Abstract 93: Alternative splicing reveals epigenetic subtypes in gastric cancer peritoneal metastasis

Abstract Background: Gastric cancer (GC) with peritoneal metastases (PM) carries a grim prognosis. Despite progress in elucidating transcriptomic mechanisms of metastasis, epigenetic factors and vulnerabilities are still not fully understood. Methods: Primary tumor (PT, n=157), primary normal (PN, n=33) and peritoneal metastases (PM, n=97) from patients with GC were retrieved and sequenced with whole transcriptome sequencing. PSI-Sigma was conducted to retrieve alternative pre-mRNA splicing (AS) changes. Differential splicing events (DSE) that were concordant between PT vs PN and PM vs PT were utilized to identify AS event hubs through non-negative matrix factorization. Transcriptomic derivatives such as epithelial-mesenchymal transition (EMT)-scores, mesenchymal subtypes were retrieved utilizing log2(FPKM) gene expression. Epigenetic subtypes of GCPM samples were retrieved through hierarchical clustering of AS event hubs and survival analyses were conducted with a Cox-proportional hazard model. Results: Nine hundred and nine overlapping DSE were identified between PT vs PN and PM vs PT comparisons, with majority being mutually exclusive exons (44.6%). Of this 909 DSEs, 45 DSE were found to be concordant across comparisons. Unsupervised clustering with gene hubs retrieved from 45 DSEs reveals 2 GCPM epigenetic clusters, characterized by divergent EMT states (p<0.001). The clusters were subsequently coined GCPM-Mesenchymal (n=47, mean EMT-score=1.06) and GCPM-Epithelial (n=50, mean EMT-score=0.17). GCPM-Mesenchymal samples were predominantly found to be nested within an inflamed immune-infiltrated peritoneal niche (p=0.002) and participants with GCPM-Mesenchymal only samples had significantly poorer survival outcomes upon PM diagnosis (Log-rank, p=0.037). Conclusions: This study sheds light on alternative splicing in transcoelomic metastasis and highlights potential for splicing-based patient stratification in GCPM. Citation Format: Joseph J. Zhao, Xiaonan Fan, Jia Jia Chan, Daryl Kai Ann Chia, Robert Walsh, Haoran Ma, Wei Peng Yong, Jimmy So, Patrick Tan, Yvonne Tay, Raghav Sundar. Alternative splicing reveals epigenetic subtypes in gastric cancer peritoneal metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 93.