PMC9378866_01
Abdominal computed tomography scan. (A) The baseline CT scan performed on August 26, 2021 showed multiple large hypodense lesions in the liver. Contrast-enhanced CT showed ring-shaped enhanced nodules with the maximum diameter of 17 mm. (B) After 2 months of treatment with imatinib, a CT scan was performed on October 25, 2021, a relapse of disease (growth of the longest lesion's diameter from 17 to 25 mm) of the hepatic lesion and multiple hepatic metastases with slight reinforcement was observed. (C) The venous phase of the CT scan performed on November 25, 2021 demonstrated decreased hypodense lesions (growth of the longest lesion's diameter from 25 to 23 mm) with peripheral rim enhancement. (D) After two cycles of sunitinib, a CT scan was performed on January 19, 2022 and revealed a smaller, irregular hypodense intrahepatic metastatic mass.
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A computed tomography (CT) scan indicated small liver lesions with multiple hypodense nodules about 30-33 Hu value, and in contrast-enhanced CT observed ring-shaped enhanced nodules with a maximum diameter of 17 mm ( Figure 1A ). The capsule endoscopy found an ulcerated bulge covered with yellow-white digesta and bloodstains ( Supplementary Figures 1A-C ). Approximately 2 months later, the patient complained of epigastric pain and CT indicated more enlarged nodules with a maximum diameter of 25 mm, increased parietal thickness, and increasing nodules ( Figure 1B ). CT demonstrated a well-defined, shrunk homogeneous soft-tissue mass on November 25, 2021 ( Figure 1C ). By Jan 19, 2022, CT scans showed partial lesion absorption ( Figure 1D ).
Macroscopic and microscopic findings of the resected tumor. (A) The resected specimen of the small intestine measured 10 x 5 x 2 cm. (B) Postoperative pathology indicated that the tumor was a high-risk GIST: the lesion had significant nuclear pleomorphism with mitotic >10/50 HPF (hematoxylin and eosin staining). The spindle or ovoid cells are deeply stained with coarse chromatin and obvious atypia (x400). (C) Immunochemical staining showing that the tissue was CD117+ (x200). (D) Immunochemical staining showing that the tissue Dog-1+ (x200).
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Immunohistochemistry results were CD117 (+), Dog-1 (+), smooth muscle actin (+), Vim (+), CK (-), CD34 (-), and SOX-10 (-) ( Figures 2A-D ). KIT p.V560E and the reduced number of RB1 copies. KIT p.V560E indicated that the valine in the 560 codon of the KIT gene was mutated to glutamate, and it was within the exon 11 of KIT, and KIT mutation accounts for 60% of GISTs ( Supplementary Figures 2A, B ). We also analyzed the sensitivity and applicability to immunotherapy: microsatellite stable; microsatellite instability where the tumor mutational burden (TMB) was rated medium of 2.23 Muts/Mb (mutational load per million bases), lower than 57% of patients with GISTs (small intestine); and no mismatch-repair gene deficiency detected ( Supplementary Figures 2C, D ).
Target drug susceptibilities. (A) The inhibition rate of the highest concentration: regorafenib, sunitinib, and imatinib were 99.28, 98.89, and 0.00, respectively (the control cells received no treatment, and the cell viability was 100%). (B) Half-maximal inhibitory concentration (IC50): regorafenib, sunitinib, and imatinib were 1.57, 0.89, and >20, respectively (definition: sensitive, IC50<0.5; undefined, 0.5<IC50<1; resistant, IC50>1).
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Subsequently, we also established the organoid model with small intestinal during surgical resection ( Supplementary Figures 3A-C ) to assess the drug response to currently widely used KIT-targeted drugs. Briefly, the patient tumor tissue was minced and digested into small cell clusters ( Supplementary Figure 3A ) and passed through a 70-mum filter. On complete gelation, the culture medium was added and cultured until enough PDOs were formed ( Supplementary Figures 3B, C ). Both the hematoxylin-eosin and immunochemical staining demonstrated that cultured PDOs retained key phenotypic characteristics of the parent GISTs like nuclear pleomorphism, mitotic rate, and immunoreactive profiles ( Supplementary Figures 3D, E ). The concentration-response curves manifested that PDOs were resistant to both imatinib (IC50: >20x) and regorafenib (IC50: 1.57x), and sensitive to sunitinib (IC50: 0.89x) ( Figure 3 ).
Timeline of the diagnostic and therapeutic process.
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The diagnosis and treatment strategy timeline schematic is presented in  Figure 4 .