Nanoscale chromatin profiling of gastric adenocarcinoma reveals cancer-associated cryptic promoters and somatically acquired regulatory elements

Abstract

Chromatin alterations are fundamental hallmarks of cancer. To study chromatin alterations in primary gastric adenocarcinomas, we perform nanoscale chromatin immunoprecipitation sequencing of multiple histone modifications in five gastric cancers and matched normal tissues. We identify hundreds of somatically altered promoters and predicted enhancers. Many cancer-associated promoters localize to genomic sites lacking previously annotated transcription start sites (cryptic promoters), driving expression of nearby genes involved in gastrointestinal cancer, embryonic development and tissue specification. Cancer-associated promoters overlap with embryonic stem cell regions targeted by polycomb repressive complex 2, exhibiting promoter bivalency and DNA methylation loss. We identify somatically acquired elements exhibiting germline allelic biases and non-coding somatic mutations creating new promoters. Our findings demonstrate the feasibility of profiling chromatin from solid tumours with limited tissue to identify regulatory elements, transcriptional patterns and regulatory genetic variants associated with cancer.

Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma

“…Regions exhibiting somatic promoters were significantly enriched in regions associated with EZH2 (P < 0.01) and SUZ12 (P < 0.01) binding ( Fig. 5A; Supplementary Table S12), confirming earlier findings on a smaller cohort (38). Both EZH2 and SUZ12 are components of the Polycomb repressor complex 2 (PRC2) epigenetic regulator complex, which is upregulated in many cancer types, including gastric cancer (90)(91)(92)(93)(94)(95).…”

“…CHANCE analysis also revealed that the large majority (81%) of samples exhibited successful enrichment (Supplementary Table S2). We have previously also shown that Nano-ChIP signals exhibit a good concordance with orthogonal ChIP-qPCR results (38 Fig. S1).…”

“…In an earlier study (38), we reported a transcript isoform of the MET receptor tyrosine kinase driven by an internal alternative promoter, which has been independently confirmed in other cancer types (65). However, functional implications of this MET variant (Var) remain unclear.…”

“…Our study applied microscale histone modification profiling [Nano-chromatin immunoprecipitation sequencing (Nano-ChIP-seq)] to profile primary cancers (37,38), which allows the measurement of epigenomic modifications in vivo, compared with laboratory-cultured cell lines that may harbor epigenomic artifacts due to in vitro culture (39,40). By comparing the epigenomic promoter profiles of primary gastric cancers and matched normal tissues, we observed pervasive alterations in promoter usage in gastric cancer, and an important role for somatic promoters in enhancing gastric cancer transcript, protein isoform, and immunogenic diversity.…”

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

“…S5a in the Supplementary Appendix). 17 Exons 1 and 2 of MET encode the hepatocyte growth factor ligand binding domain and, analogous to the epidermal growth factor receptor, EGFRvIII, isoform 18 , this isoform may result in ligand-independent MET activation. In addition, gene fusions involving MET were found in three cases (Table S5 in the Supplementary Appendix).…”