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

ARID1A型 癌症研究 表观遗传学 生物 表观遗传学 染色质 增强子 癌症 溴尿嘧啶 遗传学 DNA甲基化 基因 基因表达 突变
作者
Chang Xu,Kie Kyon Huang,Jia Hao Law,Joy Shijia Chua,Taotao Sheng,Natasha Flores,Melissa Pool Pizzi,Atsushi Okabe,Angie Lay Keng Tan,Feng Zhu,Vikrant Kumar,Xiaoyin Lu,Ana Morales Benitez,Benedict Shi Xiang Lian,Haoran Ma,Shamaine Wei Ting Ho,Kalpana Ramnarayanan,Chukwuemeka George Anene-Nzelu,Milad Razavi-Mohseni,Siti Aishah Binte Abdul Ghani,Su Ting Tay,Xuewen Ong,Ming Hui Lee,Yu Amanda Guo,Hassan Ashktorab,Duane T. Smoot,Shang Li,Anders J. Skanderup,M Beer,Roger Foo,Joel Shi Hao Wong,Kaushal Sanghvi,Wei Peng Yong,Raghav Sundar,Atsushi Kaneda,Shyam Prabhakar,Paweł K. Mazur,Jaffer A. Ajani,Khay Guan Yeoh,Jimmy Bok Yan So,Patrick Tan
出处
期刊:Gut [BMJ]
卷期号:72 (9): 1651-1663 被引量:9
标识
DOI:10.1136/gutjnl-2022-328332
摘要

Objective Gastric cancer (GC) is a leading cause of cancer mortality, with ARID1A being the second most frequently mutated driver gene in GC. We sought to decipher ARID1A -specific GC regulatory networks and examine therapeutic vulnerabilities arising from ARID1A loss. Design Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of ARID1A inactivation across molecular subtypes. Single-cell transcriptomic profiles of ARID1A -mutated GCs were analysed to examine tumour microenvironmental changes arising from ARID1A loss. 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 of ARID1A -mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. Results We observed prevalent ARID1A inactivation 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 at ARID1A -occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as NFKB1 and NFKB2 . Promoter activation in ARID1A -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 to ARID1A -genomic status. Conclusion Our results suggest a therapeutic strategy for ARID1A -mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.
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