included 54 patients; 20 non-smokers, 9 ex-smokers, 14 mild to moderate smokers and 11 heavy smokers. Fifteen normal volunteers were also studied as controls. Disease stage was clinically and radiologically determined, rheumatoid factor (RF) and anti-CCP antibodies were measured in serum. Higher percentage of severe disease (stage III) was seen in heavy smoker patients than mild to moderate smokers (54.6% versus 35.7%) and in moderate smokers than ex-smokers (35.7% versus 33.6%). Lowest percentage of severe disease was seen in non-smokers (15%). RF and anti-CCP were significantly higher in smoker than non-smoker and in heavy than mild to moderate smoker patients (p�<�0.01, p�<�0.05 and p�<�0.01, p�<�0.001, respectively). In smoker patients, both RF and anti-CCP antibodies correlated significantly and positively with smoking index (r�=�0.581, p�<�0.001; r�=�0.661, p�<�0.001). Also, smoking index and anti-CCP correlated significantly and positively with disease stage (r�=�0.424, p�<�0.05; r�=�0.523, p�<�0.01). It appears from our results that, tobacco smoking mostly play a role in progression of rheumatoid arthritis through tissue protein citrullination. So all rheumatoid arthritis patients must quit completely to achieve a good control.
Alsalahy, Mahmoud M.; Nasser, Hamdy S.; Hashem, Manal M.; Elsayed, Sahar M.
Conditioned medium from amniotic mesenchymal tissue cells reduces progression of bleomycin-induced lung fibrosis
Background and aims We have demonstrated recently that transplantation of placental membrane-derived cells reduces bleomycin-induced lung fibrosis in mice, despite a limited presence of transplanted cells in host lungs. Because placenta-derived cells are known to release factors with potential immunomodulatory and trophic activities, we hypothesized that transplanted cells may promote lung tissue repair via paracrine-acting molecules. To test this hypothesis, we examined whether administration of conditioned medium (CM) generated from human amniotic mesenchymal tissue cells (AMTC) was able to reduce lung fibrosis in this same animal model. Methods Bleomycin-challenged mice were either treated with AMTC-CM or control medium, or were left untreated (Bleo group). After 9 and 14 days, the distribution and severity of lung fibrosis were assessed histologically with a scoring system. Collagen deposition was also evaluated by quantitative image analysis. Results At day 14, lung fibrosis scores in AMTC-CM-treated mice were significantly lower (P<0.05) compared with mice of the Bleo group, in terms of fibrosis distribution [1.0 (interquartile range, IQR 0.9) versus 3.0 (IQR 1.8)], fibroblast proliferation [0.8 (IQR 0.4) versus 1.6 (IQR 1.0)], collagen deposition [1.4 (IQR 0.5) versus 2.0 (IQR 1.2)] and alveolar obliteration [2.3 (IQR 0.8) versus 3.2 (IQR 0.5)]. No differences were observed between mice of the Bleo group and mice treated with control medium. Quantitative analysis of collagen deposition confirmed these findings. Importantly, AMTC-CM treatment significantly reduced the fibrosis progression between the two observation time-points. Conclusions This pilot study supports the notion that AMTC exert anti-fibrotic effects through release of yet unknown soluble factors.
Cargnoni, Anna; Ressel, Lorenzo; Rossi, Daniele; Poli, Alessandro; Arienti, Davide; Lombardi, Guerino; Parolini, Ornella
Gene expression profiling of subcutaneous adipose tissue in morbid obesity using a focused microarray: Distinct expression of cell-cycle- and differentiation-related genes
BACKGROUND: Obesity results from an imbalance between food intake and energy expenditure, which leads to an excess of adipose tissue. The excess of adipose tissue and adipocyte dysfunction associated with obesity are linked to the abnormal regulation of adipogenesis. The objective of this study was to analyze the expression profile of cell-cycle- and lipid-metabolism-related genes of adipose tissue in morbid
Sara Rodr�guez-Acebes; Nuria Palacios; Jos� I Botella-Carretero; Nuria Olea; Lorena Crespo; Roberto Peromingo; Diego G�mez-Coronado; Miguel A Lasunci�n; Clotilde V�zquez; Javier Mart�nez-Botas
Progress on ThermoBrachytherapy Surface Applicator for Superficial Tissue Diseases
This work reports the ongoing development of a combination applicator for simultaneous heating of superficial tissue disease using a 915 MHz DCC (dual concentric conductor) array and High Dose Rate (HDR) brachytherapy delivered via an integrated conformal catheter array. The progress includes engineering design changes in the waterbolus, DCC configurations and fabrication techniques of the conformal multilayer applicator. The dosimetric impact of the thin copper DCC array is also assessed. Steady state fluid dynamics of the new waterbolus bag indicates nearly uniform flow with less than 1�C variation across a large (19�32cm) bolus. Thermometry data of the torso phantom acquired with computer controlled movement of fiberoptic temperature probes inside thermal mapping catheters indicate feasibility of real time feedback control for the DCC array. MR (magnetic resonance) scans of a torso phantom indicate that the waterbolus thickness across the treatment area is controlled by the pressure applied by the surrounding inflatable airbladder and applicator securing straps. The attenuation coefficient of the DCC array was measured as 3� 0.001% and 2.95�0.03 % using an ion chamber and OneDose� dosimeters respectively. The performance of the combination applicator on patient phantoms provides valuable feedback to optimize the applicator prior use in the patient clinic.
Arunachalam, Kavitha; Craciunescu, Oana I.; Maccarini, Paolo F.; Schlorff, Jaime L.; Markowitz, Edward; Stauffer, Paul R.
Helicobacter pylori and gastric mucosa-associated lymphoid tissue lymphoma: Recent progress in pathogenesis and management
Recent progress in the research regarding the molecular pathogenesis and management of gastric mucosa-associated lymphoid tissue (MALT) lymphoma is reviewed. In approximately 90% of cases, Helicobacter pylori (H. pylori) infection plays the causative role in the pathogenesis, and H. pylori eradication is nowadays the first-line treatment for this disease, which leads to complete disease remission in 50%-90% of cases. In H. pylori-dependent cases, microbe-generated immune responses, including interaction between B and T cells involving CD40 and CD40L co-stimulatory molecules, are considered to induce the development of MALT lymphoma. In H. pylori-independent cases, activation of the nuclear factor-?B pathway by oncogenic products of specific chromosomal translocations such as t(11;18)/API2-MALT1, or inactivation of tumor necrosis factor alpha-induced protein 3 (A20) are considered to contribute to the lymphomagenesis. Recently, a large-scale Japanese multicenter study confirmed that the long-term clinical outcome of gastric MALT lymphoma after H. pylori eradication is excellent. Treatment modalities for patients not responding to H. pylori eradication include a �watch and wait� strategy, radiotherapy, chemotherapy, rituximab immunotherapy, and a combination of these. Because of the indolent behavior of MALT lymphoma, second-line treatment should be tailored in consideration of the clinical stage and extent of the disease in each patient.
Nakamura, Shotaro; Matsumoto, Takayuki
Determination of amplicon boundaries at 20q13.2 in tissue samples of human gastric adenocarcinomas by high-resolution microarray comparative genomic hybridization.
Comparative genomic hybridization (CGH) of gastric adenocarcinomas frequently shows gains and amplifications of chromosome 20. However, the underlying genetic lesion is unknown and conventional CGH results do not allow specification of the target region. In order to investigate this chromosomal aberration with a higher resolution and sensitivity, microarray-based CGH was performed with both scanning and high-resolution arrays of chromosome 20 in a series of 27 gastric adenocarcinomas. Locus-specific fragments of genomic DNA from bacterial artificial chromosome (BAC) clones were spotted as microarrays. A scanning array contained a set of 27 BAC clones covering chromosome 20q. A high-resolution array contained 27 overlapping BAC clones at 20q13.2. This high-resolution array was used to narrow down the amplicon at 20q13.2 in tumours showing amplification of this chromosomal region with the scanning array. Positive copy number changes on chromosome 20q were detected in 12 of 27 cases (44%). These changes included gain of the whole arm of chromosome 20q in 8 of 27 (30%) cases, amplification restricted to 20q12.1 in one case, and amplifications restricted to 20q13 in three cases (11%). The three tumours showing amplification restricted to 20q13 were analysed further using the high-resolution array. In one tumour, the whole contig was amplified at a constant level. One of the other two tumours had a clear proximal breakpoint, while the other tumour had a clear distal breakpoint within the 20q13.2 region. The proximal and the distal breakpoint were approximately 800 kb apart. In the present study, an amplicon at 20q13.2 has been narrowed down to 800 kb which is likely to harbour one or more putative oncogenes relevant to gastric carcinogenesis, for which ZNF217 and CYP24 are good candidates. PMID:12845628
Weiss, Marjan M; Snijders, Antoine M; Kuipers, Ernst J; Ylstra, Bauke; Pinkel, Daniel; Meuwissen, Stefan G M; van Diest, Paul J; Albertson, Donna G; Meijer, Gerrit A
TMA for all: a new method for the construction of tissue microarrays without recipient paraffin block using custom-built needles
BACKGROUND: TMAs are becoming a useful tool for research and quality control methods, mostly for immunohistochemistry and in situ hybridization. METHODS: A new technique that allows building TMA blocks with more than 300 tissue cores without using a recipient paraffin block for the tissue cores and without using a commercial TMA builder instrument is described. This technique is based on
Andr�a Pires; Felipe Andreiuolo; Simone de Souza
Transcriptional Assessment by Microarray Analysis and Large-Scale Meta-analysis of the Metabolic Capacity of Cardiac and Skeletal Muscle Tissues to Cope With Reduced Nutrient Availability in Gilthead Sea Bream (Sparus aurata L.).
The effects of nutrient availability on the transcriptome of cardiac and skeletal muscle tissues were assessed in juvenile gilthead sea bream fed with a standard diet at two feeding levels: (1) full ration size and (2) 70�% satiation followed by a finishing phase at the maintenance ration. Microarray analysis evidenced a characteristic transcriptomic profile for each muscle tissue following changes in oxidative capacity (heart?>?red skeletal muscle?>?white skeletal muscle). The transcriptome of heart and secondly that of red skeletal muscle were highly responsive to nutritional changes, whereas that of glycolytic white skeletal muscle showed less ability to respond. The highly expressed and nutritionally regulated genes of heart were mainly related to signal transduction and transcriptional regulation. In contrast, those of white muscle were enriched in gene ontology (GO) terms related to proteolysis and protein ubiquitination. Microarray meta-analysis using the bioinformatic tool Fish and Chips ( http://fishandchips.genouest.org/index.php ) showed the close association of a representative cluster of white skeletal muscle with some of cardiac and red skeletal muscle, and many GO terms related to mitochondrial function appeared to be common links between them. A second round of cluster comparisons revealed that mitochondria-related GOs also linked differentially expressed genes of heart with those of liver from cortisol-treated gilthead sea bream. These results show that mitochondria are among the first responders to environmental and nutritional stress stimuli in gilthead sea bream, and functional phenotyping of this cellular organelle is highly promising to obtain reliable markers of growth performance and well-being in this fish species. PMID:24626932
Calduch-Giner, Josep A; Echasseriau, Yann; Crespo, Diego; Baron, Daniel; Planas, Josep V; Prunet, Patrick; P�rez-S�nchez, Jaume
A Survey of Trachoma: The Histopathology and the Mechanism of Progressive Cicatrization of Eyelid Tissues
The aim of this study is to demonstrate the spectrum of conditions encompassed by the term �trachomatous cicatrization of eyelid tissue�, to discuss the mechanisms of scar tissue formation and to describe sequelae in this potentially blinding condition. Specimens of eyelid tissues were taken from 27 upper eyelids of 21 patients with entropion who underwent surgical procedures and 2 post-mortem
Mustafa Guzey; Ilyas Ozardali; Emel Basar; Gonul Aslan; Ahmet Satici; Sezin Karadede
Analysis of Variance for Gene Expression Microarray Data
Spotted cDNA microarrays are emerging as a powerful and cost-effective tool for large- scale analysis of gene expression. Microarrays can be used to measure the relative quantities of speci� c mRNAs in two or more tissue samples for thousands of genes simultaneously. While the power of this technology has been recognized, many open questions remain about appropriate analysis of microarray
M. Kathleen Kerr; Mitchell Martin; Gary A. Churchill
New hypotheses on the function of the avian shell gland derived from microarray analysis comparing tissue from juvenile and sexually mature hens.
Activation of the shell gland region of the avian oviduct is mediated by ovarian steroids. To understand more extensively how shell glands are maintained and function, we have compared gene expression in the shell glands from juvenile and laying hens using a chicken cDNA microarray. Average expression profiles of juvenile and sexually mature shell glands were compared resulting in the identification of 266 differentially regulated genes. Reverse transcription quantitative polymerase chain reaction confirmed expression differences. The differentially expressed genes included several with known involvement in shell gland function, including ion transport and shell matrix proteins. There were also many unpredicted differentially expressed genes, and for some we propose hypotheses for their functions. These include those encoding (a) osteoprotegerin, a decoy death receptor for receptor activator of nuclear factor NFkB ligand (RANKL) and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), that in the shell gland, may prevent apoptosis and/or may have an endocrine effect by preventing RANKL's action on bone osteoclasts that mobilize stored calcium; (b) prostatic acid phosphatase (ACPP) and prostate stem cell antigen (PSCA) that could play a role in sperm physiology within the shell gland; (c) urea transporter (SLC14A2) that could provide a novel anti-microbial defence; (d) bactericidal/permeability-increasing protein-like 2 (BPIL2), and other potential anti-microbials that have not previously been documented in the chicken. These new hypotheses, if borne out experimentally, will lead to a greater understanding of shell gland function including the processes involved in eggshell formation and anti-microbial activity. PMID:19303879
Dunn, I C; Wilson, P W; Lu, Z; Bain, M M; Crossan, C L; Talbot, R T; Waddington, D
MicroRNA-203 inhibits the progression of esophageal squamous cell carcinoma with restored epithelial tissue architecture in vivo.
MicroRNA (miR)-203 has been shown to induce squamous differentiation of epidermal stem cells through the suppression of p63. The aim of this study was to assess the tumor suppressor effect of miR-203 in esophageal squamous cell carcinoma (ESCC) with focus on the regulation of the cell fate decisions and organization of tumor tissue architecture in�vivo. Our investigation establishing stable clones from ESCC cell lines with induced miR-203 expression resulted in significant growth inhibition in a mouse xenograft model. Small foci were observed in xenograft tumors with stratified squamous differentiation in conjunction with restored baso-apical polarity. The expression of the basement membrane protein laminine was localized at the center of the foci and the basal cell marker p75NTR was expressed in the innermost layer. The expression of ki67 and p63 was co-localized at the center layers, while involucrin was expressed in the outer layers. Flow cytometry revealed that the p75NTR-positive cells expressing p63 and Bmi1 were well maintained, while the expression of p63 was suppressed in the p75NTR-negative cells. Our cDNA microarray analysis demonstrated the upregulation of genes involved in regulating tissue architecture, such as BMP-4 and ZO-1 in the mir-203 transfectant. Investigation using surgically removed ESCC specimens revealed that the expression of miR-203 significantly correlated with a favorable prognosis. These results demonstrated that miR-203 regulated both basal and supra-basal cell components to induce differentiation with restored epithelial tissue architecture, leading to significant tumor growth inhibition in�vivo. Those results suggest the use of miR-203 as a novel therapeutic and diagnostic target in patients with ESCC. PMID:24692008
Okumura, Tomoyuki; Shimada, Yutaka; Moriyama, Makoto; Takei, Yoshinori; Omura, Tetsuya; Sekine, Shinichi; Nagata, Takuya; Shimizu, Kazuharu; Tsukada, Kazuhiro
Gene expression profile analysis of primary glioblastomas and non-neoplastic brain tissue: identification of potential target genes by oligonucleotide microarray and real-time quantitative PCR
The prognosis of glioblastomas is still extremely poor and the discovery of novel molecular therapeutic targets can be important\\u000a to optimize treatment strategies. Gene expression analyses comparing normal and neoplastic tissues have been used to identify\\u000a genes associated with tumorigenesis and potential therapeutic targets. We have used this approach to identify differentially\\u000a expressed genes between primary glioblastomas and non-neoplastic brain
Carlos A. Scrideli; Carlos G. Carlotti Jr; Oswaldo K. Okamoto; Vanessa S. Andrade; Maria A. A. Cortez; F�bio J. N. Motta; Agda K. Lucio-Eterovic; Luciano Neder; S�rgio Rosemberg; Sueli M. Oba-Shinjo; Suely K. N. Marie; Lu�z G. Tone
Tissue Engineering Approach to Study the Progression of Breast Tumor Metastasis in Bone.
National Technical Information Service (NTIS)
Most patients dying of breast cancer suffer painful bone metastasis. It is our hypothesis that the invasive growth and progression of breast metastatic lesions in bone requires the participation of various constituents from 'soil'. A reconstitution of suc...
D. Nie M. Che
Tissue Engineering Approach to Study the Progression of Breast Tumor Metastasis in Bone.
National Technical Information Service (NTIS)
Most patients dying of breast cancer suffer painful bone metastasis. It is our hypothesis that the invasive growth and progression of breast metastatic lesions in bone requires the participation of various constituents from 'soil'. A reconstitution of suc...
M. Che D. Nie
Microarray profiling of skeletal muscle tissues from equally obese, non-diabetic insulin-sensitive and insulin-resistant Pima Indians
��Abstract\\u000a \\u000a \\u000a Aims\\/hypothesis. We carried out global transcript profiling to identify differentially expressed skeletal muscle genes in insulin resistance,\\u000a a major risk factor for Type II (non-insulin-dependent) diabetes mellitus. This approach also complemented the ongoing genomic\\u000a linkage analyses to identify genes linked to insulin resistance and diabetes in Pima Indians.\\u000a \\u000a \\u000a \\u000a \\u000a Methods. We compared gene expression profiles of skeletal muscle tissues from
X. Yang; R. E. Pratley; S. Tokraks; C. Bogardus; P. A. Permana
The role of abscisic acid in plant tissue culture: a review of recent progress
Abscisic acid (ABA) plays a significant role in the regulation of many physiological processes of plants. It is often used\\u000a in tissue culture systems to promote somatic embryogenesis and enhance somatic embryo quality by increasing desiccation tolerance\\u000a and preventing precocious germination. ABA is also employed to induce somatic embryos to enter a quiescent state in plant\\u000a tissue culture systems and
Manoj K. Rai; N. S. Shekhawat; Harish; Amit K. Gupta; M. Phulwaria; Kheta Ram; U. Jaiswal
Visualization-based discovery and analysis of genomic aberrations in microarray data
BACKGROUND: Chromosomal copy number changes (aneuploidies) play a key role in cancer progression and molecular evolution. These copy number changes can be studied using microarray-based comparative genomic hybridization (array CGH) or gene expression microarrays. However, accurate identification of amplified or deleted regions requires a combination of visual and computational analysis of these microarray data. RESULTS: We have developed ChARMView, a
Chad L. Myers; Xing Chen; Olga G. Troyanskaya
The BMP signaling gradient patterns dorsoventral tissues in a temporally progressive manner along the anteroposterior axis
Summary Patterning of the vertebrate anteroposterior (AP) axis proceeds temporally from anterior to posterior. How dorsoventral (DV) axial patterning relates to AP temporal patterning is unknown. We examined the temporal activity of BMP signaling in patterning ventrolateral cell fates along the AP axis, using transgenes that rapidly turn �off� or �on� BMP signaling. We show that BMP signaling patterns rostral DV cell fates at the onset of gastrulation, while progressively more caudal DV cell fates are patterned at progressively later intervals during gastrulation. Increased BMP signal duration is not required to pattern more caudal DV cell fates, rather distinct temporal intervals of signaling are required. This progressive action is regulated downstream of, or in parallel to BMP signal transduction at the level of Smad1/5 phosphorylation. We propose that a temporal cue regulates a cell's competence to respond to BMP signaling, allowing the acquisition of a cell's DV and AP identity simultaneously.
Tucker, Jennifer A.; Mintzer, Keith A.; Mullins, Mary C.
Paracrine and Endocrine Effects of Adipose Tissue on Cancer Development and Progression
The past few years have provided substantial evidence for the vital role of the local tumor microenvironment for various aspects of tumor progression. With obesity and its pathophysiological sequelae still on the rise, the adipocyte is increasingly moving center stage in the context of tumor stroma-related studies. To date, we have limited insight into how the systemic metabolic changes associated with obesity and the concomitant modification of the paracrine and endocrine panel of stromal adipocyte-derived secretory products (�adipokines�) influence the incidence and progression of obesity-related cancers. Here, we discuss the role of adipocyte dysfunction associated with obesity and its potential impact on cancer biology.
Park, Jiyoung; Euhus, David M.
The role of tissue transglutaminase (TG2) in regulating the tumour progression of the mouse colon carcinoma CT26
The multifunctional enzyme tissue transglutaminase (TG2) is reported to both mediate and inhibit tumour progression. To elucidate\\u000a these different roles of TG2, we established a series of stable-transfected mouse colon carcinoma CT26 cells expressing a\\u000a catalytically active (wild type) and a transamidating-inactive TG2 (Cys277Ser) mutant. Comparison of the TG2-transfected cells\\u000a with the empty vector control indicated no differences in cell
Panayiotis Kotsakis; Zhuo Wang; Russell John Collighan; Martin Griffin
Viable Tumor Tissue Adherent to Needle Applicators after Local Ablation: A Risk Factor for Local Tumor Progression
Background��Local tumor progression (LTP) is a serious complication after local ablation of malignant liver tumors, negatively influencing\\u000a patient survival. LTP may be the result of incomplete ablation of the treated tumor. In this study, we determined whether\\u000a viable tumor cells attached to the needle applicator after ablation was associated with LTP and disease-free survival.\\u000a \\u000a \\u000a \\u000a \\u000a Methods��In this prospective study, tissue was
Nikol Snoeren; Joost Huiskens; Arjen M. Rijken; Richard van Hillegersberg; Arian R. van Erkel; Gerrit D. Slooter; Joost M. Klaase; Petrousjka M. van den Tol; Fibo J. W. Ten Kate; Maarten C. Jansen; Thomas M. van Gulik
Identifying molecular features for prostate cancer with Gleason 7 based on microarray gene expression profiles.
Prostate cancer represents the first leading cause of cancer among western male population, with different clinical behavior ranging from indolent to metastatic disease. Although many molecules and deregulated pathways are known, the molecular mechanisms involved in the development of prostate cancer are not fully understood. The aim of this study was to explore the molecular variation underlying the prostate cancer, based on microarray analysis and bioinformatics approaches. Normal and prostate cancer tissues were collected by macrodissection from prostatectomy pieces. All prostate cancer specimens used in our study were Gleason score 7. Gene expression microarray (Agilent Technologies) was used for Whole Human Genome evaluation. The bioinformatics and functional analysis were based on Limma and Ingenuity software. The microarray analysis identified 1119 differentially expressed genes between prostate cancer and normal prostate, which were up- or down-regulated at least 2-fold. P-values were adjusted for multiple testing using Benjamini-Hochberg method with a false discovery rate of 0.01. These genes were analyzed with Ingenuity Pathway Analysis software and were established 23 genetic networks. Our microarray results provide new information regarding the molecular networks in prostate cancer stratified as Gleason 7. These data highlighted gene expression profiles for better understanding of prostate cancer progression. PMID:22203922
B?l?cescu, Loredana; B?l?cescu, O; Cri?an, N; Fetica, B; Petru?, B; Bung?rdean, C?t?lina; Rus, Meda; Tudoran, Oana; Meurice, G; Irimie, Al; Drago?, N; Berindan-Neagoe, Ioana
Extracellular Matrix, Nuclear and Chromatin Structure, and Gene Expression in Normal Tissues and Malignant Tumors: A Work in Progress
Almost three decades ago, we presented a model where the extracellular matrix (ECM) was postulated to influence gene expression and tissue-specificity through the action of ECM receptors and the cytoskeleton. This hypothesis implied that ECM molecules could signal to the nucleus and that the unit of function in higher organisms was not the cell alone, but the cell plus its microenvironment. We now know that ECM invokes changes in tissue and organ architecture and that tissue, cell, nuclear, and chromatin structure are changed profoundly as a result of and during malignant progression. Whereas some evidence has been generated for a link between ECM-induced alterations in tissue architecture and changes in both nuclear and chromatin organization, the manner by which these changes actively induce or repress gene expression in normal and malignant cells is a topic in need of further attention. Here, we will discuss some key findings that may provide insights into mechanisms through which ECM could influence gene transcription and how tumor cells acquire the ability to overcome these levels of control.
Spencer, Virginia A.; Xu, Ren; Bissell, Mina J.
Tissue microarray cytometry reveals positive impact of homeodomain interacting protein kinase 2 in colon cancer survival irrespective of p53 function.
The human p53 gene is a tumor suppressor mutated in half of colon cancers. Although p53 function appears important for proliferation arrest and apoptosis induced by cancer therapeutics, the prognostic significance of p53 mutations remains elusive. This suggests that p53 function is modulated at a posttranslational level and that dysfunctions affecting its modulators can have a prognostic impact. Among p53 modulators, homeodomain interacting protein kinase (HIPK) 2 emerges as a candidate "switch" governing p53 transition from a cytostatic to a proapoptotic function. Thus, we investigated the possible prognostic role of HIPK2 on a retrospective series of 80 colon cancer cases by setting up a multiplexed cytometric approach capable of exploring correlative protein expression at the single tumor cell level on TMA. Crossing the data with quantitative PCR and p53 gene sequencing and p53 functional assays, we observed the following: despite a strong impact on p21 transcription, the presence of disabling p53 mutations has no prognostic value, and the increased expression of the HIPK2 protein in tumor cells compared with paired normal tissue cells has a strong impact on survival. Unexpectedly, HIPK2 effect does not appear to be mediated by p53 function because it is also observed in p53-disabling mutated backgrounds. Thus, our results point to a prominent and p53-independent role of HIPK2 in colon cancer survival. PMID:21514416
Soubeyran, Isabelle; Mahouche, Isabelle; Grigoletto, Aude; Leste-Lasserre, Thierry; Drutel, Guillaume; Rey, Christophe; Pedeboscq, Stephane; Blanchard, France; Brouste, Veronique; Sabourin, Jean-Christophe; B�couarn, Yves; Reiffers, Josy; Ichas, Fran�ois; De Giorgi, Francesca
Tissue Microarray Cytometry Reveals Positive Impact of Homeodomain Interacting Protein Kinase 2 in Colon Cancer Survival Irrespective of p53 Function
The human p53 gene is a tumor suppressor mutated in half of colon cancers. Although p53 function appears important for proliferation arrest and apoptosis induced by cancer therapeutics, the prognostic significance of p53 mutations remains elusive. This suggests that p53 function is modulated at a posttranslational level and that dysfunctions affecting its modulators can have a prognostic impact. Among p53 modulators, homeodomain interacting protein kinase (HIPK) 2 emerges as a candidate �switch� governing p53 transition from a cytostatic to a proapoptotic function. Thus, we investigated the possible prognostic role of HIPK2 on a retrospective series of 80 colon cancer cases by setting up a multiplexed cytometric approach capable of exploring correlative protein expression at the single tumor cell level on TMA. Crossing the data with quantitative PCR and p53 gene sequencing and p53 functional assays, we observed the following: despite a strong impact on p21 transcription, the presence of disabling p53 mutations has no prognostic value, and the increased expression of the HIPK2 protein in tumor cells compared with paired normal tissue cells has a strong impact on survival. Unexpectedly, HIPK2 effect does not appear to be mediated by p53 function because it is also observed in p53-disabling mutated backgrounds. Thus, our results point to a prominent and p53-independent role of HIPK2 in colon cancer survival.
Soubeyran, Isabelle; Mahouche, Isabelle; Grigoletto, Aude; Leste-Lasserre, Thierry; Drutel, Guillaume; Rey, Christophe; Pedeboscq, Stephane; Blanchard, France; Brouste, Veronique; Sabourin, Jean-Christophe; Becouarn, Yves; Reiffers, Josy; Ichas, Francois; De Giorgi, Francesca
Towards determining soft tissue properties for modelling spine surgery: current progress and challenges.
Current complication rates for adolescent scoliosis surgery necessitate the development of better surgical planning tools to improve outcomes. Here we present our approach to developing finite element models of the thoracolumbar spine for deformity surgery simulation, with patient-specific model anatomy based on low-dose pre-operative computed tomography scans. In a first step towards defining patient-specific tissue properties, an initial 'benchmark' set of properties were used to simulate a clinically performed pre-operative spinal flexibility assessment, the fulcrum bending radiograph. Clinical data for ten patients were compared with the simulated results for this assessment and in cases where these data differed by more than 10%, soft tissue properties for the costo-vertebral joint (CVJt) were altered to achieve better agreement. Results from these analyses showed that changing the CVJt stiffness resulted in acceptable agreement between clinical and simulated flexibility in two of the six cases. In light of these results and those of our previous studies in this area, it is suggested that spinal flexibility in the fulcrum bending test is not governed by any single soft tissue structure acting in isolation. More detailed biomechanical characterisation of the fulcrum bending test is required to provide better data for determination of patient-specific soft tissue properties. PMID:22198729
Little, J Paige; Adam, Clayton
Evolution of matrix metalloprotease and tissue inhibitor expression during heart failure progression in the infarcted rat
Objective: Characterize the timecourse of matrix metalloproteinase (MMP-1, -2, -3, -7, -9, -11, -12, -13, and -14) and endogenous tissue inhibitors of MMPs (TIMP-1, -2, -3, and -4) upregulation during left ventricular (LV) remodeling following myocardial infarction (MI) in rats. Methods: The descending left coronary artery of male rats (Rattus norvegicus) was ligated to produce a MI. LV function and
J. Thomas Peterson; Hua Li; Lisa Dillon; John W. Bryant
A cell-regulatory mechanism involving feedback between contraction and tissue formation guides wound healing progression.
Wound healing is a process driven by cells. The ability of cells to sense mechanical stimuli from the extracellular matrix that surrounds them is used to regulate the forces that cells exert on the tissue. Stresses exerted by cells play a central role in wound contraction and have been broadly modelled. Traditionally, these stresses are assumed to be dependent on variables such as the extracellular matrix and cell or collagen densities. However, we postulate that cells are able to regulate the healing process through a mechanosensing mechanism regulated by the contraction that they exert. We propose that cells adjust the contraction level to determine the tissue functions regulating all main activities, such as proliferation, differentiation and matrix production. Hence, a closed-regulatory feedback loop is proposed between contraction and tissue formation. The model consists of a system of partial differential equations that simulates the evolution of fibroblasts, myofibroblasts, collagen and a generic growth factor, as well as the deformation of the extracellular matrix. This model is able to predict the wound healing outcome without requiring the addition of phenomenological laws to describe the time-dependent contraction evolution. We have reproduced two in vivo experiments to evaluate the predictive capacity of the model, and we conclude that there is feedback between the level of cell contraction and the tissue regenerated in the wound. PMID:24681636
Valero, Clara; Javierre, Etelvina; Garc�a-Aznar, Jos� Manuel; G�mez-Benito, Mar�a Jos�
Inflammation and adipose tissue: effects of progressive load training in rats
INTRODUCTION: Cytokines (IL-6, IL-10 and TNF-?) are increased after exhaustive exercise in the rat retroperitoneal (RPAT) and mesenteric adipose tissue (MEAT) pads. On the other hand, these cytokines show decreased expression in these depots in response to a chronic exercise protocol. However, the effect of exercise with overload combined with a short recovery period on pro- and anti-inflammatory cytokine expression
F�bio S Lira; Jos� C Rosa; Gustavo D Pimentel; Victor AF Tarini; Ricardo M Arida; Fl�vio Faloppa; Eduardo S Alves; Cl�udia O do Nascimento; Lila M Oyama; Mar�lia Seelaender; Marco T de Mello; Ronaldo VT Santos
Rapid protein display profiling of cancer progression directly from human tissue using a protein biochip
The complicated, changing pattern of protein expression should contain important infor- mation about the pathologic process taking place in the cells of actual tissue. Utilization of this information for the selection of druggable targets could be possible if a means existed to rapidly analyze and display changes in protein expression in defined microscopic cellular subpopulations. As a demonstration of feasi-
Cloud P. Paweletz; John W. Gillespie; David K. Ornstein; Nicole L. Simone; Monica R. Brown; Kristina A. Cole; Quan-Hong Wang; Jing Huang; Nan Hu; Tai-Tung Yip; William E. Rich; Elise C. Kohn; W. Marston Linehan; Thomas Weber; Phil Taylor; Mike R. Emmert-Buck; Lance A. Liotta; Emanuel F. Petricoin III
TLR9 expression in glioma tissues correlated to glioma progression and the prognosis of GBM patients
Background Our study aims to evaluate the expression of TLR9 in glioma tissues, examine the association between TLR9 expression, clinicopathological variables, and glioma patient outcome, we further characterized the direct effects of TLR9 agonist CpG ODN upon the proliferation and invasion of glioma cells in vitro. Methods RT-PCR and immunofluorescence were used to determine the expression of TLR9 in glioma cell lines and clinical glioma samples. Tissue microarry and immunohistochemistry were applied to evaluated TLR9 expression in 292 newly diagnosed glioma and 13 non-neoplastic brain tissues. We further investigated the effect of CpG ODN on the proliferation and invasion of glioma cells in vitro with MTT assays and matrigel transwell assay respectively. Results RT-PCR showed that TLR9 expressed in all the glioma samples and glioma cell lines we examined. The tissue array analysis indicated that TLR9 expression is correlated with malignancy of glioma (p < 0.01). Multivariate Cox regression analysis revealed that TLR9 expression is an independent prognostic factor for PFS of GBM patients(P = 0.026). TLR9 agonist CpG ODN has no significant effect on glioma proliferation, but matrigel transwell analysis showed that TLR9 agonist CpG ODN can significantly enhance glioma invasion in vitro. Conclusions Our data indicated that TLR9 expression increases according to the histopathological grade of glioma, and the TLR9 expression level is related to the PFS of GBM patients. In addition, our findings warrant caution in the directly injection of TLR9 agonist CpG ODN into glioma tissues for the glioma immunotherapy.
Inflammation and adipose tissue: effects of progressive load training in rats
Introduction Cytokines (IL-6, IL-10 and TNF-?) are increased after exhaustive exercise in the rat retroperitoneal (RPAT) and mesenteric adipose tissue (MEAT) pads. On the other hand, these cytokines show decreased expression in these depots in response to a chronic exercise protocol. However, the effect of exercise with overload combined with a short recovery period on pro- and anti-inflammatory cytokine expression is unknown. In the present study, we investigated the regulation of cytokine production in the adipose tissue of rats after an overtraining-inducing exercise protocol. Methods Male Wistar rats were divided into four groups: Control (C), Trained (Tr), Overtrained (OT) and recovered overtrained (R). Cytokines (IL-6, TNF-? and IL-10) levels and Toll Like Receptor 4 (TLR4), Nuclear Factor kBp65 (NF-kBp65), Hormone Sensitive Lipase (HSL) and, Perilipin protein expression were assessed in the adipose tissue. Furthermore, we analysed plasma lipid profile, insulin, testosterone, corticosterone and endotoxin levels, and liver triacylglycerol, cytokine content, as well as apolipoprotein B (apoB) and TLR4 expression in the liver. Results OT and R groups exhibited reduced performance accompanied by lower testosterone and increased corticosterone and endotoxin levels when compared with the control and trained groups. IL-6 and IL-10 protein levels were increased in the adipose tissue of the group allowed to recover, in comparison with all the other studied groups. TLR-4 and NF-kBp65 were increased in this same group when compared with both control and trained groups. The protein expression of HSL was increased and that of Perilipin, decreased in the adipose in R in relation to the control. In addition, we found increased liver and serum TAG, along with reduced apoB protein expression and IL-6 and IL-10 levels in the of R in relation to the control and trained groups. Conclusion In conclusion, we have shown that increases in pro-inflammatory cytokines in the adipose tissue after an overtraining protocol may be mediated via TLR-4 and NF-kBp65 signalling, leading to an inflammatory state in this tissue.
Microarray data analysis and mining
Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target identification. Large-scale microarray studies are also becoming crucial to a new way of conceiving experimental biology. A main issue in microarray transcription profiling is data analysis and mining. When microarrays became a methodology of general use, considerable effort
Marco Botta; Raffaele A. Calogero; Enrico Caserta; Alessandro Guffanti
Fabrication of Glyconanoparticle Microarrays
We report a new type of microarray, based on glyconanoparticles (GNPs), to study glycan-lectin interactions. GNPs, synthesized by conjugating carbohydrate ligands on silica nanoparticles, were printed on a photoactive surface followed by covalent immobilization by light activation. The GNP microarrays could be probed by lectins labeled with fluorescein as well as fluorescein-doped silica nanoparticles (FSNPs). Results showed that FSNP as the label enhanced the signals for the higher affinity ligands than the lower ones.
Tong, Qi; Wang, Xin; Wang, Hui; Kubo, Takuya; Yan, Mingdi
Fabrication of glyconanoparticle microarrays.
We report a new type of microarray, based on glyconanoparticles (GNPs), to study glycan-lectin interactions. GNPs, synthesized by conjugating carbohydrate ligands on silica nanoparticles, were printed on a photoactive surface followed by covalent immobilization by light activation. The GNP microarrays could be probed by lectins labeled with fluorescein as well as fluorescein-doped silica nanoparticles (FSNPs). Results showed that FSNP as the label enhanced the signals for the higher affinity ligands than the lower ones. PMID:22385080
Tong, Qi; Wang, Xin; Wang, Hui; Kubo, Takuya; Yan, Mingdi
Mixed connective tissue disease presenting with progressive scleroderma symptoms in a 10-year-old girl
Mixed connective tissue disease (MCTD) is a systemic inflammatory disease affecting connective tissue with the underlying autoimmunological mechanism. The core of MCTD is an appearance of symptoms of several other inflammatory diseases of connective tissue � systemic lupus erythematosus, systemic scleroderma, poly- or dermatomyositis, rheumatoid arthritis at the same time, accompanied by a high level of anti-ribonucleoprotein antibodies (anti-U1RNP). The disease was described more than 40 years ago by Sharp et al. During recent years, many efforts to better understand clinical and serological features of MCTD have been made. Diagnosis of MCTD can be difficult. Obligatory international diagnostic criteria are required to be fulfilled. Several versions of such criteria have been proposed, but the most widely used one was described by Kasukawa. There is no consensus about treatment � a choice of drugs depends on symptoms. We present a case of a 10-year-old girl with sclerodactyly and trophic damages of fingers accompanied by symptoms of Raynaud's phenomenon. After an almost 2-year course of the disease, a diagnosis of MCTD has been established.
Latuskiewicz-Potemska, Joanna; Biernacka-Zielinska, Malgorzata; Stanczyk, Jerzy; Smolewska, Elzbieta
Long noncoding RNA expression signatures of bladder cancer revealed by microarray
Dysregulation of long noncoding RNAs (lncRNAs) has been regarded as a primary feature of several human cancers. However, the genome-wide expression and functional significance of lncRNAs in bladder cancer remains unclear. The aim of this study was to identify aberrantly expressed lncRNAs that may play an important role in contributing to bladder cancer pathogenesis. In this study, we described lncRNAs profiles in four pairs of human bladder cancer and matched normal bladder tissues by microarray. We finally determined 3,324 differentially expressed human lncRNAs and 2,120 differentially expressed mRNAs (?2-fold change). A total of 110 lncRNAs were significantly differentially expressed between the tumor and the control groups (?8-fold change). Four lncRNAs (TNXA, CTA-134P22.2, CTC-276P9.1 and KRT19P3) were selected for further confirmation of microarray results using quantitative PCR (qPCR), and a strong correlation was identified between the qPCR results and microarray data. We also observed that numerous lncRNA expression levels were significantly correlated with the expression of tens of protein coding genes by construction of the lncRNA-mRNA co-expression network. Kyoto Encyclopedia of Genes and Genomes annotation showed a significant association with p53, bladder cancer, cell cycle and propanoate metabolism pathway gene expression in the bladder cancer group compared with the normal tissue group, indicating that deregulated lncRNAs may act by regulating protein-coding genes in these pathways. We demonstrated the expression profiles of human lncRNAs in bladder cancer by microarray. We identified a collection of aberrantly expressed lncRNAs in bladder cancer compared with matched normal tissue. It is likely that these deregulated lncRNAs play a key or partial role in the development and/or progression of bladder cancer.
Magnetic Analysis of Post-mortem Hippocampal Tissue from Alzheimer's Patients: Changes with Progression of the Disease.
NASA Astrophysics Data System (ADS)
Increases of iron in the human brain with age have been observed and may be accompanied by the development of neurodegenerative diseases, such as Alzheimer's. We have measured the magnetic characteristics of several sets of slides of hippocampal tissue from deceased Alzheimer patients. The slides were made available by the Harvard Brain Bank. The pathology of the tissue was classified in the Braak stages I to VI used to describe the progression of the disease. In general, the slides from patients with higher Braak stages and development of fibrillary tangles and plaques had greater magnetic moments than did those with Braak stage II. However, the peak values were at stage IV and V. To mitigate errors due to the inevitable differences in masses of the tissue on individual slides and their precise location in the hippocampus, ratios of magnetic properties were also observed. Ratios of Anhysteretic Remanent Magnetizaton (ARM) to Isothermal Remanent Magnetization (IRM) were obtained and showed a decrease from Stage II to the more advanced stages, with the minimum values at stages IV and V. The acquisition and demagnetization of IRM are consistent with the presence of magnetite, but also indicate a magnetically harder phase.
Fuller, M.; Zinin, P.; Favia, J.; Tatsumi, L.; Kletetschka, G.; Adachi, T.
On-chip lectin microarray for glycoprofiling of different gastritis types and gastric cancer.
An on-chip lectin microarray based glycomic approach is employed to identify glyco markers for different gastritis and gastric cancer. Changes in protein glycosylation have impact on biological function and carcinogenesis. These altered glycosylation patterns in serum proteins and membrane proteins of tumor cells can be unique markers of cancer progression and hence have been exploited to diagnose various stages of cancer through lectin microarray technology. In the present work, we aimed to study the alteration of glycan structure itself in different stages of gastritis and gastric cancer thoroughly. In order to perform the study from both serum and tissue glycoproteins in an efficient and high-throughput manner, we indigenously developed and employed lectin microarray integrated on a microfluidic lab-on-a-chip platform. We analyzed serum and gastric biopsy samples from 8 normal, 15 chronic Type-B gastritis, 10 chronic Type-C gastritis, and 6 gastric adenocarcinoma patients and found that the glycoprofile obtained from tissue samples was more distinctive than that of the sera samples. We were able to establish signature glycoprofile for the three disease groups, that were absent in healthy normal individuals. In addition, our findings elucidated certain novel signature glycan expression in chronic gastritis and gastric cancer. In silico analysis showed that glycoprofile of chronic gastritis and gastric adenocarcinoma formed close clusters, confirming the previously hypothesized linkage between them. This signature can be explored further as gastric cancer marker to develop novel analytical tools and obtain in-depth understanding of the disease prognosis. PMID:24959308
Roy, Bibhas; Chattopadhyay, Gautam; Mishra, Debasish; Das, Tamal; Chakraborty, Suman; Maiti, Tapas K
Applications of Functional Protein Microarrays in Basic and Clinical Research
The protein microarray technology provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. It is viewed as a new tool that overcomes the limitation of DNA microarrays. On the basis of its application, protein microarrays fall into two major classes: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be directly spotted on a slide to form the so-called �reverse-phase� protein microarray. In the last decade, applications of functional protein microarrays in particular have flourished in studying protein function and construction of networks and pathways. In this chapter, we will review the recent advancements in the protein microarray technology, followed by presenting a series of examples to illustrate the power and versatility of protein microarrays in both basic and clinical research. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade.
Zhu, Heng; Qian, Jiang
Expression microarrays in equine sciences.
Microarrays have become an important research tool for life science researchers. Expression microarrays are capable of profiling the gene expression pattern of tens of thousands of genes in a single experiment. It appears to be the platform of choice for parallel gene expression profiling. Various equine-specific gene expression microarrays have been generated and used. However, homologous microarrays are not yet commercially available for the horse. An alternative is the use of heterologous microarrays, mainly microarrays specific for mice or humans. Although the use of microarrays in equine research is still in its infancy, gene expression microarrays have shown their potential in equine research. This review presents the previous, current and potential use of expression microarrays in equine research. PMID:19027176
Ramery, Eve; Closset, Rodrigue; Art, Tatiana; Bureau, Fabrice; Lekeux, Pierre
MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes
Summary: The microarrays performed by scientific teams grow exponentially. These microarray data could be useful for researchers around the world, but unfortunately they are underused. To fully exploit these data, it is necessary (i) to extract these data from a repository of the high-throughput gene expression data like Gene Expression Omnibus (GEO) and (ii) to make the data from different microarrays comparable with tools easy to use for scientists. We have developed these two solutions in our server, implementing a database of microarray marker genes (Marker Genes Data Base). This database contains the marker genes of all GEO microarray datasets and it is updated monthly with the new microarrays from GEO. Thus, researchers can see whether the marker genes of their microarray are marker genes in other microarrays in the database, expanding the analysis of their microarray to the rest of the public microarrays. This solution helps not only to corroborate the conclusions regarding a researcher's microarray but also to identify the phenotype of different subsets of individuals under investigation, to frame the results with microarray experiments from other species, pathologies or tissues, to search for drugs that promote the transition between the studied phenotypes, to detect undesirable side effects of the treatment applied, etc. Thus, the researcher can quickly add relevant information to his/her studies from all of the previous analyses performed in other studies as long as they have been deposited in public repositories. Availability: Marker-gene database tool: http://ibb.uab.es/mgdb Contact: email@example.com
Huerta, Mario; Munyi, Marc; Exposito, David; Querol, Enric; Cedano, Juan
High levels of carbonic anhydrase IX in tumour tissue and plasma are biomarkers of poor prognostic in patients with non-small cell lung cancer
Background:Carbonic anhydrase IX (CAIX) is an enzyme upregulated by hypoxia during tumour development and progression. This study was conducted to assess if the expression of CAIX in tumour tissue and\\/or plasma can be a prognostic factor in patients with non-small cell lung cancer (NSCLC).Methods:Tissue microarrays containing 555 NSCLC tissue samples were generated for quantification of CAIX expression. The plasma level
M ?lie; N M Mazure; V Hofman; R E Ammadi; C Ortholan; C Bonnetaud; K Havet; N Venissac; B Mograbi; J Mouroux; J Pouyss�gur; P Hofman
T1 relaxation maps allow differentiation between pathologic tissue subsets in relapsing-remitting and secondary progressive multiple sclerosis.
In an attempt to clarify whether T1 relaxation time mapping may assist in characterizing the pathological brain tissue substrate of multiple sclerosis (MS), we compared the T1 relaxation times of lesions, areas of normal-appearing white matter (NAWM) located proximal to lesions, and areas of NAWM located distant from lesions in 12 patients with the relapsing-remitting and 12 with the secondary progressive (SP) subtype of disease. Nine healthy volunteers served as controls. Calculated mean T1 values were averaged across all patients within each clinical group, and comparisons were made by means of the Mann-Whitney U-test. Significant differences were found between all investigated brain regions within each clinical subgroup. Significant differences were also detected for each investigated brain region among clinical subgroups. While T1 values of NAWM were significantly higher in patients with SP disease than in normal white matter (NWM) of controls, no differences were detected when corresponding brain areas of patients with RR MS were compared with NWM of controls. T1 maps identify areas of the brain that are damaged to a different extent in patients with MS, and may be of help in monitoring disease progression. PMID:15471373
Castriota-Scanderbeg, A; Fasano, F; Filippi, M; Caltagirone, C
Tissue Inhibitor of Metalloproteinase-4 Is Elevated in Early-Stage Breast Cancers with Accelerated Progression and Poor Clinical Course
An increasing number of breast cancer patients are diagnosed with small, localized, early-stage tumors. These patients are typically thought to have a good prognosis for long-term disease-free survival, but epidemiological studies indicate that up to 30% may have a recurrence within 3 to 5 years of diagnosis. Identifying patients with a high risk of recurrence and/or progression is important because they could be more aggressively treated at diagnosis to improve their chances for disease-free survival. Recent evidence suggests that elevated levels of the matrix metalloproteinase inhibitor, tissue inhibitor of metalloproteinase (TIMP)-4, are associated with malignant progression of ductal carcinoma in situ, a precancerous lesion. To examine the association of TIMP-4 with survival outcomes, we conducted a retrospective immunohistochemical analysis of 314 cases from patients with early-stage disease, defined as tumors smaller than 2 cm and no spread to lymph nodes (tumor-node-metastasis staging: T1N0MX). We found that tumors with elevated levels of TIMP-4 were correlated with a reduced probability of long-term disease-free survival, especially in patients with estrogen receptor-negative tumors. Our findings prompt further evaluation of TIMP-4 as a simple prognostic marker that may help identify patients with early-stage breast cancer who could benefit from more aggressive treatment at diagnosis.
Liss, Michaelann; Sreedhar, Nandhini; Keshgegian, Albert; Sauter, Guido; Chernick, Michael R.; Prendergast, George C.; Wallon, U. Margaretha
Tissue inhibitor of metalloproteinase-4 is elevated in early-stage breast cancers with accelerated progression and poor clinical course.
An increasing number of breast cancer patients are diagnosed with small, localized, early-stage tumors. These patients are typically thought to have a good prognosis for long-term disease-free survival, but epidemiological studies indicate that up to 30% may have a recurrence within 3 to 5 years of diagnosis. Identifying patients with a high risk of recurrence and/or progression is important because they could be more aggressively treated at diagnosis to improve their chances for disease-free survival. Recent evidence suggests that elevated levels of the matrix metalloproteinase inhibitor, tissue inhibitor of metalloproteinase (TIMP)-4, are associated with malignant progression of ductal carcinoma in situ, a precancerous lesion. To examine the association of TIMP-4 with survival outcomes, we conducted a retrospective immunohistochemical analysis of 314 cases from patients with early-stage disease, defined as tumors smaller than 2 cm and no spread to lymph nodes (tumor-node-metastasis staging: T1N0MX). We found that tumors with elevated levels of TIMP-4 were correlated with a reduced probability of long-term disease-free survival, especially in patients with estrogen receptor-negative tumors. Our findings prompt further evaluation of TIMP-4 as a simple prognostic marker that may help identify patients with early-stage breast cancer who could benefit from more aggressive treatment at diagnosis. PMID:19700750
Liss, Michaelann; Sreedhar, Nandhini; Keshgegian, Albert; Sauter, Guido; Chernick, Michael R; Prendergast, George C; Wallon, U Margaretha
Designing Microarray Experiments
NASA Astrophysics Data System (ADS)
Gene expression microarrays have become an important exploratory tool in many screening experiments that aim to discover the genes that change expression in two or more biological conditions and can be used to build molecular profiles for both diagnostic and prognostic use. The still very high costs of microarrays and the difficulty in generating the biological samples are critical issues of microarraybased screening experiments, and the experimental design plays a crucial role in how informative an experiment is going to be. In this chapter, we describe some of the major issues related to the design of either randomized control trials or observational studies and discuss the choice of powerful sample sizes, the selection of informative experimental conditions, and experimental strategies that can minimize confounding. We conclude with a discussion of some of the open problems in the design and analysis of microarray experiments that need further research.
Sebastiani, Paola; Milton, Jacqui; Wang, Ling
This paper describes G-protein-coupled receptor (GPCR) microarrays on porous glass substrates and functional assays based on the binding of a europium-labeled GTP analogue. The porous glass slides were made by casting a glass frit on impermeable glass slides and then coating with gamma-aminopropyl silane (GAPS). The emitted fluorescence was captured on an imager with a time-gated intensified CCD detector. Microarrays of the neurotensin receptor 1, the cholinergic receptor muscarinic 2, the opioid receptor mu, and the cannabinoid receptor 1 were fabricated by pin printing. The selective agonism of each of the receptors was observed. The screening of potential antagonists was demonstrated using a cocktail of agonists. The amount of activation observed was sufficient to permit determinations of EC50 and IC50. Such microarrays could potentially streamline drug discovery by helping integrate primary screening with selectivity and safety screening without compromising the essential functional information obtainable from cellular assays. PMID:16262381
Hong, Yulong; Webb, Brian L; Su, Hui; Mozdy, Eric J; Fang, Ye; Wu, Qi; Liu, Li; Beck, Jonathan; Ferrie, Ann M; Raghavan, Srikanth; Mauro, John; Carre, Alain; M�eller, Dirk; Lai, Fang; Rasnow, Brian; Johnson, Michael; Min, Hosung; Salon, John; Lahiri, Joydeep
Abating progressive tissue injury and preserving function after CNS trauma: The role of inflammation modulatory therapies.
Brain and spinal cord injuries result in cognitive and/or sensorimotor impairments that can significantly diminish the quality of life for the patient and their carers, and result in healthcare system costs totaling in the billions. The current gold-standard of acute care for spinal cord injury is to administer high doses of glucocorticoids within 8 h of injury; administration after 8 h may be without effect or detrimental to the outcome of the patient. Therefore, improved pharmacological approaches for limiting the extent of tissue damage and neurological dysfunction in the acute injury setting are urgently needed. Early intervention in CNS injury by antagonizing or controlling the post-injury inflammatory process with pharmaceutical agents is a major focus of current clinical and preclinical investigations. In this editorial overview, recent clinical trials and preclinical studies of brain and spinal cord injuries are discussed, including studies focusing on the use of broad-spectrum immunosuppressive drugs (eg, minocycline); growth factors (eg, erythropoietin); dual anti-inflammatory and anti-vasospasm drugs, such as Rho and ROCK kinase inhibitors; and broad-spectrum anti-inflammatory drugs, such as PDE4 inhibitors. These new approaches hold great promise to improve outcomes for patients with brain and spinal injuries. PMID:21189657
Pearse, Damien; Jarnagin, Kurt
Hybridization and Selective Release of DNA Microarrays
DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.
Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K
Creation of a digital slide and tissue microarray resource from a multi-institutional predictive toxicology study in the rat: an initial report from the PredTox group.
The widespread use of digital slides has only recently come to the fore with the development of high-throughput scanners and high performance viewing software. This development, along with the optimisation of compression standards and image transfer techniques, has allowed the technology to be used in wide reaching applications including integration of images into hospital information systems and histopathological training, as well as the development of automated image analysis algorithms for prediction of histological aberrations and quantification of immunohistochemical stains. Here, the use of this technology in the creation of a comprehensive library of images of preclinical toxicological relevance is demonstrated. The images, acquired using the Aperio ScanScope CS and XT slide acquisition systems, form part of the ongoing EU FP6 Integrated Project, Innovative Medicines for Europe (InnoMed). In more detail, PredTox (abbreviation for Predictive Toxicology) is a subproject of InnoMed and comprises a consortium of 15 industrial (13 large pharma, 1 technology provider and 1 SME) and three academic partners. The primary aim of this consortium is to assess the value of combining data generated from 'omics technologies (proteomics, transcriptomics, metabolomics) with the results from more conventional toxicology methods, to facilitate further informed decision making in preclinical safety evaluation. A library of 1709 scanned images was created of full-face sections of liver and kidney tissue specimens from male Wistar rats treated with 16 proprietary and reference compounds of known toxicity; additional biological materials from these treated animals were separately used to create 'omics data, that will ultimately be used to populate an integrated toxicological database. In respect to assessment of the digital slides, a web-enabled digital slide management system, Digital SlideServer (DSS), was employed to enable integration of the digital slide content into the 'omics database and to facilitate remote viewing by pathologists connected with the project. DSS also facilitated manual annotation of digital slides by the pathologists, specifically in relation to marking particular lesions of interest. Tissue microarrays (TMAs) were constructed from the specimens for the purpose of creating a repository of tissue from animals used in the study with a view to later-stage biomarker assessment. As the PredTox consortium itself aims to identify new biomarkers of toxicity, these TMAs will be a valuable means of validation. In summary, a large repository of histological images was created enabling the subsequent pathological analysis of samples through remote viewing and, along with the utilisation of TMA technology, will allow the validation of biomarkers identified by the PredTox consortium. The population of the PredTox database with these digitised images represents the creation of the first toxicological database integrating 'omics and preclinical data with histological images. PMID:18479893
Mulrane, Laoighse; Rexhepaj, Elton; Smart, Valerie; Callanan, John J; Orhan, Diclehan; Eldem, T�rkan; Mally, Angela; Schroeder, Susanne; Meyer, Kirstin; Wendt, Maria; O'Shea, Donal; Gallagher, William M
DNA microarrays in neuropsychopharmacology
Recent advances in experimental genomics, coupled with the wealth of sequence information available for a variety of organisms, have the potential to transform the way pharmacological research is performed. At present, high-density DNA microarrays allow researchers to quickly and accurately quantify gene-expression changes in a massively parallel manner. Although now well established in other biomedical fields, such as cancer and
Eric R. Marcotte; Lalit K. Srivastava
[3] Troubleshooting Microarray Hybridizations
Microarray experiments are being performed more widely than ever before, but even seasoned investigators can experience technical problems with hybridizations. This chapter provides guidelines for recognizing, rectifying, and avoiding common trouble areas. Specifically, it addresses frequent complications related to artifacts of printing, RNA sample preparation and quality, fluorophore labeling, hybridization conditions, and posthybridization washes. Emphasis is placed on investigating problems
Brian Eads; Amy Cash; Kevin Bogart; James Costello; Justen Andrews
NSDL National Science Digital Library
This is an educator-led demonstration of microarray technology using a model created from a pizza box and ping-pong balls. This �macroarray� model demonstrates how single-stranded DNA segments affixed to a solid support are used to separate and identify DNA segments in a solution.
Malone, Molly; Semadeni, Andrew; Freudenrich, Craig C.; Starr, Harmony
Recent developments in DNA microarrays.
DNA microarrays are used to quantify tens of thousands of DNA or RNA sequences in a single assay. Upon their introduction approximately six years ago, DNA microarrays were viewed as a disruptive technology that would fundamentally alter the scientific landscape. Supporting this view, the number of applications of DNA microarray technology has since expanded exponentially. Here, we review recent advances in microarray technology and selected new applications of the technology. PMID:12057691
Shoemaker, Daniel D; Linsley, Peter S
DNA Microarray Methodology Flash Animation
NSDL National Science Digital Library
This Flash animation from Davidson College demonstrates how DNA microarray experiments are performed and can be used as a starting point to teach students the basics of microarray technology. The microarray allows scientists to measure simultaneously the expression of the entire genome in one experiment.
Verna Miller Case (Davidson College;); A. Malcolm Campbell (Davidson College;)
Recent developments in DNA microarrays
DNA microarrays are used to quantify tens of thousands of DNA or RNA sequences in a single assay. Upon their introduction approximately six years ago, DNA microarrays were viewed as a disruptive technology that would fundamentally alter the scientific landscape. Supporting this view, the number of applications of DNA microarray technology has since expanded exponentially. Here, we review recent advances
Daniel D Shoemaker; Peter S Linsley
Tissue prostate-specific antigen facilitates refractory prostate tumor progression via enhancing ARA70-regulated androgen receptor transactivation.
Despite being well recognized as the best biomarker for prostate cancer, pathophysiologic roles of prostate-specific antigen (PSA) remain unclear. We report here that tissue PSA may be involved in the hormone-refractory prostate cancer progression. Histologic analyses show that the increased tissue PSA levels are correlated with lower cell apoptosis index and higher cell proliferation rate in hormone-refractory tumor specimens. By stably transfecting PSA cDNA into various prostate cancer cell lines, we found that PSA could promote the growth of androgen receptor (AR)-positive CWR22rv1 and high-passage LNCaP (hormone-refractory prostate cancer cells) but not that of AR-negative PC-3 and DU145 cells. Surprisingly, the protease activity of PSA is not crucial for PSA to stimulate growth and promote AR transactivation. We further showed that increased PSA could enhance ARA70-induced AR transactivation via modulating the p53 pathway that results in the decreased apoptosis and increased cell proliferation in prostate cancer cells. Knockdown of PSA in LNCaP and CWR22rv1 cells causes cell apoptosis and cell growth arrest at the G(1) phase. In vitro colony formation assay and in vivo xenografted tumor results showed the suppression of prostate cancer growth via targeting PSA expression. Collectively, our findings suggest that, in addition to being a biomarker, PSA may also become a new potential therapeutic target for prostate cancer. PSA small interfering RNA or smaller molecules that can degrade PSA protein may be developed as alternative approaches to treat the prostate cancer. PMID:18757426
Niu, Yuanjie; Yeh, Shuyuan; Miyamoto, Hiroshi; Li, Gonghui; Altuwaijri, Saleh; Yuan, Jianqun; Han, Ruifa; Ma, Tengxiang; Kuo, Hann-Chorng; Chang, Chawnshang
High glucose and hyperinsulinemia stimulate connective tissue growth factor expression: A potential mechanism involved in progression to fibrosis in nonalcoholic steatohepatitis
Nonalcoholic steatohepatitis (NASH) may progress to liver fibrosis and cirrhosis. Mechanisms directly involved in the development of fibrosis have been poorly investigated. Because connective tissue growth factor (CTGF) is an intermediate key molecule involved in the pathogenesis of fibrosing chronic liver diseases and is potentially induced by hyperglycemia, the aims of this study were to (1) study the expression of
Valerie Paradis; Gabriel Perlemuter; Franck Bonvoust; Delphine Dargere; Beatrice Parfait; Michel Vidaud; Marc Conti; Stephane Huet; Nathalie Ba; Catherine Buffet; Pierre Bedossa
Compressive Sensing DNA Microarrays
Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.
Compressive Sensing DNA Microarrays
Abstract�Compressive,Sensing Microarrays,(CSM) are DNA- based sensors that operate,using group,testing and,compressive sensing (CS) principles. In contrast to conventional DNA microar- rays, in which each genetic sensor is designed to respond to a single target, in a CSM each sensor responds to a set of targets. We study the problem,of designing,CSMs that simultaneously account for both the constraints from,compressive,sensing theory and,the biochemistry,of
Wei Dai; Mona A. Sheikh; Olgica Milenkovic; Richard G. Baraniukyy
NSDL National Science Digital Library
In this activity, learners use microarray technology to determine which genes are turned on and off at various points in the differentiation of pluripotent stem cells on their way to becoming pancreatic β cells. An introductory PowerPoint, reading, video clip and an animation provide learners with background information needed to interpret the results of a paper microarray simulation. Learners will position cDNA strips on mini-microarrays to discover which genes are expressing, to what degree they are expressing, and which are not. They use these findings to trace the differentiation of embryonic stem cells that give rise to pancreatic β cells and other cell types. The role of growth factors and proximity of other cell types is central to learners understanding how researchers may direct the ultimate fate of stem cells. The value of this in treating diabetes is also discussed. This activity is recommended for learners studying Biology at the High School (honors, IB and AP) or Undergraduate level.
Colvard, Mary
Analyzing schizophrenia by DNA microarrays.
To understand the pathological processes of schizophrenia, we must embrace the analysis of the diseased human brain: we will never be able to recapitulate the pathology of uniquely human disorders in an animal model. Based on the outcome of the transcriptome profiling experiments performed to date, it appears that schizophrenia is associated with a global gene expression disturbance across many cortical regions. In addition, transcriptome changes are present in multiple cell types, including specific subclasses of principal neurons, interneurons, and oligodendrocytes. Furthermore, transcripts related to synaptic transmission, energy metabolism, and inhibitory neurotransmission are routinely found underexpressed in the postmortem brain tissue of subjects with schizophrenia. To put these transcriptome data in biological context, we must make our data publicly available and report our findings in a proper, expanded Minimum Information About a Microarray Experiment format. Cell-type specific expression profiling and sequencing-based transcript assessments should be expanded, with particular attention to understanding splice-variant changes in various mental disorders. Deciphering the pathophysiology of mental disorders depends on integrating data from across many research fields and techniques. Leads from postmortem transcriptome profiling will be essential to generate model animals, perform tissue culture experiments, and develop or evaluate novel drugs to treat this devastating disorder. PMID:20801428
Horv�th, Szatm�r; Janka, Zolt�n; Mirnics, K�roly
Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays.
There is a mounting evidence of the existence of autoantibodies associated to cancer progression. Antibodies are the target of choice for serum screening because of their stability and suitability for sensitive immunoassays. By using commercial protein microarrays containing 8000 human proteins, we examined 20 sera from colorectal cancer (CRC) patients and healthy subjects to identify autoantibody patterns and associated antigens. Forty-three proteins were differentially recognized by tumoral and reference sera (p value <0.04) in the protein microarrays. Five immunoreactive antigens, PIM1, MAPKAPK3, STK4, SRC, and FGFR4, showed the highest prevalence in cancer samples, whereas ACVR2B was more abundant in normal sera. Three of them, PIM1, MAPKAPK3, and ACVR2B, were used for further validation. A significant increase in the expression level of these antigens on CRC cell lines and colonic mucosa was confirmed by immunoblotting and immunohistochemistry on tissue microarrays. A diagnostic ELISA based on the combination of MAPKAPK3 and ACVR2B proteins yielded specificity and sensitivity values of 73.9 and 83.3% (area under the curve, 0.85), respectively, for CRC discrimination after using an independent sample set containing 94 sera representative of different stages of progression and control subjects. In summary, these studies confirmed the presence of specific autoantibodies for CRC and revealed new individual markers of disease (PIM1, MAPKAPK3, and ACVR2B) with the potential to diagnose CRC with higher specificity and sensitivity than previously reported serum biomarkers. PMID:19638618
Babel, Ingrid; Barderas, Rodrigo; D�az-Uriarte, Ram�n; Mart�nez-Torrecuadrada, Jorge Luis; S�nchez-Carbayo, Marta; Casal, J Ignacio
Pancreatic Tissue Microarray (TMA) - SEER Residual Tissue Repository Program
SEER is an authoratitive source of information on cancer incidence and survival in the United States. SEER currently collects and publishes cancer incidence and survival data from population-based cancer registries covering approximately 28 percent of the U.S. population.
Surface chemistries for antibody microarrays
Enzyme-linked immunosorbent assay (ELISA) microarrays promise to be a powerful tool for the detection of disease biomarkers. The original technology for printing ELISA microarray chips and capturing antibodies on slides was derived from the DNA microarray field. However, due to the need to maintain antibody structure and function when immobilized, surface chemistries used for DNA microarrays are not always appropriate for ELISA microarrays. In order to identify better surface chemistries for antibody capture, a number of commercial companies and academic research groups have developed new slide types that could improve antibody function in microarray applications. In this review we compare and contrast the commercially available slide chemistries, as well as highlight some promising recent advances in the field.
Seurynck-Servoss, Shannon L.; Baird, Cheryl L.; Rodland, Karin D.; Zangar, Richard C.
TNT Metabolites in Animal Tissues: Quarterly Technical Progress Report No. 2, January 1, 1989-March 31, 1989.
National Technical Information Service (NTIS)
The overall objectives of this project are: (1) to provide quantitative analytical procedures for the analysis of TNT and at least eight of its metabolites in animal tissues, and (2) to obtain representative samples of tissues from animals from designated...
L. R. Shugart
Evaluation of gene importance in microarray data based upon probability of selection
BACKGROUND: Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking to metabolic characteristics that contribute to disease development and progression. The microarray approach offers an
Li M. Fu; Casey S. Fu-liu
Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray
PURPOSE: Retinitis pigmentosa (RP) is a genetically heterogeneous disorder characterized by progressive loss of vision. The aim of this study was to identify the causative mutations in 272 Spanish families using a genotyping microarray. METHODS: 272 unrelated Spanish families, 107 with autosomal recessive RP (arRP) and 165 with sporadic RP (sRP), were studied using the APEX genotyping microarray. The families
A. Avila-Fernandez; D. Cantalapiedra; E. Aller; E. Vallespin; J. Aguirre-Lamban; F. Blanco-Kelly; M. Corton; R. Riveiro-Alvarez; R. Allikmets; M. J. Trujillo-Tiebas; J. M. Millan; F. P. M. Cremers; C. Ayuso
Molecular profiling of bladder cancer using cDNA microarrays: defining histogenesis and biological phenotypes.
This study was designed to characterize the expression profiles of nine bladder cancer cell lines (T24, J82, 5637, HT1376, RT4, SCaBER, TCCSUP, UMUC-3, and HT1197) using cDNA microarrays (8976 genes and expressed sequence tags). Novel targets involved in bladder cancer progression of potential clinical relevance were validated by immunohistochemistry using tissue microarrays of primary bladder tumors (n = 193 cases). Hierarchical clustering classified uroepithelial cells based on their histopathogenesis and cell cycle alterations. Keratin 10 and caveolin-1 transcripts were more abundant in tumor cells from squamous and invasive origin. Their combined expression was shown to stratify bladder tumors and define squamous differentiation. To assess the robustness of the clustering analysis, a bootstrap resampling technique was used. This grouped tumor cell lines based on their biological properties, including cell cycle and cell adhesion features. E-cadherin, zyxin, and moesin were identified as genes differentially expressed in these clusters and related to the p53, RB, and INK4A status of the cell lines. Loss of these adhesion molecules was associated with stage and grade in primary tumors (P < 0.05), and moesin expression was also associated with survival (P = 0.01). Deregulation of cell cycle and apoptotic pathways, such as mutations or altered expression of p53, pRB, and INK4A (p16), is necessary for uroepithelial transformation. However, it appears that deregulation of cell adhesion is a common event associated with tumor progression in uroepithelial neoplasms. PMID:12460915
Sanchez-Carbayo, Marta; Socci, Nicholas D; Charytonowicz, Elizabeth; Lu, Minglan; Prystowsky, Michael; Childs, Geoffrey; Cordon-Cardo, Carlos
Progress in developing a living human tissue-engineered tri-leaflet heart valve assembled from tissue produced by the self-assembly approach.
The aortic heart valve is constantly subjected to pulsatile flow and pressure gradients which, associated with cardiovascular risk factors and abnormal hemodynamics (i.e. altered wall shear stress), can cause stenosis and calcification of the leaflets and result in valve malfunction and impaired circulation. Available options for valve replacement include homograft, allogenic or xenogenic graft as well as the implantation of a mechanical valve. A tissue-engineered heart valve containing living autologous cells would represent an alternative option, particularly for pediatric patients, but still needs to be developed. The present study was designed to demonstrate the feasibility of using a living tissue sheet produced by the self-assembly method, to replace the bovine pericardium currently used for the reconstruction of a stented human heart valve. In this study, human fibroblasts were cultured in the presence of sodium ascorbate to produce tissue sheets. These sheets were superimposed to create a thick construct. Tissue pieces were cut from these constructs and assembled together on a stent, based on techniques used for commercially available replacement valves. Histology and transmission electron microscopy analysis showed that the fibroblasts were embedded in a dense extracellular matrix produced in vitro. The mechanical properties measured were consistent with the fact that the engineered tissue was resistant and could be cut, sutured and assembled on a wire frame typically used in bioprosthetic valve assembly. After a culture period in vitro, the construct was cohesive and did not disrupt or disassemble. The tissue engineered heart valve was stimulated in a pulsatile flow bioreactor and was able to sustain multiple duty cycles. This prototype of a tissue-engineered heart valve containing cells embedded in their own extracellular matrix and sewn on a wire frame has the potential to be strong enough to support physiological stress. The next step will be to test this valve extensively in a bioreactor and at a later date, in a large animal model in order to assess in vivo patency of the graft. PMID:24813743
Dub�, Jean; Bourget, Jean-Michel; Gauvin, Robert; Lafrance, Hugues; Roberge, Charles J; Auger, Fran�ois A; Germain, Lucie
Microarray analysis of activated mixed glial (microglia) and monocyte-derived macrophage gene expression
Since macrophage activation can now be studied at a global level using modern microarray and proteomic analyses, discovery of novel macrophage activation genes is inevitable and important for understanding HIV-associated dementia (HAD). We isolated two different types of primary human macrophages: microglia and monocyte-derived macrophages (MDM) from brain tissue and whole blood, respectively. The microarray analysis of differentially regulated macrophage
Andrew V. Albright; Francisco Gonz�lez-Scarano
Chronic treatment with tempol does not significantly ameliorate renal tissue hypoxia or disease progression in a rodent model of polycystic kidney disease.
In the present study, we tested whether polycystic kidney disease (PKD) is associated with renal tissue hypoxia and oxidative stress, which, in turn, contribute to the progression of cystic disease and hypertension. Lewis polycystic kidney (LPK) rats and Lewis control (Lewis) rats were treated with tempol (1�mmol/L in drinking water) from 3 to 13�weeks of age or remained untreated. The LPK rats developed polyuria, uraemia and proteinuria. At 13�weeks of age, LPK rats had greater mean arterial pressure (1.5-fold), kidney weight (sixfold) and plasma creatinine (3.5-fold) than Lewis rats. Kidneys from LPK rats were cystic and fibrotic. Renal hypoxia was evidenced by staining for pimonidazole adducts and hypoxia-inducible factor (HIF)-1? in cells lining renal cysts and upregulation of HIF-1? and its downstream targets vascular endothelial growth factor (VEGF), glucose transporter-1 (Glut-1) and heme oxygenase 1 (HO-1). However, total HO activity did not differ greatly between kidney tissue from LPK compared with Lewis rats. Renal oxidative and/or nitrosative stress was evidenced by ninefold greater immunofluorescence for 3-nitrotyrosine in kidney tissue from LPK compared with Lewis rats and a�>�10-fold upregulation of mRNA for p47phox and gp91phox. Total renal superoxide dismutase (SOD) activity was sevenfold less and expression of SOD1 mRNA was 70% less in kidney tissue from LPK compared with Lewis rats. In LPK rats, tempol treatment reduced immunofluorescence for 3-nitrotyrosine and HIF1A mRNA while upregulating VEGF and p47phox mRNA expression, but otherwise had little impact on disease progression, renal tissue hypoxia or hypertension. Our findings do not support the hypothesis that oxidative stress drives hypoxia and disease progression in PKD. PMID:23006058
Ding, Alice; Kalaignanasundaram, Priyadharshani; Ricardo, Sharon D; Abdelkader, Amany; Witting, Paul K; Broughton, Brad R S; Kim, Hyun B; Wyse, Benjamin F; Phillips, Jacqueline K; Evans, Roger G
Characteristic attributes in cancer microarrays
Rapid advances in genome sequencing and gene expression microarray technologies are providing unprecedented opportunities to identify specific genes involved in complex biological processes, such as development, signal transduction, and disease. The vast amount of data generated by these technologies has presented new challenges in bioinformatics. To help organize and interpret microarray data, new and efficient computational methods are needed to:
Indra Neil Sarkar; Paul J. Planet; T. E. Bael; S. E. Stanley; Mark Siddall; Robert Desalle; David H. Figurski
Microarray core detection by geometric restoration.
Whole-slide imaging of tissue microarrays (TMAs) holds the promise of automated image analysis of a large number of histopathological samples from a single slide. This demands high-throughput image processing to enable analysis of these tissue samples for diagnosis of cancer and other conditions. In this paper, we present a completely automated method for the accurate detection and localization of tissue cores that is based on geometric restoration of the core shapes without placing any assumptions on grid geometry. The method relies on hierarchical clustering in conjunction with the Davies-Bouldin index for cluster validation in order to estimate the number of cores in the image wherefrom we estimate the core radius and refine this estimate using morphological granulometry. The final stage of the algorithm reconstructs circular discs from core sections such that these discs cover the entire region of each core regardless of the precise shape of the core. The results show that the proposed method is able to reconstruct core locations without any evidence of localization. Furthermore, the algorithm is more efficient than existing methods based on the Hough transform for circle detection. The algorithm's simplicity, accuracy, and computational efficiency allow for automated high-throughput analysis of microarray images. PMID:22684152
Azar, Jimmy C; Busch, Christer; Carlbom, Ingrid B
Microarrays in primary breast cancer - lessons from chemotherapy studies
Current development in molecular techniques has extended the opportunities to explore genetic alterations in malignant tissue. There is a need to improve prognostication and, in particular, to understand the mechanisms of treatment resistance in different tumours. Gene analyses by microarrays allow concomitant analyses of several genes in concert, providing new opportunities for tumour classification and understanding of key biological disturbances.
P E L�nning; C M Perou; P O Brown; D Botstein
Data-adaptive test statistics for microarray data
Motivation: An important task in microarray data analysis is the selection of genes that are differentially expressed between different tissue samples, such as healthy and diseased. However, micro- array data contain an enormous number of dimensions (genes) and very few samples (arrays), a mismatch which poses fundamental statistical problems for the selection process that have defied easy resolution. Results: In
Sach Mukherjee; Stephen J. Roberts; Mark J. Van Der Laan
Clinical Application of cDNA Microarrays in Oncology
DNA microarrays represent an important new tool to analyze human tissues. The technology enables inves- tigators to measure the expression of several thousand mRNA species simultaneously in a biological specimen. This process, called transcriptional profiling, represents a technological breakthrough in the analysis of biologi- cal specimens. It may be used to screen for individual genes that are differentially expressed between
LAJOS PUSZTAI; MARK AYERS; JAMES STEC; GABRIEL N. HORTOB�GYIa
Deciphering gene expression profiles generated from DNA microarrays and their applications in oral medicine.
Genome-wide monitoring of gene expression profiles using DNA microarrays provides a unique approach to exploring the biological processes underlying oral diseases and disorders by providing a comprehensive survey of a cell's or tissue's transcriptional mapping. This revolutionary technology allows for the simultaneous assessment of the transcription levels of tens of thousands of genes, and of their relative expression between normal and diseased cells. As microarray data analysis evolves, there is a widespread hope that microarrays will significantly impact our ability to explore the genetic changes associated with disease etiology and development, ultimately leading to the discovery of new biomarkers for disease diagnosis and prognosis prediction as well as new therapeutic tools. The goal of this manuscript is to review 2 of the most commonly used microarray technologies, provide an overview of data analyses involved in a typical microarray experiment, and comment upon the application of microarrays to oral medicine. PMID:15153870
Kuo, Winston Patrick; Whipple, Mark E; Epstein, Joel B; Jenssen, Tor-Kristian; Santos, Gustavo S; Ohno-Machado, Lucila; Sonis, Stephen T
Differentiated miRNA expression and validation of signaling pathways in apoE gene knockout mice by cross-verification microarray platform
The microRNA (miRNA) regulation mechanisms associated with atherosclerosis are largely undocumented. Specific selection and efficient validation of miRNA regulation pathways involved in atherosclerosis development may be better assessed by contemporary microarray platforms applying cross-verification methodology. A screening platform was established using both miRNA and genomic microarrays. Microarray analysis was then simultaneously performed on pooled atherosclerotic aortic tissues from 10 Apolipoprotein E (apoE) knockout mice (apoE?/?) and 10 healthy C57BL/6 (B6) mice. Differentiated miRNAs were screened and cross-verified against an mRNA screen database to explore integrative mRNA�miRNA regulation. Gene set enrichment analysis was conducted to describe the potential pathways regulated by these mRNA�miRNA interactions. High-throughput data analysis of miRNA and genomic microarrays of knockout and healthy control mice revealed 75 differentially expressed miRNAs in apoE?/? mice at a threshold value of 2. The six miRNAs with the greatest differentiation expression were confirmed by real-time quantitative reverse-transcription PCR (qRT�PCR) in atherosclerotic tissues. Significantly enriched pathways, such as the type 2 diabetes mellitus pathway, were observed by a gene-set enrichment analysis. The enriched molecular pathways were confirmed through qRT�PCR evaluation by observing the presence of suppressor of cytokine signaling 3 (SOCS3) and SOCS3-related miRNAs, miR-30a, miR-30e and miR-19b. Cross-verified high-throughput microarrays are optimally accurate and effective screening methods for miRNA regulation profiles associated with atherosclerosis. The identified SOCS3 pathway is a potentially valuable target for future development of targeted miRNA therapies to control atherosclerosis development and progression.
Han, Hui; Wang, Yu-Hong; Qu, Guang-Jin; Sun, Ting-Ting; Li, Feng-Qing; Jiang, Wei; Luo, Shan-Shun
Microarray platform for omics analysis
NASA Astrophysics Data System (ADS)
Microarray technology has revolutionized genetic analysis. However, limitations in genome analysis has lead to renewed interest in establishing 'omic' strategies. As we enter the post-genomic era, new microarray technologies are needed to address these new classes of 'omic' targets, such as proteins, as well as lipids and carbohydrates. We have developed a microarray platform that combines self- assembling monolayers with the biotin-streptavidin system to provide a robust, versatile immobilization scheme. A hydrophobic film is patterned on the surface creating an array of tension wells that eliminates evaporation effects thereby reducing the shear stress to which biomolecules are exposed to during immobilization. The streptavidin linker layer makes it possible to adapt and/or develop microarray based assays using virtually any class of biomolecules including: carbohydrates, peptides, antibodies, receptors, as well as them ore traditional DNA based arrays. Our microarray technology is designed to furnish seamless compatibility across the various 'omic' platforms by providing a common blueprint for fabricating and analyzing arrays. The prototype microarray uses a microscope slide footprint patterned with 2 by 96 flat wells. Data on the microarray platform will be presented.
Mecklenburg, Michael; Xie, Bin
Sweet tasting chips: microarray-based analysis of glycans.
Glycosylation, a ubiquitous post-translational modification of proteins and lipids that generates enormous functional diversity, is rapidly gaining attention in the postgenomic era. The systematic study of glycans, that is glycomics, has been driven by the development of new analytical tools well suited to the inherent complexities of carbohydrate analysis, such as lectin-based microarray technologies. Recent work has demonstrated the utility of these analytical tools for glycomics in both clinical and research settings, for example identifying novel biomarkers associated with disease progression or studying HIV-1 exit mechanisms. This review highlights these new lectin-based microarray technologies and their role in the emerging field of glycomics. PMID:19716334
Hsu, Ku-Lung; Mahal, Lara K
Three-dimensional lithographically-defined organotypic tissue arrays for quantitative analysis of morphogenesis and neoplastic progression
Here we describe a simple micromolding method to construct three-dimensional arrays of organotypic epithelial tissue structures that approximate in vivo histology. An elastomeric stamp containing an array of posts of defined geometry and spacing is used to mold microscale cavities into the surface of type I collagen gels. Epithelial cells are seeded into the cavities and covered with a second layer of collagen. The cells reorganize into hollow tissues corresponding to the geometry of the cavities. Patterned tissue arrays can be produced in 3-4 h and will undergo morphogenesis over the following one to three days. The protocol can easily be adapted to study a variety of tissues and aspects of normal and neoplastic development.
Nelson, Celeste M.; Inman, Jamie L.; Bissell, Mina J.
TNT metabolites in animal tissues: Quarterly technical progress report No. 2, January 1, 1989--March 31, 1989
The overall objectives of this project are: (1) to provide quantitative analytical procedures for the analysis of TNT and at least eight of its metabolites in animal tissues, and (2) to obtain representative samples of tissues from animals from designated Army sites and to determine the presence or absence of TNT and its metabolites in these samples. The study is divided into two Phases corresponding to the stated overall objectives of the project. 3 figs., 2 tabs.
Shugart, L.R.
TNT metabolites in animal tissues: Quarterly technical progress report (No. 3), April 1, 1989--June 30, 1989
The overall objectives of this project are: (1) to provide quantitative analytical procedures for the analysis of TNT and at least eight of its metabolites in animal tissues, and (2) to obtain representative samples of tissues from animals from designated Army sites and to determine the presence or absence of TNT and its metabolites in these samples. The study is divided into two Phases corresponding to the stated overall objectives of the project.
Shugart, L.R.
Dot by dot: analyzing the glycome using lectin microarrays.
The glycome, that is, the cohort of carbohydrates within a cell or tissue, plays a key part in diverse biological interactions involved in health and disease. Glycans are structurally complex and notoriously difficult to analyze. Lectin microarrays, a sensitive and high-throughput method for glycomic profiling, provide a global view of the glycome. In recent work, this technology has been successfully applied to a wide range of studies, from identification of glycan-based stem cell markers to the detection of pathogens and early diagnosis of disease. This review focuses on advances in the field of lectin microarrays. PMID:23856055
Ribeiro, Jo�o P; Mahal, Lara K
The bioinformatics of microarrays to study cancer: Advantages and disadvantages
NASA Astrophysics Data System (ADS)
Microarrays are devices designed to analyze simultaneous expression of thousands of genes. However, the process will adds noise into the information at each stage of the study. To analyze these thousands of data is necessary to use bioinformatics tools. The traditional analysis begins by normalizing data, but the obtained results are highly dependent on how it is conducted the study. It is shown the need to develop new strategies to analyze microarray. Liver tissue taken from an animal model in which is chemically induced cancer is used as an example.
Rodr�guez-Segura, M. A.; Godina-Nava, J. J.; Villa-Trevi�o, S.
Microarray Analysis of Microbial Weathering
NASA Astrophysics Data System (ADS)
Microarray analysis of the heavy metal resistant bacterium, Cupriavidus metallidurans CH34 was used to investigate the genes involved in the weathering. The results demonstrated that large porin and membrane transporter genes were unregulated.
Olsson-Francis, K.; van Houdt, R.; Leys, N.; Mergeay, M.; Cockell, C. S.
Analysis of Protein Expression in Cell Microarrays: A Tool for Antibody-based Proteomics
Tissue microarray (TMA) technology provides a possibility to explore protein expression patterns in a multitude of normal and disease tissues in a high-throughput setting. Although TMAs have been used for analysis of tissue samples, robust methods for studying in vitro cultured cell lines and cell aspirates in a TMA format have been lacking. We have adopted a technique to homogeneously
Ann-Catrin Andersson; Sara Str�mberg; Helena B�ckvall; Caroline Kampf; Mathias Uhlen; Kenneth Wester; Fredrik Pont�n
Imaging the morphological change of tissue structure during the early phase of esophageal tumor progression using multiphoton microscopy
NASA Astrophysics Data System (ADS)
Esophageal cancer is a common malignancy with a very poor prognosis. Successful strategies for primary prevention and early detection are critically needed to control this disease. Multiphoton microscopy (MPM) is becoming a novel optical tool of choice for imaging tissue architecture and cellular morphology by two-photon excited fluorescence. In this study, we used MPM to image microstructure of human normal esophagus, carcinoma in situ (CIS), and early invasive carcinoma in order to establish the morphological features to differentiate these tissues. The diagnostic features such as the appearance of cancerous cells, the significant loss of stroma, the absence of the basement membrane were extracted to distinguish between normal and cancerous esophagus tissue. These results correlated well with the paired histological findings. With the advancement of clinically miniaturized MPM and the multi-photon probe, combining MPM with standard endoscopy will therefore allow us to make a real-time in vivo diagnosis of early esophageal cancer at the cellular level.
Xu, Jian; Kang, Deyong; Xu, Meifang; Zhu, Xiaoqin; Zhuo, Shuangmu; Chen, Jianxin
Development of a Highly Sensitive Glycan Microarray for Quantifying AFP-L3 for Early Prediction of Hepatitis B Virus-Related Hepatocellular Carcinoma
The ?-fetoprotein fraction L3 (AFP-L3), which is synthesized by malignant cells and incorporates a fucosylated oligosaccharide, has been investigated as a diagnostic and prognostic marker for hepatocellular carcinoma (HCC). Quantification of AFP-L3 by conventional enzyme-linked immunosorbent assay (ELISA) has not always produced reliable results for serum samples with low AFP, and thus we evaluated the clinical utility of quantifying AFP-L3 using a new and highly sensitive glycan microarray assay. Sera from 9 patients with chronic hepatitis B and 32 patients with hepatitis B virus (HBV)-related HCC were tested for AFP-L3 level using the glycan microarray. Additionally, we compared receiver operator characteristic curves for the ELISA and glycan microarray methods for determination of the AFP-L3: AFP-L1 ratio in patient samples. This ratio was calculated for 8 HCC patients who underwent transarterial embolization therapy pre- or post-treatment with AFP-L3. Glycan microarrays showed that the AFP-L3 ratio of HBV-related HCC patients was significantly higher than that measured for chronic hepatitis B patients. Overall parameters for estimating AFP-L3% in HCC samples were as follows: sensitivity, 53.13%; specificity, 88.89%; and area under the curve, 0.75. The elevated AFP-L3% in the 8 patients with HBV-related HCC was strongly associated with HCC progression. Following one month of transarterial embolization therapy, the relative mean AFP-L3% decreased significantly. In addition, we compared Fut8 gene expression between paired tumor and non-tumor tissues from 24 patients with HBV-related HCC. The Fut8 mRNA expression was significantly increased in tumorous tissues in these patients than that in non-tumor tissue controls. Higher expression of Fut8 mRNA in tumorous tissues in these patients was associated with poor differentiation than well and moderate differentiation. Our results describe a new glycan microarray for the sensitive and rapid quantification of fucosylated AFP; this method is potentially applicable to screening changes in AFP-L3 level for assessment of HCC progression.
Chou, Ruey-Hwang; Yen, Chia-Jui; Huang, Wei-Chien; Wu, Chung-Yi; Yu, Yung-Luen
Fluorescent and luminescent probes for measurement of oxidative and nitrosative species in cells and tissues: Progress, pitfalls, and prospects
Chemical probes for free radicals in biology are important tools; fluorescence and chemiluminescence offer high detection sensitivity. This article reviews progress in the development of probes for �reactive oxygen and nitrogen� species, emphasizing the caution needed in their use. Reactive species include hydrogen peroxide; hydroxyl, superoxide, and thiyl radicals; carbonate radical-anion; and nitric oxide, nitrogen dioxide, and peroxynitrite. Probes based
Peter Wardman
Identification of differentially expressed genes in cutaneous squamous cell carcinoma by microarray expression profiling
Background Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. This study examined and identified differentially expressed genes in cutaneous squamous cell carcinoma (SCC). Results Three different biopsies of 5 immunosuppressed organ-transplanted recipients each normal skin (all were pooled), actinic keratosis (AK) (two were pooled), and invasive SCC and additionally 5 normal skin tissues from immunocompetent patients were analyzed. Thus, total RNA of 15 specimens were used for hybridization with Affymetrix HG-U133A microarray technology containing 22,283 genes. Data analyses were performed by prediction analysis of microarrays using nearest shrunken centroids with the threshold 3.5 and ANOVA analysis was independently performed in order to identify differentially expressed genes (p < 0.05). Verification of 13 up- or down-regulated genes was performed by quantitative real-time reverse transcription (RT)-PCR and genes were additionally confirmed by sequencing. Broad coherent patterns in normal skin vs. AK and SCC were observed for 118 genes. Conclusion The majority of identified differentially expressed genes in cutaneous SCC were previously not described.
Nindl, Ingo; Dang, Chantip; Forschner, Tobias; Kuban, Ralf J; Meyer, Thomas; Sterry, Wolfram; Stockfleth, Eggert
Identification of autoantibody biomarkers for primary Sj?gren's syndrome using protein microarrays
Sj�gren's syndrome (SS) is a chronic, progressive autoimmune disease primarily affecting women. Diagnosis of SS requires an invasive salivary gland tissue biopsy and a long delay from the start of the symptoms to final diagnosis has been frequently observed. In this study, we aim to identify salivary autoantibody biomarkers for primary SS (pSS) using a protein microarray approach. Immune-response protoarrays were used to profile saliva autoantibodies from patients with pSS (n=14), patients with systemic lupus erythematosus (SLE, n=13), and healthy control subjects (n=13). We identified 24 potential autoantibody biomarkers that can discriminate patients with pSS from both patients with SLE and healthy individuals. Four saliva autoantibody biomarkers, anti-transglutaminase, anti-histone, anti-SSA, and anti-SSB, were further tested in independent pSS (n=34), SLE (n=34), and healthy control (n=34) subjects and all were successfully validated with ELISA. This study has demonstrated the potential of a high-throughput protein microarray approach for the discovery of autoantibody biomarkers. The identified saliva autoantibody biomarkers may lead to a clinical tool for simple, noninvasive detection of pSS at low cost.
Hu, Shen; Vissink, Arjan; Arellano, Martha; Roozendaal, Caroline; Zhou, Hui; Kallenberg, Cees G. M.; Wong, David T.
Identification of autoantibody biomarkers for primary Sj�gren's syndrome using protein microarrays.
Sj�gren�s syndrome (SS) is a chronic, progressive autoimmune disease primarily affecting women. Diagnosis of SS requires an invasive salivary gland tissue biopsy and a long delay from the start of the symptoms to final diagnosis has been frequently observed. In this study,we aim to identify salivary autoantibody biomarkers for primary SS (pSS) using a protein microarray approach. Immune-response protoarrays were used to profile saliva autoantibodies from patients with pSS (n = 514), patients with systemic lupus erythematosus(SLE, n = 513), and healthy control subjects (n = 513). We identified 24 potential autoantibody biomarkers that can discriminate patients with pSS from both patients with SLE and healthy individuals. Four saliva autoantibody biomarkers, anti-transglutaminase, anti-histone, anti-SSA, and anti-SSB, were further tested in independent pSS (n = 534), SLE (n = 534), and healthy control (n = 534) subjects and all were successfully validated with ELISA. This study has demonstrated the potential of a high-throughput protein microarray approach for the discovery of autoantibody biomarkers. The identified saliva autoantibody biomarkers may lead to a clinical tool for simple, noninvasive detection of pSS at low cost. PMID:21413148
Hu, Shen; Vissink, Arjan; Arellano, Martha; Roozendaal, Caroline; Zhou, Hui; Kallenberg, Cees G M; Wong, David T
Molecular diagnostics of ocular diseases: the application of antibody microarray.
Proteomic analyses as applied to ocular aqueous humor provide evidence that this approach may be used to identify ocular disease with particular reference to cataract and glaucoma. Protein alterations bear pathogenic relevance for disease development. Among the different methods available, antibody microarray seems to be the most readily transferable to the clinic. However, this method still bears some limitations, such as the relatively small number of proteins analyzed and the poor specificity. Proteomic analysis is able to depict the pathogenesis of common ocular diseases and to produce data of both diagnostic and prognostic relevance. Proteome alterations detected in the aqueous humor of glaucomatous patients reflect degeneration occurring in target tissues - that is, the trabecular meshwork, retina and optic nerve head. Performed studies indicate good performances of aqueous humor analysis by antibody microarray for glaucoma diagnosis. Future development is addressed to improve antibody microarray specificity and to set up minimally invasive procedures for aqueous humor sampling. PMID:22845483
Izzotti, Alberto; Centofanti, Marco; Sacc�, Sergio Claudio
Oncogene interactions are required for glioma development and progression as revealed by a tissue specific transgenic mouse model
The aggressive and invasive nature of brain tumors has hampered progress in the design and implementation of efficacious therapies. The recent success of targeted therapies in other tumor types makes this an attractive area for research yet complicating matters is the ability of brain tumors to circumvent the targeted pathways to develop drug resistance. Effective therapies will likely need to target more than one signaling pathway or target multiple nodes within a given pathway. Key to identifying these targets is the elucidation of the driver and passenger molecules within these pathways. Animal models provide a useful tool with many advantages in the study of these pathways. These models provide a means to dissect the critical components of tumorigenesis, as well as serve as agents for preclinical testing. This review focuses on the use of the RCAS/tv-a mouse model of brain tumors and describes their unique ability to provide insight into the role of Oncogene cooperation in tumor development and progression.
Moore, Lynette M.; Holmes, Kristen M.; Fuller, Gregory N.; Zhang, Wei
Recent progress in defining mechanisms and potential targets for prevention of normal tissue injury after radiation therapy
The ability to optimize treatments for cancer on the basis of relative risks for normal tissue injury has important implications in oncology, because higher doses of radiation might, in some diseases, improve both local control and survival. To achieve this goal, a thorough understanding of the molecular mechanisms responsible for radiation-induced toxicity will be essential. Recent research has demonstrated that ionizing radiation triggers a series of genetic and molecular events, which might lead to chronic persistent alterations in the microenvironment and an aberrant wound-healing response. Disrupted epithelial-stromal cell communication might also be important. With the application of a better understanding of fundamental biology to clinical practice, new approaches to treating and preventing normal tissue injury can focus on correcting these disturbed molecular processes.
Anscher, Mitchell S. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States)]. E-mail: firstname.lastname@example.com; Chen, Liguang [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Rabbani, Zahid [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Kang Song [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Larrier, Nicole [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Huang Hong [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Samulski, Thaddeus V. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Dewhirst, Mark W. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Brizel, David M. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Folz, Rodney J. [Department of Medicine, Duke University Medical Center, Durham, NC (United States); Vujaskovic, Zeljko [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States)
Disturbance of the gut-associated lymphoid tissue is associated with disease progression in chronic HIV infection
Why and how HIV makes people sick is highly debated. Recent evidence implicates heightened immune activation due to breakdown\\u000a of the gastrointestinal barrier as a determining factor of lentiviral pathogenesis. HIV-mediated loss of Th17 cells from the\\u000a gut-associated lymphoid tissue (GALT) impairs mucosal integrity and innate defense mechanisms against gut microbes. Translocation\\u000a of microbial products from the gut, in turn,
Ursula Hofer; Roberto F. Speck
Noninvasive near-infrared fluorescent protein-based imaging of tumor progression and metastases in deep organs and intraosseous tissues
NASA Astrophysics Data System (ADS)
Whole-body imaging of experimental tumor growth is more feasible within the near-infrared (NIR) optical window because of the highest transparency of mammalian tissues within this wavelength spectrum, mainly due to improved tissue penetration and lower autofluorescence. We took advantage from the recently cloned infrared fluorescent protein (iRFP) together with a human immunodeficiency virus (HIV)-based lentiviral vector to produce virally transduced tumor cells that permanently express this protein. We then noninvasively explored metastatic spread as well as primary tumor growth in deep organs and behind bone barriers. Intrabone tumor growth was investigated through intracranial and intratibial injections of glioblastoma and osteosarcoma cells, respectively, and metastasis was assessed by tail vein injection of melanoma cells. We found that the emitted fluorescence is captured as sharp images regardless of the organ or tissue considered. Furthermore, by overlaying fluorescence spots with the white light, it was possible to afford whole-body images yet never observed before. This approach allowed us to continuously monitor the growth and dissemination of tumor cells with a small number of animals, minimal animal handling, and without the need for any additive. This iRFP-based system provides high-resolution readouts of tumorigenesis that should greatly facilitate preclinical trials with anticancer therapeutic molecules.
Jiguet-Jiglaire, Carine; Cayol, Myl�ne; Mathieu, Sylvie; Jeanneau, Charlotte; Bouvier-Labit, Corinne; Ouafik, L.'houcine; El-Battari, Assou
Comparing Bacterial DNA Microarray Fingerprints
Detecting subtle genetic differences between microorganisms is an important problem in molecular epidemiology and microbial forensics. In a typical investigation, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial strains, where the patterns of DNA fragment sizes are proxies for a microbe's genotype. The limited genomic sample captured on a gel is often insufficient to discriminate nearly identical strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if the number of probes on the microarray is sufficiently large, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate the statistical fingerprinting problem for 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.
Willse, Alan R.; Chandler, Darrell P.; White, Amanda M.; Protic, Miroslava; Daly, Don S.; Wunschel, Sharon C.
Utility of tissue microarrays for profiling prognostic biomarkers in clinically localized prostate cancer: the expression of BCL-2, E-cadherin, Ki-67 and p53 as predictors of biochemical failure after radical prostatectomy with nested control for clinical and pathological risk factors
A cure cannot be assured for all men with clinically localized prostate cancer undergoing radical treatment. Molecular markers would be invaluable if they could improve the prediction of occult metastatic disease. This study was carried out to investigate the expression of BCL-2, Ki-67, p53 and E-cadherin in radical prostatectomy specimens. We sought to assess their ability to predict early biochemical relapse in a specific therapeutic setting. Eighty-two patients comprising 41 case pairs were matched for pathological stage, Gleason grade and preoperative prostate-specific antigen (PSA) concentration. One patient in each pair had biochemical recurrence (defined as PSA ? 0.2 ng mL?1 within 2 years of surgery) and the other remained biochemically free of disease (defined as undetectable PSA at least 3 years after surgery). Immunohistochemical analysis was performed to assess marker expression on four replicate tissue microarrays constructed with benign and malignant tissue from each radical prostatectomy specimen. Ki-67, p53 and BCL-2, but not E-cadherin, were significantly upregulated in prostate adenocarcinoma compared with benign prostate tissue (P < 0.01). However, no significant differences in expression of any of the markers were observed when comparing patients who developed early biochemical relapse with patients who had no biochemical recurrence. This study showed that expression of p53, BCL-2 and Ki-67 was upregulated in clinically localized prostate cancer compared with benign prostate tissue, with no alteration in E-cadherin expression. Biomarker upregulation had no prognostic value for biochemical recurrence after radical prostatectomy, even after considering pathological stage, whole tumour Gleason grade and preoperative serum PSA level.
Nariculam, Joseph; Freeman, Alex; Bott, Simon; Munson, Phillipa; Cable, Noriko; Brookman-Amissah, Nicola; Williamson, Magali; Kirby, Roger S.; Masters, John; Feneley, Mark
Extracellular Matrix, Nuclear and Chromatin Structure and GeneExpression in Normal Tissues and Malignant Tumors: A Work inProgress
Almost three decades ago, we presented a model where theextracellular matrix (ECM) was postulated to influence gene expressionand tissue-specificity through the action of ECM receptors and thecytoskeleton. This hypothesis implied that ECM molecules could signal tothe nucleus and that the unit of function in higher organisms was not thecell alone, but the cell plus its microenvironment. We now know that ECMinvokes changes in tissue and organ architecture and that tissue, cell,nuclear, and chromatin structure are changed profoundly as a result ofand during malignant progression. Whereas some evidence has beengenerated for a link between ECM-induced alterations in tissuearchitecture and changes in both nuclear and chromatin organization, themanner by which these changes actively induce or repress gene expressionin normal and malignant cells is a topic in need of further attention.Here, we will discuss some key findings that may provide insights intomechanisms through which ECM could influence gene transcription and howtumor cells acquire the ability to overcome these levels ofcontrol.
Spencer, Virginia A.; Xu, Ren; Bissell, Mina J.
Chromatin patterns associated with lung adenocarcinoma progression
The development and progression of lung adenocarcinoma, one of the most common cancers, is driven by the interplay of genetic and epigenetic changes and the role of chromatin structure in malignant transformation remains poorly understood. We used systematic nucleosome distribution and chromatin accessibility microarray mapping platforms to analyze the genome-wide chromatin structure from normal tissues and from primary lung adenocarcinoma of different grades and stages. We identified chromatin-based patterns across different patients with lung adenocarcinoma of different cancer grade and stage. Low-grade cancers had nucleosome distributions very different compared with the corresponding normal tissue but had nearly identical chromatin accessibility. Conversely, nucleosome distributions of high-grade cancers showed few differences. Substantial disruptions in chromosomal accessibility were seen in a patient with a high-grade and high-stage tumor. These data imply that chromatin structure changes during the progression of lung adenocarcinoma. We have therefore developed a model in which low-grade lung adenocarcinomas are linked to changes in nucleosome distributions, whereas higher-grade tumors are linked to large-scale chromosomal changes. These results provide a foundation for the development of a comprehensive framework linking the general and locus-specific roles of chromatin structure to lung cancer progression. We propose that this strategy has the potential to identify a new class of chromatin-based diagnostic, prognostic and therapeutic markers in cancer progression.
Druliner, Brooke R.; Fincher, Justin A.; Sexton, Brittany S.; Vera, Daniel L.; Roche, Michael; Lyle, Stephen; Dennis, Jonathan H.
DNA microarrays: Types, Applications and their future
This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000�s of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.
Bumgarner, Roger
Error-correcting microarray design.
We describe a microarray design based on the concept of error-correcting codes from digital communication theory. Currently, microarrays are unable to efficiently deal with "drop-outs," when one or more spots on the array are corrupted. The resulting information loss may lead to decoding errors in which no quantitation of expression can be extracted for the corresponding genes. This issue is expected to become increasingly problematic as the number of spots on microarrays expands to accommodate the entire genome. The error-correcting approach employs multiplexing (encoding) of more than one gene onto each spot to efficiently provide robustness to drop-outs in the array. Decoding then allows fault-tolerant recovery of the expression information from individual genes. The error-correcting method is general and may have important implications for future array designs in research and diagnostics. PMID:12620393
Khan, Arshad H; Ossadtchi, Alex; Leahy, Richard M; Smith, Desmond J
Fusion Transcript Discovery in Formalin-Fixed Paraffin-Embedded Human Breast Cancer Tissues Reveals a Link to Tumor Progression
The identification of gene fusions promises to play an important role in personalized cancer treatment decisions. Many rare gene fusion events have been identified in fresh frozen solid tumors from common cancers employing next-generation sequencing technology. However the ability to detect transcripts from gene fusions in RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissues, which exist in very large sample repositories for which disease outcome is known, is still limited due to the low complexity of FFPE libraries and the lack of appropriate bioinformatics methods. We sought to develop a bioinformatics method, named gFuse, to detect fusion transcripts in FFPE tumor tissues. An integrated, cohort based strategy has been used in gFuse to examine single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76 patients. In total, 118 fusion events were detected transcriptome-wide at base-pair resolution across the 212 samples. We selected 77 candidate fusions based on their biological relevance to cancer and supported 61% of these using TaqMan assays. Direct sequencing of 19 of the fusion sequences identified by TaqMan confirmed them. Three unique fused gene pairs were recurrent across the 212 patients with 6, 3, 2 individuals harboring these fusions respectively. We show here that a high frequency of fusion transcripts detected at the whole transcriptome level correlates with poor outcome (P<0.0005) in human breast cancer patients. This study demonstrates the ability to detect fusion transcripts as biomarkers from archival FFPE tissues, and the potential prognostic value of the fusion transcripts detected.
Ma, Yan; Ambannavar, Ranjana; Stephans, James; Jeong, Jennie; Dei Rossi, Andrew; Liu, Mei-Lan; Friedman, Adam J.; Londry, Jason J.; Abramson, Richard; Beasley, Ellen M.; Baker, Joffre; Levy, Samuel; Qu, Kunbin
Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models
High-throughput DNA microarray provides an effective approach to the monitoring of expression levels of thousands of genes in a sample simultaneously. One promising application of this technology is the molecular diagnostics of cancer, e.g. to distinguish normal tissue from tumor or to classify tumors into different types or subtypes. One problem arising from the use of microarray data is how
Yongxi Tan; Leming M. Shi; Weida Tong; G. T. Gene Hwang; Charles Wang
DNA microarray analysis in a mouse model for endometriosis and validation of candidate factors with human adenomyosis
Gene expression profiling can be of benefit in identifying critical factors in the process of disease initiation and development. However, in endometriosis it has proven difficult to identify common genes between DNA microarray studies, presumably because of tissue homogeneity in lesions and diversity in the patients� conditions. We attempted DNA microarray analysis in a mouse model for endometriosis with stable
Ken Takeshi Kusakabe; Hideaki Abe; Tomohiro Kondo; Keiko Kato; Toshiya Okada; Yoshinori Otsuki
Rapid Spoligotyping of Mycobacterium tuberculosis Complex Bacteria by Use of a Microarray System with Automatic Data Processing and Assignment
Membrane-based spoligotyping has been converted to DNA microarray format to qualify it for high-throughput testing. We have shown the assay's validity and suitability for direct typing from tissue and detecting new spoligotypes. Advantages of the microarray methodology include rapidity, ease of operation, automatic data processing, and affordability.
Ruettger, Anke; Nieter, Johanna; Skrypnyk, Artem; Engelmann, Ines; Ziegler, Albrecht; Moser, Irmgard; Monecke, Stefan; Ehricht, Ralf
Immunoprofiling using NAPPA protein microarrays.
Protein microarrays provide an efficient method to immunoprofile patients in an effort to rapidly identify disease immunosignatures. The validity of using autoantibodies in diagnosis has been demonstrated in type 1 diabetes, rheumatoid arthritis, and systemic lupus, and is now being strongly considered in cancer. Several types of protein microarrays exist including antibody and antigen arrays. In this chapter, we describe the immunoprofiling application for one type of antigen array called NAPPA (nucleic acids programmable protein array). We provide a guideline for setting up the screening study and designing protein arrays to maximize the likelihood of obtaining quality data. PMID:21370064
Sibani, Sahar; LaBaer, Joshua
Immunoprofiling Using NAPPA Protein Microarrays
Protein microarrays provide an efficient method to immunoprofile patients in an effort to rapidly identify disease immunosignatures. The validity of using autoantibodies in diagnosis has been demonstrated in type 1 diabetes, rheumatoid arthritis, and systemic lupus, and is now being strongly considered in cancer. Several types of protein microarrays exist including antibody and antigen arrays. In this chapter, we describe the immunoprofiling application for one type of antigen array called NAPPA (nucleic acids programmable protein array). We provide a guideline for setting up the screening study and designing protein arrays to maximize the likelihood of obtaining quality data.
Sibani, Sahar; LaBaer, Joshua
Microarray Analysis for Studying the Abiotic Stress Responses in Plants
\\u000a Plants respond and adapt to drought, high-salinity and cold stresses in order to survive. Molecular and genomic studies have\\u000a shown that many genes with various functions are induced by drought, high-salinity and cold stresses, and that the various\\u000a signaling factors including transcription factors are involved in the stress responses. The development of microarray-based\\u000a expression profiling methods has allowed significant progress
Motoaki Seki; Masanori Okamoto; Akihiro Matsui; Jong-Myong Kim; Yukio Kurihara; Junko Ishida; Taeko Morosawa; Makiko Kawashima; Taiko Kim To; Kazuo Shinozaki
Image microarrays (IMA): Digital pathology's missing tool
Introduction: The increasing availability of whole slide imaging (WSI) data sets (digital slides) from glass slides offers new opportunities for the development of computer-aided diagnostic (CAD) algorithms. With the all-digital pathology workflow that these data sets will enable in the near future, literally millions of digital slides will be generated and stored. Consequently, the field in general and pathologists, specifically, will need tools to help extract actionable information from this new and vast collective repository. Methods: To address this limitation, we designed and implemented a tool (dCORE) to enable the systematic capture of image tiles with constrained size and resolution that contain desired histopathologic features. Results: In this communication, we describe a user-friendly tool that will enable pathologists to mine digital slides archives to create image microarrays (IMAs). IMAs are to digital slides as tissue microarrays (TMAs) are to cell blocks. Thus, a single digital slide could be transformed into an array of hundreds to thousands of high quality digital images, with each containing key diagnostic morphologies and appropriate controls. Current manual digital image cut-and-paste methods that allow for the creation of a grid of images (such as an IMA) of matching resolutions are tedious. Conclusion: The ability to create IMAs representing hundreds to thousands of vetted morphologic features has numerous applications in education, proficiency testing, consensus case review, and research. Lastly, in a manner analogous to the way conventional TMA technology has significantly accelerated in situ studies of tissue specimens use of IMAs has similar potential to significantly accelerate CAD algorithm development.
Hipp, Jason; Cheng, Jerome; Pantanowitz, Liron; Hewitt, Stephen; Yagi, Yukako; Monaco, James; Madabhushi, Anant; Rodriguez-canales, Jaime; Hanson, Jeffrey; Roy-Chowdhuri, Sinchita; Filie, Armando C.; Feldman, Michael D.; Tomaszewski, John E.; Shih, Natalie NC.; Brodsky, Victor; Giaccone, Giuseppe; Emmert-Buck, Michael R.; Balis, Ulysses J.
Lung cancer in uranium miners: A tissue resource and pilot study. Progress report, September 25, 1992--May 31, 1993
This project involves two related activities directed toward understanding respiratory carcinogenesis in radon-exposed former uranium miners. The first activity involves a continuation of the tissue resource of lung cancer cases from former underground uranium miners and comparison cases from non-miners. The second activity is a pilot study for a proposed longitudinal study of respiratory carcinogenesis in former uranium miners. The objectives are to facilitate the investigation of molecular changes in radon exposed lung cancer cases and to develop methods for prospectively studying clinical, cytologic, cytogenetic, and molecular changes in the multi-event process of respiratory carcinogenesis, and to assess the feasibility of recruiting former uranium miners into a longitudinal study that collects multiple biologic specimens.
Samet, J.M.
Periostin: novel tissue and urinary biomarker of progressive renal injury induces a coordinated mesenchymal phenotype in tubular cells
Background Periostin acts as an adhesion molecule during bone formation. Knowledge of its expression in kidney injury is scant. Methods We investigated periostin function and expression in vivo in Sprague�Dawley rats after 5/6 nephrectomy (Nx), in DBA2J mice with streptozotocin-induced diabetic nephropathy (SZ-DN) and unilateral ureteral obstruction (UUO) and in vitro in mouse distal collecting tubular cells (MDCT) and in tissue and urine from chronic kidney disease (CKD) patients. Results Periostin messenger RNA was increased after 5/6Nx and SZ-DN demonstrating generalizability of the increment in renal injury. Periostin was expressed predominantly in distal tubule (DT) epithelial cell cytoplasm in situ, in cells shed into the lumen, and, in lesser abundance, in glomeruli undergoing obsolescence, arterioles and in the tubulointerstitium in extracellular and intracellular locations. In affected DT after 5/6Nx, periostin expression appeared de novo, E-cadherin became undetectable and tubule cells displayed the mesenchymal marker proteins fibroblast-specific protein-1 (FSP1) and matrix metalloproteinase-9 (MMP9). Periostin overexpression in cultured MDCT cells dramatically induced MMP9 and FSP1 protein and suppressed E-cadherin. Periostin short interfering RNA blocked these changes. Urine periostin excretion increased over time after 5/6Nx, and it was also excreted in the urine of CKD patients. Urine periostin enzyme-linked immunosorbent assay at a cutoff of 32.66 pg/mg creatinine demonstrated sensitivity and specificity for distinguishing patients with CKD from healthy people (92.3 and 95.0%, respectively) comparing favorably with urine neutrophil gelatinase-associated lipocalin. Conclusion These data demonstrate that periostin is a mediator and marker of tubular dedifferentiation and a promising tissue and urine biomarker for kidney injury in experimental models and in clinical renal disease.
Satirapoj, Bancha; Wang, Ying; Chamberlin, Mina P.; Dai, Tiane; LaPage, Janine; Phillips, Lynetta; Nast, Cynthia C.; Adler, Sharon G.
Microfluidic Microarray Systems and Methods Thereof.
National Technical Information Service (NTIS)
Disclosed are systems that include a manifold in fluid communication with a microfluidic chip having a microarray, an illuminator, and a detector in optical communication with the microarray. Methods for using these systems for biological detection are al...
G. A. Hux J. A. A. West K. W. Hukari
Meta-coexpression conservation analysis of microarray data: a \\
BACKGROUND: Alterations in brain-derived neurotrophic factor (BDNF) gene expression contribute to serious pathologies such as depression, epilepsy, cancer, Alzheimer's, Huntington and Parkinson's disease. Therefore, exploring the mechanisms of BDNF regulation represents a great clinical importance. Studying BDNF expression remains difficult due to its multiple neural activity-dependent and tissue-specific promoters. Thus, microarray data could provide insight into the regulation of this
Tamara Aid-Pavlidis; Pavlos Pavlidis; T�nis Timmusk
Microarray analysis of replicative senescence
Background: Limited replicative capacity is a defining characteristic of most normal human cells and culminates in senescence, an arrested state in which cells remain viable but display an altered pattern of gene and protein expression. To survey widely the alterations in gene expression, we have developed a DNA microarray analysis system that contains genes previously reported to be involved in
Dawne N. Shelton; Edwin Chang; Peter S. Whittier; Donghee Choi; Walter D. Funk
Toxicogenomics using yeast DNA microarrays
Development of genomics and bioinformatics enable us to analyze the global gene expression profiles of cells by DNA microarray. Changes in gene expression patterns indicate changes in its physiological conditions. Following the exposure of an organism or cell to toxic chemicals or other environmental stresses, the global genetic responses can be expeditiously and easily analyzed. Baker's yeast, Saccharomyces cerevisiae, is
Daisuke Yasokawa; Hitoshi Iwahashi
Chaotic mixer improves microarray hybridization
Hybridization is an important aspect of microarray experimental design which influences array signal levels and the repeatability of data within an array and across different arrays. Current methods typically require 24h and use target inefficiently. In these studies, we compare hybridization signals obtained in conventional static hybridization, which depends on diffusional target delivery, with signals obtained in a dynamic hybridization
Mark K McQuain; Kevin Seale; Joel Peek; Timothy S Fisher; Shawn Levy; Mark A Stremler; Frederick R Haselton
DNA Microarray Methodology - Flash Animation
NSDL National Science Digital Library
This animation demonstrates how DNA microarray experiments are performed. DNA chips are used to determine which genes are activated and which genes are repressed when two populations are compared. In this case, the comparison is between yeast cells grown under either aerobic or anaerobic conditions. This animation is very effective for many different education levels. Teachers and students love this one.
Campbell, A. M.
Robust DNA microarray image analysis
DNA microarrays are an increasingly important tool that allow biologists to gain insight into the function of thousands of genes in a single experiment. Common to all array-based approaches is the necessity to analyze digital images of the scanned DNA array. The ultimate image analysis goal is to automatically quantify every individual array element (spot), providing information about the amount
Norbert Br�ndle; Horst Bischof; Hilmar Lapp
Overexpression of carbonic anhydrase IX (CAIX) in vulvar cancer is associated with tumor progression and development of locoregional lymph node metastases
Carbonic anhydrase IX (CAIX) is a strictly membranous expressed metalloenzyme involved in cell adhesion, pH homeostasis, and\\u000a cancer progression. The protein is specifically overexpressed in a wide variety of malignant tumors. This study was designed\\u000a to assess the role of CAIX in primary vulvar cancer. One hundred forty-two well-characterized primary vulvar carcinomas were\\u000a analyzed on a tissue microarray (TMA). Three
Matthias Choschzick; Linn Woelber; Stephan Hess; Christine zu Eulenburg; J�rg Schwarz; Ronald Simon; Sven Mahner; Fritz Jaenicke; Volkmar M�ller
DNA Microarray Applications in Environmental Microbiology
Although the majority of microarray reports are concerned with gene expression profiling in health-related studies, the use of DNA microarray technology is expanding into new fields and new applications. In environmental microbiology, developments are also focusing on the detection of specific sequences in complex environmental samples and on genomic comparisons. Despite the fact that some limitations still exist, microarrays offer
Jaroslaw Letowski; Roland Brousseau; Luke Masson
The Microarray Revolution: Perspectives from Educators
ERIC Educational Resources Information Center
In recent years, microarray analysis has become a key experimental tool, enabling the analysis of genome-wide patterns of gene expression. This review approaches the microarray revolution with a focus upon four topics: 1) the early development of this technology and its application to cancer diagnostics; 2) a primer of microarray research,�
Brewster, Jay L.; Beason, K. Beth; Eckdahl, Todd T.; Evans, Irene M.
Chasing the dream: plant EST microarrays
DNA microarray technology is poised to make an important contribution to the field of plant biology. Stimulated by recent funding programs, expressed sequence tag sequencing and microarray production either has begun or is being contemplated for most economically important plant species. Although the DNA microarray technology is still being refined, the basic methods are well established. The real challenges lie
Todd Richmond; Shauna Somerville
Fluorescent and luminescent probes for measurement of oxidative and nitrosative species in cells and tissues: progress, pitfalls, and prospects.
Chemical probes for free radicals in biology are important tools; fluorescence and chemiluminescence offer high detection sensitivity. This article reviews progress in the development of probes for "reactive oxygen and nitrogen" species, emphasizing the caution needed in their use. Reactive species include hydrogen peroxide; hydroxyl, superoxide, and thiyl radicals; carbonate radical-anion; and nitric oxide, nitrogen dioxide, and peroxynitrite. Probes based on reduced dyes lack selectivity and may require a catalyst for reaction: despite these drawbacks, dichlorodihydrofluorescein and dihydrorhodamine have been used in well over 2,000 studies. Use in cellular systems requires loading into cells, and minimizing leakage. Reactive species can compete with intracellular antioxidants, changes in fluorescence or luminescence possibly reflecting changes in competing antioxidants rather than free radical generation rate. Products being measured can react further with radicals, and intermediate probe radicals are often reactive toward antioxidants and especially oxygen, to generate superoxide. Common probes for superoxide and nitric oxide require activation to a reactive intermediate; activation is not achieved by the radical of interest and the response is thus additionally sensitive to this first step. Rational use of probes requires understanding and quantitation of the mechanistic pathways involved, and of environmental factors such as oxygen and pH. We can build on this framework of knowledge in evaluating new probes. PMID:17761297
Wardman, Peter
An ensemble method for gene discovery based on DNA microarray data
The advent of DNA microarray technology has offered the promise of casting new insights onto deciphering secrets of life by\\u000a monitoring activities of thousands of genes simultaneously. Current analyses of microarray data focus on precise classification\\u000a of biological types, for example, tumor versus normal tissues. A further scientific challenging task is to extract disease-relevant\\u000a genes from the bewildering amounts of
Xia Li; Shaoqi Rao; Tianwen Zhang; Zheng Guo; Qingpu Zhang; Kathy L. Moser; Eric J. Topol
Loss of chromosome 13q is a frequently acquired event in genetic progression of soft tissue sarcomas in the abdominal cavity.
Soft tissue sarcomas (STSs) arising in the abdominal cavity constitute a group of aggressive tumours, typically of very large size and with a high recurrence rate in the affected patients. While some distinct genetic etiologies have been described, the genetic background of this tumour group is not well characterised. Here we have assessed gross chromosomal alterations in a series of such tumours obtained from 26 patients. CGH alterations were found in tumours from 23 of the patients (88%), the most frequent being loss of 13q21 (46%) and gain of 17p and/or q (46%). Furthermore, mutations of C-KIT exon 11 were demonstrated in five tumours from four patients, and the two myxoid liposarcomas exhibited a translocation t(12;16)(q13;p11). From the pattern of chromosomal alterations detected, a genetic progression of events was clearly evident in the tumours. Taken together with analysis of subsequent relapses from the same patients, the common CGH alteration +12q13 was suggested to be a relatively early event in the genetic progression, similar to t(12;16)(q13;p11) and C-KIT mutations. Moreover, -1p21-22, -13q21, -14q, -Xp22, +9q34, +17p, +17q, and +20q13 would all represent relative later events. The most consistent alteration was loss of 13q, that was found to target the 13q14-21 and 13q34 regions as determined by CGH and Southern blot analyses. Loss of 13q was identified independently of +12q13 and C-KIT mutation and the patient's sex, and was observed in all common subtypes of STS, suggesting that it is a general and late event in the genetic progression. The findings provide a starting point for further dissection of the target genes involved in development of STSs in the abdominal cavity. PMID:15586219
Weng, Wen-Hui; Lerner, Mikael; Grand�r, Dan; Ahl�n, Jan; Villablanca, Andrea; Pang, See-Tong; Wejde, Johan; Lui, Weng-Onn; Larsson, Catharina
Traumatic Brain Injury in Young Rats Leads to Progressive Behavioral Deficits Coincident with Altered Tissue Properties in Adulthood
Abstract Traumatic brain injury (TBI) affects many infants and children, and results in enduring motor and cognitive impairments with accompanying changes in white matter tracts, yet few experimental studies in rodent juvenile models of TBI (jTBI) have examined the timeline and nature of these deficits, histologically and functionally. We used a single controlled cortical impact (CCI) injury to the parietal cortex of rats at post-natal day (P) 17 to evaluate behavioral alterations, injury volume, and morphological and molecular changes in gray and white matter, with accompanying measures of electrophysiological function. At 60 days post-injury (dpi), we found that jTBI animals displayed behavioral deficits in foot-fault and rotarod tests, along with a left turn bias throughout their early developmental stages and into adulthood. In addition, anxiety-like behaviors on the zero maze emerged in jTBI animals at 60?dpi. The final lesion constituted only ?3% of brain volume, and morphological tissue changes were evaluated using MRI, as well as immunohistochemistry for neuronal nuclei (NeuN), myelin basic protein (MBP), neurofilament-200 (NF200), and oligodendrocytes (CNPase). White matter morphological changes were associated with a global increase in MBP immunostaining and reduced compound action potential amplitudes at 60?dpi. These results suggest that brain injury early in life can induce long-term white matter dysfunction, occurring in parallel with the delayed development and persistence of behavioral deficits, thus modeling clinical and longitudinal TBI observations.
Ajao, David O.; Pop, Viorela; Kamper, Joel E.; Adami, Arash; Rudobeck, Emil; Huang, Lei; Vlkolinsky, Roman; Hartman, Richard E.; Ashwal, Stephen; Obenaus, Andre
DNA microarray technology and its applications in dermatology.
The use of DNA microarray technology in biomedical research has dramatically increased during the past years. In the present report, we provide an overview on the basic DNA microarray technology and biostatistical methods for gene expression analysis. A focus is then put on its applications in dermatological research. In recent years, a series of gene expression studies have been performed for various dermatological diseases, such as malignant melanoma, psoriasis and lupus erythematosus. These analyses have identified interesting target genes as well as putative disease susceptibility loci. However, further functional studies will be needed for a more complete understanding of the pathogenesis of these diseases. This may be performed by means of the recently developed RNA interference technology. Besides its role in large-scale gene expression studies, DNA microarray technology has proved to be a valuable tool for genomic screens of genetic alterations, e.g. single nucleotide polymorphisms. These play a role in tumour development and progression, and also function as genetic markers for disease susceptibility. Taken together, DNA microarray technology opens enormous perspectives for dermatologists. It may help us understand the complex pathogenesis of a wide variety of dermatologic diseases and identify their genetic background. PMID:15447719
Kunz, M; Ibrahim, S M; Koczan, D; Scheid, S; Thiesen, H J; Gross, G
Association of tissue promoter methylation levels of APC, TGF?2, HOXD3 and RASSF1A with prostate cancer progression.
Aberrant promoter methylation is known to silence tumor-suppressor genes in prostate cancer (PCa). We correlated quantitative promoter methylation levels of APC, TGF?2 and RASSF1A in 219 radical prostatectomies diagnosed between 1998 and 2001 with clinicopathological follow-up data available including Gleason Pattern (GP), Gleason Score (GS) and pathological stage and explored their potential in predicting biochemical recurrence using univariate and multivariate analyses. We observed that the average methylation levels of APC increased significantly from GS ? 6 to GS7, and pT2 to pT3a, and that of TGF?2 increased from GS ? 6 to GS7, but not for RASSF1A. PCa samples were also stratified into high methylation (HM) and low methylation (LM) groups based on the PMR scores of all cases analyzed for each marker. The HM frequency of APC was greater in pT3a than pT2, and in GS ? 8 than GS ? 6. The HM frequency also increased significantly from GP3 to GP4 for APC, TGF?2 and RASSF1A. APC methylation level was a significant predictor of biochemical recurrence in univariate analysis (p-value = 0.028). Finally, we combined methylation data of these three genes with the previously reported novel methylation biomarker HOXD3. Quantitative methylation assessment of a multiplex panel of markers, consisting of APC, HOXD3 and TGF?2, outperforms any single marker for the prediction of biochemical recurrence (p-value = 0.017). Our study demonstrated that quantitative increase in promoter methylation levels of APC, HOXD3 and TGF?2 are associated with PCa progression. PMID:21207416
Liu, Liyang; Kron, Ken J; Pethe, Vaijayanti V; Demetrashvili, Nino; Nesbitt, Michael E; Trachtenberg, John; Ozcelik, Hilmi; Fleshner, Neil E; Briollais, Laurent; van der Kwast, Theodorus H; Bapat, Bharati
Protein Microarrays for Quantitative Detection of PAI-1 in Serum
Objective Plasminogen activator inhibitor-1 (PAI-1), one crucial component of the plasminogen activator system, is a major player in the pathogenesis of many vascular diseases as well as in cancer. High levels of PAI-1 in breast cancer tissue are associated with poor prognosis. The aim of this study is to evaluate rigorously the potential of serum PAI-1 concentration functioning as a general screening test in diagnostic or prognostic assays. Methods A protein-microarray-based sandwich fluorescence immunoassay (FIA) was developed to detect PAI-1 in serum. Several conditions of this microarray-based FIA were optimized to establish an efficacious method. Serum specimens of 84 healthy women and 285 women with breast cancer were analyzed using the optimized FIA microarray. Results The median serum PAI-1 level of breast cancer patients was higher than that of healthy women (109.7 ng/ml vs. 63.4 ng/ml). Analysis of covariance revealed that PAI-1 levels of the two groups were significantly different (P<0.001) when controlling for an age effect on PAI-1 levels. However, PAI-1 values in TNM stage I?IV patients respectively were not significantly different from each other. Conclusion This microarray-based sandwich FIA holds potential for quantitative analysis of tumor markers such as PAI-1.
Ma, Xu
Analysis of microarray experiments of gene expression profiling
The study of gene expression profiling of cells and tissue has become a major tool for discovery in medicine. Microarray experiments allow description of genome-wide expression changes in health and disease. The results of such experiments are expected to change the methods employed in the diagnosis and prognosis of disease in obstetrics and gynecology. Moreover, an unbiased and systematic study of gene expression profiling should allow the establishment of a new taxonomy of disease for obstetric and gynecologic syndromes. Thus, a new era is emerging in which reproductive processes and disorders could be characterized using molecular tools and fingerprinting. The design, analysis, and interpretation of microarray experiments require specialized knowledge that is not part of the standard curriculum of our discipline. This article describes the types of studies that can be conducted with microarray experiments (class comparison, class prediction, class discovery). We discuss key issues pertaining to experimental design, data preprocessing, and gene selection methods. Common types of data representation are illustrated. Potential pitfalls in the interpretation of microarray experiments, as well as the strengths and limitations of this technology, are highlighted. This article is intended to assist clinicians in appraising the quality of the scientific evidence now reported in the obstetric and gynecologic literature.
Tarca, Adi L.; Romero, Roberto; Draghici, Sorin
Retraction. "Immunohistochemical prognostic markers in diffuse large B-cell lymphoma: validation of tissue microarray as a prerequisite for broad clinical applications (a study from the Lunenburg Lymphoma Biomarker Consortium)" (J Clin Pathol 2009;62:128�38;doi:10.1136/jcp.2008.057257).
The Journal of Clinical Pathology wishes to inform its readers of the authors' retraction of the following article for redundancy. The original article by D de Jong, W Xie, Rosenwald, M Chhanabhai, P Gaulard,W Klapper, A Lee, B Sander, C Thorns,E Campo, T Molina, A Hagenbeek,S Horning, A Lister, J Raemaekers, G Salles, R D Gascoyne and E Weller entitled "Immunohistochemical prognostic markersi n diffuse large B-cell lymphoma: validation of tissue microarray as a prerequisite for broad clinical applications (a study from the Lunenburg Lymphoma Biomarker Consortium)" (J Clin Pathol 2009;62:128�38;doi:10.1136/jcp.2008.057257) published online on 15 September 2008, contained substantial overlap in text, data, and conclusions compared with a previous article with the same title published in Journal of Clinical Oncology on 1 March 2007 by Daphne de Jong, Andreas Rosenwald, Mukesh Chhanabhai, Philippe Gaulard,Wolfram Klapper, Abigail Lee, Birgitta Sander, Christoph Thorns, Elias Campo, Thierry Molina, Andrew Norton, Anton Hagenbeek, Sandra Horning, Andrew Lister, John Raemaekers, Randy D Gascoyne, Gilles Salles and Edie Weller (doi:10.1200/JCO.2006.09.4490). In addition, the authors did not cite the Journal of Clinical Oncology article in the paper published in Journal of Clinical Pathology. PMID:22930798
The Current Status of DNA Microarrays
NASA Astrophysics Data System (ADS)
DNA microarray technology that allows simultaneous assay of thousands of genes in a single experiment has steadily advanced to become a mainstream method used in research, and has reached a stage that envisions its use in medical applications and personalized medicine. Many different strategies have been developed for manufacturing DNA microarrays. In this chapter, we discuss the manufacturing characteristics of seven microarray platforms that were used in a recently completed large study by the MicroArray Quality Control (MAQC) consortium, which evaluated the concordance of results across these platforms. The platforms can be grouped into three categories: (1) in situ synthesis of oligonucleotide probes on microarrays (Affymetrix GeneChip� arrays based on photolithography synthesis and Agilent's arrays based on inkjet synthesis); (2) spotting of presynthesized oligonucleotide probes on microarrays (GE Healthcare's CodeLink system, Applied Biosystems' Genome Survey Microarrays, and the custom microarrays printed with Operon's oligonucleotide set); and (3) deposition of presynthesized oligonucleotide probes on bead-based microarrays (Illumina's BeadChip microarrays). We conclude this chapter with our views on the challenges and opportunities toward acceptance of DNA microarray data in clinical and regulatory settings.
Shi, Leming; Perkins, Roger G.; Tong, Weida
M@IA: a modular open-source application for microarray workflow and integrative datamining.
Microarray technology is a widely used approach to gene expression analysis. Many tools for microarray management and data analysis have been developed, and recently new methods have been proposed for deciphering biological pathways by integrating microarray data with other data sources. However, to improve microarray analysis and provide meaningful gene interaction networks, integrated software solutions are still needed. Therefore, we developed M@IA, an environment for DNA microarray data analysis allowing gene network reconstruction. M@IA is a microarray integrated application which includes all of the steps of a microarray study, from MIAME-compliant raw data storage and processing gene expression analysis. Furthermore, M@IA allows automatic gene annotation based on ontology, metabolic/signalling pathways, protein interaction, miRNA and transcriptional factor associations, as well as integrative analysis of gene interaction networks. Statistical and graphical methods facilitate analysis, yielding new hypotheses on gene expression data. To illustrate our approach, we applied M@IA modules to microarray data taken from an experiment on liver tissue. We integrated differentially expressed genes with additional biological information, thus identifying new molecular interaction networks that are associated with fibrogenesis. M@IA is a new application for microarray management and data analysis, offering functional insights into microarray data by the combination of gene expression data and biological knowledge annotation based on interactive graphs. M@IA is an interactive multi-user interface based on a flexible modular architecture and it is freely available for academic users at http://maia.genouest.org. PMID:18430991
Le B�chec, Antony; Zindy, Pierre; Sierocinski, Thomas; Petritis, Dimitri; Bihou�e, Audrey; Le Meur, Nolwenn; L�ger, Jean; Th�ret, Nathalie
Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency
Background Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear. We present a computational method for inferring genetic regulatory networks from micorarray data automatically with transcription factor analysis and conditional independence testing to explore the potential significant gene regulatory networks that are correlated with cancer, tumor grade and stage in the prostate cancer. Results To deal with missing values in microarray data, we used a K-nearest-neighbors (KNN) algorithm to determine the precise expression values. We applied web services technology to wrap the bioinformatics toolkits and databases to automatically extract the promoter regions of DNA sequences and predicted the transcription factors that regulate the gene expressions. We adopt the microarray datasets consists of 62 primary tumors, 41 normal prostate tissues from Stanford Microarray Database (SMD) as a target dataset to evaluate our method. The predicted results showed that the possible biomarker genes related to cancer and denoted the androgen functions and processes may be in the development of the prostate cancer and promote the cell death in cell cycle. Our predicted results showed that sub-networks of genes SREBF1, STAT6 and PBX1 are strongly related to a high extent while ETS transcription factors ELK1, JUN and EGR2 are related to a low extent. Gene SLC22A3 may explain clinically the differentiation associated with the high grade cancer compared with low grade cancer. Enhancer of Zeste Homolg 2 (EZH2) regulated by RUNX1 and STAT3 is correlated to the pathological stage. Conclusions We provide a computational framework to reconstruct the genetic regulatory network from the microarray data using biological knowledge and constraint-based inferences. Our method is helpful in verifying possible interaction relations in gene regulatory networks and filtering out incorrect relations inferred by imperfect methods. We predicted not only individual gene related to cancer but also discovered significant gene regulation networks. Our method is also validated in several enriched published papers and databases and the significant gene regulatory networks perform critical biological functions and processes including cell adhesion molecules, androgen and estrogen metabolism, smooth muscle contraction, and GO-annotated processes. Those significant gene regulations and the critical concept of tumor progression are useful to understand cancer biology and disease treatment.
Functional assessment of time course microarray data
Motivation Time-course microarray experiments study the progress of gene expression along time across one or several experimental conditions. Most developed analysis methods focus on the clustering or the differential expression analysis of genes and do not integrate functional information. The assessment of the functional aspects of time-course transcriptomics data requires the use of approaches that exploit the activation dynamics of the functional categories to where genes are annotated. Methods We present three novel methodologies for the functional assessment of time-course microarray data. i) maSigFun derives from the maSigPro method, a regression-based strategy to model time-dependent expression patterns and identify genes with differences across series. maSigFun fits a regression model for groups of genes labeled by a functional class and selects those categories which have a significant model. ii) PCA-maSigFun fits a PCA model of each functional class-defined expression matrix to extract orthogonal patterns of expression change, which are then assessed for their fit to a time-dependent regression model. iii) ASCA-functional uses the ASCA model to rank genes according to their correlation to principal time expression patterns and assess functional enrichment on a GSA fashion. We used simulated and experimental datasets to study these novel approaches. Results were compared to alternative methodologies. Results Synthetic and experimental data showed that the different methods are able to capture different aspects of the relationship between genes, functions and co-expression that are biologically meaningful. The methods should not be considered as competitive but they provide different insights into the molecular and functional dynamic events taking place within the biological system under study.
Nueda, Maria Jose; Sebastian, Patricia; Tarazona, Sonia; Garcia-Garcia, Francisco; Dopazo, Joaquin; Ferrer, Alberto; Conesa, Ana
Self-Assembling Protein Microarrays
NASA Astrophysics Data System (ADS)
Protein microarrays provide a powerful tool for the study of protein function. However, they are not widely used, in part because of the challenges in producing proteins to spot on the arrays. We generated protein microarrays by printing complementary DNAs onto glass slides and then translating target proteins with mammalian reticulocyte lysate. Epitope tags fused to the proteins allowed them to be immobilized in situ. This obviated the need to purify proteins, avoided protein stability problems during storage, and captured sufficient protein for functional studies. We used the technology to map pairwise interactions among 29 human DNA replication initiation proteins, recapitulate the regulation of Cdt1 binding to select replication proteins, and map its geminin-binding domain.
Ramachandran, Niroshan; Hainsworth, Eugenie; Bhullar, Bhupinder; Eisenstein, Samuel; Rosen, Benjamin; Lau, Albert Y.; C. Walter, Johannes; LaBaer, Joshua
How Can Microarrays Unlock Asthma?
Asthma is a complex disease regulated by the interplay of a large number of underlying mechanisms which contribute to the overall pathology. Despite various breakthroughs identifying genes related to asthma, our understanding of the importance of the genetic background remains limited. Although current therapies for asthma are relatively effective, subpopulations of asthmatics do not respond to these regimens. By unlocking the role of these underlying mechanisms, a source of novel and more effective treatments may be identified. In the new age of high-throughput technologies, gene-expression microarrays provide a quick and effective method of identifying novel genes and pathways, which would be impossible to discover using an individual gene screening approach. In this review we follow the history of expression microarray technologies and describe their contributions to advancing our current knowledge and understanding of asthma pathology.
Faiz, Alen; Burgess, Janette K.
DNA Microarrays for Identifying Fishes
In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological\\u000a characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study,\\u000a a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species\\u000a from European seas based on
M. Kochzius; M. N�lte; H. Weber; N. Silkenbeumer; S. Hj�rleifsdottir; G. O. Hreggvidsson; V. Marteinsson; K. Kappel; S. Planes; F. Tinti; A. Magoulas; E. Garcia Vazquez; C. Turan; C. Hervet; D. Campo Falgueras; A. Antoniou; M. Landi; D. Blohm
The gene expression signatures of melanoma progression
Because of the paucity of available tissue, little information has previously been available regarding the gene expression profiles of primary melanomas. To understand the molecular basis of melanoma progression, we compared the gene expression profiles of a series of nevi, primary melanomas, and melanoma metastases. We found that metastatic melanomas exhibit two dichotomous patterns of gene expression, which unexpectedly reflect gene expression differences already apparent in comparing laser-capture microdissected radial and vertical phases of a large primary melanoma. Unsupervised hierarchical clustering accurately separated nevi and primary melanomas. Multiclass significance analysis of microarrays comparing normal skin, nevi, primary melanomas, and the two types of metastatic melanoma identified 2,602 transcripts that significantly correlated with sample class. These results suggest that melanoma pathogenesis can be understood as a series of distinct molecular events. The gene expression signatures identified here provide the basis for developing new diagnostics and targeting therapies for patients with malignant melanoma.
Haqq, Christopher; Nosrati, Mehdi; Sudilovsky, Daniel; Crothers, Julia; Khodabakhsh, Daniel; Pulliam, Brian L.; Federman, Scot; Miller, James R.; Allen, Robert E.; Singer, Mark I.; Leong, Stanley P. L.; Ljung, Britt-Marie; Sagebiel, Richard W.; Kashani-Sabet, Mohammed
The gene expression signatures of melanoma progression.
Because of the paucity of available tissue, little information has previously been available regarding the gene expression profiles of primary melanomas. To understand the molecular basis of melanoma progression, we compared the gene expression profiles of a series of nevi, primary melanomas, and melanoma metastases. We found that metastatic melanomas exhibit two dichotomous patterns of gene expression, which unexpectedly reflect gene expression differences already apparent in comparing laser-capture microdissected radial and vertical phases of a large primary melanoma. Unsupervised hierarchical clustering accurately separated nevi and primary melanomas. Multiclass significance analysis of microarrays comparing normal skin, nevi, primary melanomas, and the two types of metastatic melanoma identified 2,602 transcripts that significantly correlated with sample class. These results suggest that melanoma pathogenesis can be understood as a series of distinct molecular events. The gene expression signatures identified here provide the basis for developing new diagnostics and targeting therapies for patients with malignant melanoma. PMID:15833814
Haqq, Christopher; Nosrati, Mehdi; Sudilovsky, Daniel; Crothers, Julia; Khodabakhsh, Daniel; Pulliam, Brian L; Federman, Scot; Miller, James R; Allen, Robert E; Singer, Mark I; Leong, Stanley P L; Ljung, Britt-Marie; Sagebiel, Richard W; Kashani-Sabet, Mohammed
S100A4 overexpression proves to be independent marker for breast cancer progression
Background Breast cancer is the most common cancer and cause of deaths in women around the world. Oncogene amplification usually occurs late in tumor progression and correlates well with aggressiveness of tumor. In fact the function of the S100A4 protein and its role in metastasis is unclear at present. The purpose of the study was to determine the expression of S100A4 protein in the invasion status and metastatic potential of breast cancer by using tissue microarray and to determine its role in breast cancer based on the expression of S100A4 gene product. Methods S100A4 protein expression was examined by immunohistochemistry (IHC) using commercially available tissue microarray containing malignant and normal breast tissue cores from 216 patients. Results S100A4 was absent in normal breast tissues while positive in 45.1% of infiltrating ductal carcinoma (IDC) node negative and 48.8% of infiltrating lobular carcinoma node negative. In paired samples, S100A4 protein was expressed in 13.5% of IDC node positive cases and 35.1% of matched lymph node metastasis. Conclusion S100A4 protein expression appears widely expressed in early and advanced breast cancer stages compared with normal breast. Our study suggests S100A4 may play a role in breast cancer progression and may prove to be an independent marker of breast cancer which appears to be down regulated in more advanced stages of breast cancer.
Ismail, Nawfal I; Kaur, Gurjeet; Hashim, Hasnah; Hassan, Mohammed S
On the classification of microarray gene-expression data.
We consider the classification of microarray gene-expression data. First, attention is given to the supervised case, where the tissue samples are classified with respect to a number of predefined classes and the intent is to assign a new unclassified tissue to one of these classes. The problems of forming a classifier and estimating its error rate are addressed in the context of there being a relatively small number of observations (tissue samples) compared to the number of variables (that is, the genes, which can number in the tens of thousands). We then proceed to the unsupervised case and consider the clustering of the tissue samples and also the clustering of the gene profiles. Both problems can be viewed as being non-standard ones in statistics and we address some of the key issues involved. The focus is on the use of mixture models to effect the clustering for both problems. PMID:22988257
Basford, Kaye E; McLachlan, Geoffrey J; Rathnayake, Suren I
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes
Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148?993 and 121?703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25?342 human and 24?109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3? end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a ?80% correlation with hybridizations performed on Affymetrix GeneChip� suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE.
Brigand, Kevin Le; Russell, Roslin; Moreilhon, Chimene; Rouillard, Jean-Marie; Jost, Bernard; Amiot, Franck; Magnone, Virginie; Bole-Feysot, Christine; Rostagno, Philippe; Virolle, Virginie; Defamie, Virginie; Dessen, Philippe; Williams, Gary; Lyons, Paul; Rios, Geraldine; Mari, Bernard; Gulari, Erdogan; Kastner, Philippe; Gidrol, Xavier; Freeman, Tom C.; Barbry, Pascal
Semiconductor quantum dots for multiplexed bio-detection on solid-state microarrays.
Understanding cellular systems requires identification and analysis of their multiple components and determination of how they act together and are regulated. Microarray technology is one of the few tools that is able to solve such problems. It is based on high-throughput recognition of a target to the probe and has the potential to simultaneously measure the presence of numerous molecules in multiplexed tests, all contained in a small drop of test fluid. Microarrays allow the parallel analysis of genomic or proteomic content in healthy versus disease-affected or altered tissues or cells. The signal read-out from the microarrays is done with organic dyes which often suffer of photobleaching, low brightness and background fluorescence. Recent data show that the use of fluorescent nanocrystals named "quantum dots" (QDs) allows to push these limits away. QDs are sufficiently bright to be detected as individual particles, extremely resistant against photobleaching and provide unique possibilities for multiplexing, thus supplying the microarray technology with a novel read-out option enabling the sensitivity of detection to reach the single-molecule level. This paper reviews QDs applications to microarray-based detection and demonstrates how the combination of microarray and QDs technologies may increase sensitivity and highly parallel capacities of multiplexed microarrays. Such a combination should provide the breakthrough results in drug discovery, cancer diagnosis and establish new therapeutic approaches through the identification of binding target molecules and better understanding of cell signalling pathways. PMID:19467882
Rousserie, Gilles; Sukhanova, Alyona; Even-Desrumeaux, Klervi; Fleury, Fabrice; Chames, Patrick; Baty, Daniel; Oleinikov, Vladimir; Pluot, Michel; Cohen, Jacques H M; Nabiev, Igor
Distinctive gene expression profiles by cDNA microarrays in endometrioid and serous carcinomas of the endometrium.
Endometrial carcinomas are classified by their morphology into two major subtypes. Endometrioid carcinomas (type I) are generally estrogen dependent, well-differentiated, superficially invasive, and have a good outcome. Serous carcinomas (type II) are hormone independent, frequently deeply invasive and widely metastatic, and have a poor prognosis. Microarray technology and analysis allows us to determine if the global gene expression profiles of these two subtypes correlate with their morphologic phenotype. Fresh tissue from 18 endometrial carcinomas was studied: 7 well-, 2 moderately, and one poorly differentiated endometrioid, 4 serous carcinomas, and 4 high-grade mixed endometrioid-serous carcinomas. Labeled cDNA probes were synthesized (Cy5 for tumor, Cy3 for reference) and applied to microarrays containing 18,098 cDNA clones or ESTs. A pool of equal amounts of total RNA from each tumor served as the reference RNA. By unsupervised cluster analysis, the endometrioid carcinomas clustered together and were separate from the serous carcinomas. The high-grade mixed carcinomas clustered with the serous carcinomas. Using a statistical algorithm based on gene expression pattern and conducting a supervised analysis of the two defined groups, we have identified 315 genes that statistically differentiate type I from type II endometrial carcinomas. In addition to corroborating the predicted overexpression of known markers (e.g., ras and catenin in endometrioid carcinomas), the cDNA microarray technique has revealed novel alterations in gene expression relevant to cell cycle, cell adhesion, signal transduction, apoptosis, and tumor progression not previously implicated in endometrial carcinomas. For serous carcinomas, these include aldolase, desmoplakin, integrin-linked kinase, PKC, and metallopeptidase. In conclusion, the gene expression profiles of type I and type II endometrial carcinomas are different. Refinement of these profiles will permit more accurate diagnostic tumor classification and the development of prognosis assays. PMID:15381901
Cao, Q Jackie; Belbin, Thomas; Socci, Nicholas; Balan, Raluca; Prystowsky, Michael B; Childs, Geoffrey; Jones, Joan G
Independent component analysis of Alzheimer's DNA microarray gene expression data
Background Gene microarray technology is an effective tool to investigate the simultaneous activity of multiple cellular pathways from hundreds to thousands of genes. However, because data in the colossal amounts generated by DNA microarray technology are usually complex, noisy, high-dimensional, and often hindered by low statistical power, their exploitation is difficult. To overcome these problems, two kinds of unsupervised analysis methods for microarray data: principal component analysis (PCA) and independent component analysis (ICA) have been developed to accomplish the task. PCA projects the data into a new space spanned by the principal components that are mutually orthonormal to each other. The constraint of mutual orthogonality and second-order statistics technique within PCA algorithms, however, may not be applied to the biological systems studied. Extracting and characterizing the most informative features of the biological signals, however, require higher-order statistics. Results ICA is one of the unsupervised algorithms that can extract higher-order statistical structures from data and has been applied to DNA microarray gene expression data analysis. We performed FastICA method on DNA microarray gene expression data from Alzheimer's disease (AD) hippocampal tissue samples and consequential gene clustering. Experimental results showed that the ICA method can improve the clustering results of AD samples and identify significant genes. More than 50 significant genes with high expression levels in severe AD were extracted, representing immunity-related protein, metal-related protein, membrane protein, lipoprotein, neuropeptide, cytoskeleton protein, cellular binding protein, and ribosomal protein. Within the aforementioned categories, our method also found 37 significant genes with low expression levels. Moreover, it is worth noting that some oncogenes and phosphorylation-related proteins are expressed in low levels. In comparison to the PCA and support vector machine recursive feature elimination (SVM-RFE) methods, which are widely used in microarray data analysis, ICA can identify more AD-related genes. Furthermore, we have validated and identified many genes that are associated with AD pathogenesis. Conclusion We demonstrated that ICA exploits higher-order statistics to identify gene expression profiles as linear combinations of elementary expression patterns that lead to the construction of potential AD-related pathogenic pathways. Our computing results also validated that the ICA model outperformed PCA and the SVM-RFE method. This report shows that ICA as a microarray data analysis tool can help us to elucidate the molecular taxonomy of AD and other multifactorial and polygenic complex diseases.
Kong, Wei; Mou, Xiaoyang; Liu, Qingzhong; Chen, Zhongxue; Vanderburg, Charles R; Rogers, Jack T; Huang, Xudong
Reverse phase protein microarrays advance to use in clinical trials
Individualizing cancer therapy for molecular targeted inhibitors requires a new class of molecular profiling technology that can map the functional state of the cancer cell signal pathways containing the drug targets. Reverse phase protein microarrays (RPMA) are a technology platform designed for quantitative, multiplexed analysis of specific phosphorylated, cleaved, or total (phosphorylated and non-phosphorylated) forms of cellular proteins from a limited amount of sample. This class of microarray can be used to interrogate tissue samples, cells, serum, or body fluids. RPMA were previously a research tool; now this technology has graduated to use in research clinical trials with clinical grade sensitivity and precision. In this review we describe the application of RPMA for multiplexed signal pathway analysis in therapeutic monitoring, biomarker discovery, and evaluation of pharmaceutical targets, and conclude with a summary of the technical aspects of RPMA construction and analysis.
Mueller, Claudius; Liotta, Lance A.; Espina, Virginia
A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis.
We provide a new oligo-microarray for Ciona intestinalis, based on the NimbleGen 12-plex�135k format. The array represents 106,285 probes, which is more than double the probe number of the currently available 44k microarray. These probes cover 99.2% of the transcripts in the KyotoHoya (KH) models, published in 2008, and they contain 81.1% of the entries in the UniGene database that are not included in the KH models. In this paper, we show that gene expression levels measured by this new 135k microarray are highly correlated with those obtained by the existing 44k microarray for genes common to both arrays. We also investigated gene expression using samples obtained from the ovary and the neural complex of adult C. intestinalis, showing that the expression of tissue-specific genes is consistent with previous reports. Approximately half of the highly expressed genes identified in the 135k microarray are not included in the previous microarray. The high coverage of gene models by this microarray made it possible to identify splicing variants for a given transcript. The 135k microarray is useful in investigating the functions of genes that are not yet well characterized. Detailed information about this 135k microarray is accessible at no charge from supplemental materials, NCBI Gene Expression Omnibus (GEO), and http://marinegenomics.oist.jp. PMID:23388151
Matsumae, Hiromi; Hamada, Mayuko; Fujie, Manabu; Niimura, Yoshihito; Tanaka, Hiroshi; Kawashima, Takeshi
Tissue Inhibitor of Metalloproteinase-1 Promotes NIH3T3 Fibroblast Proliferation by Activating p-Akt and Cell Cycle Progression
Tissue inhibitor of metalloproteinase-1 (TIMP-1) plays various roles in cell growth in different cell types. However, few studies have focused on TIMP-1�s effect on fibroblast cells. In this study, we investigated the effects of TIMP-1 overexpression on NIH3T3 fibroblast proliferation and potential transduction signaling pathways involved. Overexpression of TIMP-1, by transfection of the pLenti6/ V5-DEST-TIMP-1 plasmid, significantly promoted NIH3T3 proliferation as determined by the BrdU array. Neither 5 nor 15 nM GM6001 (matrix metalloproteinase system inhibitor) affected NIH3T3 proliferation, but 45 nM GM6001 inhibited proliferation. TIMP-1 overexpression activated the p-Akt pathway, but not the p-ERK or p-p38 pathway. In TIMP-1-transfected cells, cyclinD1 was upregulated and p21CIP1 and p27KIP1 were downregulated, which promoted cell entry into the S and G2/M phases. The PI3-K inhibitor LY294002 abolished the TIMP-1-induced effects. Overex-pression of intracellular TIMP-1 stimulated NIH3T3 fibroblast proliferation in a matrix metalloproteinase (MMP)-indepen-dent manner by activating the p-Akt pathway and related cell cycle progression.
Lu, Yang; Liu, Shuxin; Zhang, Shujia; Cai, Guangyan; Jiang, Hongwei; Su, Huabin; Li, Xiaofan; Hong, Quan; Zhang, Xueguang; Chen, Xiangmei
Tissue-specific deregulation of selected HDACs characterizes ALS progression in mouse models: pharmacological characterization of SIRT1 and SIRT2 pathways.
Acetylation homeostasis is thought to play a role in amyotrophic lateral sclerosis, and treatment with inhibitors of histone deacetylases has been considered a potential and attractive therapeutic approach, despite the lack of a thorough study of this class of proteins. In this study, we have considerably extended previous knowledge on the expression of 13 histone deacetylases in tissues (spinal cord and muscle) from mice carrying two different ALS-linked SOD1 mutations (G93A-SOD1 and G86R-SOD1). We have then focused on class III histone deacetylases SIRT1 and SIRT2 that are considered relevant in neurodegenerative diseases. SIRT1 decreases in the spinal cord, but increases in muscle during the progression of the disease, and a similar expression pattern is observed in the corresponding cell models (neuroblastoma and myoblasts). SIRT2 mRNA expression increases in the spinal cord in both G93A-SOD1 and G86R-SOD1 mice but protein expression is substantially unchanged in all the models examined. At variance with other sirtuin modulators (sirtinol, AGK2 and SRT1720), the well-known SIRT1 inhibitor Ex527 has positive effects on survival of neuronal cells expressing mutant SOD1, but this effect is neither mediated by SIRT1 inhibition nor by SIRT2 inhibition. These data call for caution in proposing sirtuin modulation as a target for treatment. PMID:24946089
Valle, C; Salvatori, I; Gerbino, V; Rossi, S; Palamiuc, L; Ren�, F; Carr�, M T
Nuclear localization and intensity of staining of nm23 protein is useful marker for breast cancer progression
Background Breast cancer is the most common cause of cancer death in the western world. The expression differences of many proteins are associated with breast cancer progression or suppression. The purpose of the study was to determine the expression of nm23 protein in the invasion status and metastatic potential of breast cancer by using tissue microarray and to determine its role in breast cancer based on the expression of nm23 gene product. Method nm23 protein expression was examined by immunohistochemistry (IHC) using commercially available tissue microarray containing malignant and normal breast tissues from 216 patients. Results a similar percentage of cases showed positive cytoplasmic/nuclear staining for nm23 in normal breast tissue (85.7%), primary breast carcinoma node negative (97.5%) and carcinoma with lymph node metastasis (92.1%). Nuclear localization of staining for nm23 protein was higher in infiltrating ductal carcinoma (IDC) node positive (24.3%) and in matched lymph mode metastasis (18.9%) compared to IDC node negative (4.9%). Strong intensity of cytoplasmic/nucleus staining was observed in IDC node negative (42.6%), in IDC node positive (57.1%), and Infiltrating lobular carcinoma (ILC) node negative (44%) compared to normal breast tissue (16.7%). Conclusion nm23 protein expression appears widely expressed in normal breast, early and advanced breast cancer stages. Interestingly our study found that strong staining intensity and nuclear localization of nm23 protein may prove to be a useful marker of breast cancer progression.
Ismail, Nawfal I; Kaur, Gurjeet; Hashim, Hasnah; Hassan, Mohammed S
Gene Expression Microarrays in Cancer Research
The advent of microarray technology has enabled scientists to simultaneously investigate the expression of thousands of genes.\\u000a This technology has been widely used in cancer research to better characterize cancer behaviors at mRNA level and to obtain\\u000a new insights into various stages of carcinogenesis. A microarray-based experiment generally involves three major components:\\u000a microarray manufacturing, sample processing, and data analysis, with
Jian Yan; Weikuan Gu
A Homogenous Microarray for Enzymatic Functional Assays
Microarrays as an emerging research tool promises to play a pivotal role in the post genomic era. However, in spite of the\\u000a fast development of this technology special requirements, such as the immobilization and delivery of bio-reagents on the chip\\u000a surface limit the utilization of microarrays, especially for small chemical compound libraries. We have developed a unique\\u000a homogenous microarray system
Haiching Ma; Yuan Wang; Amy S. Pomaybo; Connie Tsai
Probing Biology with Small Molecule Microarrays (SMM)
In the continuous drive to increase screening throughput and reduce sample requirement, microarray-based\\u000a technologies have risen to the occasion. In the past 7�years, a�number of new methodologies have\\u000a been developed for preparing small molecule microarrays from combinatorial and natural product libraries\\u000a with the goal of identifying new interactions or enzymatic activities. Recent advances and applications\\u000a of small molecule microarrays are
Nicolas Winssinger; Zbigniew Pianowski; Francois Debaene
Quality Assessment for Short Oligonucleotide Microarray Data
Quality of microarray gene expression data has emerged as a new research\\u000atopic. As in other areas, microarray quality is assessed by comparing suitable\\u000anumerical summaries across microarrays, so that outliers and trends can be\\u000avisualized, and poor quality arrays or variable quality sets of arrays can be\\u000aidentified. Since each single array comprises tens or hundreds of thousands of
Julia Brettschneider; Fran�ois Collin; Benjamin M. Bolstad; Terence P. Speed