PMC9188403_01
Preoperative Contrast-enhanced CT images and postoperative histology examination of the LGMS specimen. (A). CT images at the initial diagnosis (the lesions are indicated by arrows). (B). The LGMS tumor cells are mainly in a fascicular arrangement, infiltrative growth with unclear boundaries, with light to moderate heteromorphic and mitotic image (magnification, x10). (C). Immunohistochemical examination shows positive staining for CD117, DOG1 and SMA (magnification, x10).
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A computed tomography (CT) scan of the patient's chest revealed large masses in both lungs, enlarged mediastinal lymph nodes, left pleural effusion, pulmonary artery main, and branch embolism (Figure 1A). Histopathological results (Figure 1B) revealed that the tumor cells were composed of spindle-shaped cells arranged in sheet-like or storiform patterns. The immunohistochemical test results were as follows: DOG1 (+-), CD117 (+), SMA (+), desmin (-), and CD34 (-) (Figure 1C).
Contrast-enhanced CT images and serum CA125 level changes throughout the apatinib therapy. (A). CT images reveal that the mass grew quickly until apatinib treatment was given. After apatinib treatment, the mass was observably decreases in size one month later and continues to shrink at a follow-up period of 4 months (October 25, 2017); however, the mass increases in size 7 months later (January 4, 2018), liver and pancreas metastasis are detected 8 months later (February 26 2018). (B). Serum CA125 levels continuously increase from 231.3 U/mL (February 21, 2017) to 252.3 U/mL (June 6, 2017) until apatinib treatment is given. After apatinib treatment begins in June 8, 2017, at a follow-up period of one month, serum CA125 levels significantly decrease to 150.8 U/mL (July 27, 2017). Then, apatinib is used as maintenance therapy, and CA125 dramatically decreases to a minimum of 7.1 U/mL (October 25, 2017). Finally, the evaluation indicates PD and the patient's CA125 increases to 132.7 U/mL again in May 25, 2018.
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A CT scan indicated that the mass had observably decreased in size, achieving a partial response (PR) according to the modified RECIST criteria (Figure 2A). At a follow-up of 8 months from the first month after apatinib treatment, serum CA125 levels remained within normal limits (Figure 2B), and CT images showed no recurrence.
The mutations detected by WES and RNA sequencing. (A). Framework of the bioinformatics analysis of the article. (B). The types of single-nucleotide variations. (C). The chromosomal locations of the copy number variations. The red fragment corresponds to the under-chromosome, which shows CNVs with amplification. In blue, CNVs with deletions are reported. (D). CNV and SNP of patients in the human body. Gene font size is directly proportional to the expression of CNV and SNP, and the color of the gene is random. (E). The distribution of CNV and SNP mutations sites are shown on a human chromosome ideogram. The different types of SNP mutations are annotated under the chromosome. CNV mutations are annotated: red bar, amplification; blue bar, deletion. The chromosome number is indicated at the left of each ideogram. (F). Amino acid axis labels for domain start and stop positions, as well as exact marker locations, are clearly displayed for precision interpretation. (G). Visualization of the predicted chemical interaction between mutation genes. The 3D structure of the protein is modeled using Swiss MODEL. All the structural components of the protein including the Cbeta, all atoms, salvation and torsion angles were retrieved from Protein Data Bank (PDB) server. The visualization was drawn using PyMol. (H). Subpathway enrichment analysis of CNV and SNP mutation genes in LGMS patient (P<0.05).
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RNA-seq for further analysis in September 2018 (Figure 3A). Raw data were accessible through the EMBL-EBI database ERP120509 under the ENA, and the results were subjected to bioinformatics analysis. Classification was performed according to the variation type (Figure 3B), including missense mutations (95%), nonsense mutations (1%), splice sites (1%), frameshift mutations (1%), and inflame-del mutations (2%). The CNV and SNP variation types and sites were plotted on high-resolution chromosome ideograms (Figure 3C). MKI67, OR2J2, EPPK1, FCGBP, and OR10G4 is shown in Figure 3D and E. These mutations are responsible for functional changes in the proteins (Figure 3F). Molecular docking was used to evaluate the binding ability between ligands and receptors, and based on the molecular docking model, we found that the mutated protein had a higher probability of docking with downstream genes than did the wild-type protein (Etotal < 0, Figure 3G). These sites are considered to be mutational hotspots. Table 3). The three most significant subpathways were the PI3K-Akt, endocytosis, MAPK, and RIG-I-like receptor signaling pathways (Figure 3H).
Analyzing the potential mechanism and targets of LGMS by KEGG pathways and gene ontology. (A). Volcanic map of the DEGs: The abscissa represents the log2FC, and the ordinate represents log10 (adjusted P-value). Red dots, blue dots and gray dots show that the expression levels of the DEGs were obviously upregulated, downregulated, or had no significant difference, respectively. (B). KEGG pathway analysis of LGMS. (C). The biological processes of LGMS. (D). GO (biological process) analysis was performed by Clue GO. Different colors of nodes refer to the functional annotation of ontologies. All these genes were discovered to be involved in 23 different biological processes.
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In the LGMS sample, we screened 3311 differentially expressed genes (DEGs) (Supplementary Table 3) using RNA sequencing analysis, of which 1422 genes were upregulated and 1890 genes were downregulated (Figure 4A). Genes and Genomes (KEGG) enrichment analysis revealed that the DEGs were mainly enriched in the PI3K signaling pathway, neuroactive ligand-receptor interaction signaling pathway, and cAMP signaling pathway (Figure 4B). Gene ontology (GO) analysis revealed that DEGs were significantly enriched in regulating extracellular structure organization, extracellular matrix organization, and humoral immune response mediated by circulating immunoglobulin (Figure 4C). Clue GO analysis suggested that cell signal transduction, surface receptor signal transduction pathway, and cell-cell adhesion through plasma membrane adhesion molecules were significantly enriched in the LGMS samples (Figure 4D).