Comprehensive molecular phenotyping ofARID1A-deficient gastric cancer reveals pervasive epigenomic reprogramming and therapeutic opportunities

Abstract

ObjectiveGastric cancer (GC) is a leading cause of cancer mortality, withARID1Abeing the second most frequently mutated driver gene in GC. We sought to decipherARID1A-specific GC regulatory networks and examine therapeutic vulnerabilities arising fromARID1Aloss.DesignGenomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures ofARID1Ainactivation across molecular subtypes. Single-cell transcriptomic profiles ofARID1A-mutated GCs were analysed to examine tumour microenvironmental changes arising fromARID1Aloss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks ofARID1A-mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition.ResultsWe observed prevalentARID1Ainactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment.ARID1A-depletion caused loss of H3K27ac activation signals atARID1A-occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such asNFKB1andNFKB2. Promoter activation inARID1A-mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific toARID1A-genomic status.ConclusionOur results suggest a therapeutic strategy forARID1A-mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.