380. INTEGRATIVE TRANSCRIPTOMIC AND FUNCTIONAL ANALYSIS OF CHEMOTHERAPY RESISTANCE IN ESOPHAGEAL ADENOCARCINOMA

Abstract

Abstract Background Gastroesophageal Adenocarcinoma (GEA) is one of the most lethal malignancies in North America with a 5-year survival of <20%. Currently, the standard-of-care treatment for GEA patients is docetaxel-based triplet chemotherapy. However, around 40% of patients are innately resistant to chemotherapy, and half of the initial responders develop acquired resistance during treatment. There is an urgent need to understand the molecular mechanisms driving chemotherapy resistance and identify alternative therapeutic options. Methods Primary tumor tissue was collected from 29 GEA patients to generate patient-derived organoids (PDOs). PDOs were treated with chemotherapy, and the cell viability was measured using Cell Titer Glo. A 3200-compound library was screened at a single concentration (1uM) on three chemo-resistant PDOs. Compounds that showed efficacy in all three lines were then tested in combination with chemotherapy to evaluate their synergistic effects. Single-cell RNA sequencing (scRNA) was performed for 8 chemo-sensitive and 16 chemo-resistant patients. We conducted a transcriptomic analysis to identify markers that are differentially expressed in the two groups. Pathway analysis was performed using Gene Set Enrichment Analysis. Results Cell viability of the PDOs obtained from chemo-resistant patients was significantly higher than that of chemo-sensitive patients. High-throughput (HTP) screening revealed 21 drugs that showed efficacy in all three PDOs, including inhibitors for ribosomes, oxidative phosphorylation (OXPHOS) pathway, and NFkB pathway. Correspondingly, scRNA analysis indicated that chemo-resistant patients have up-regulated ribosome biosynthesis and OXPHOS pathways, as well as increased expression of CCND1, which is a downstream target of the NFkB pathway. Furthermore, the IGF1R inhibitor Ceritinib demonstrated a significant synergistic effect when combined with chemotherapy, with a synergy score of 19.9. Conclusions GEA organoids recapitulate the chemotherapy response of patients, making them an ideal model for ex-vivo drug testing. Integrative analysis of the HTP functional screening and scRNA sequencing data revealed ribosome biogenesis, OXPHOS pathway and IGF-1R as potential therapeutic targets to overcome chemoresistance in GEA.