Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent <i>CCNE1</i> and <i>IGF2</i> enhancer hijacking in primary gastric adenocarcinoma.

Abstract

Genomic structural variations (SVs) causing rewiring of <i>cis</i>-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (<i>enhancer-based SVs</i>), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS). We applied PeNChIP-seq to 11 primary GCs and matched normal tissues combined with WGS profiles of >200 GCs. Epigenome profiles were analysed alongside matched RNA-seq data to identify tumour-associated enhancer-based SVs with altered cancer transcription. Functional validation of candidate enhancer-based SVs was performed using CRISPR/Cas9 genome editing, chromosome conformation capture assays (4C-seq, Capture-C) and Hi-C analysis of primary GCs. PeNChIP-seq/WGS revealed ~150 enhancer-based SVs in GC. The majority (63%) of SVs linked to target gene deregulation were associated with increased tumour expression. Enhancer-based SVs targeting <i>CCNE1</i>, a key driver of therapy resistance, occurred in 8% of patients frequently juxtaposing diverse distal enhancers to <i>CCNE1</i> proximal regions. <i>CCNE1</i>-rearranged GCs were associated with high <i>CCNE1</i> expression, disrupted <i>CCNE1</i> topologically associating domain (TAD) boundaries, and novel TAD interactions in <i>CCNE1</i>-rearranged primary tumours. We also observed <i>IGF2</i> enhancer-based SVs, previously noted in colorectal cancer, highlighting a common non-coding genetic driver alteration in gastric and colorectal malignancies. Integrated paired-end NanoChIP-seq and WGS of gastric tumours reveals tumour-associated regulatory SV in regions associated with both simple and complex genomic rearrangements. Genomic rearrangements may thus exploit enhancer-hijacking as a common mechanism to drive oncogene expression in GC.