Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrentCCNE1andIGF2enhancer hijacking in primary gastric adenocarcinoma

Abstract

ObjectiveGenomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), 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).DesignWe 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.ResultsPeNChIP-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 CCNE1, a key driver of therapy resistance, occurred in 8% of patients frequently juxtaposing diverse distal enhancers to CCNE1 proximal regions. CCNE1-rearranged GCs were associated with high CCNE1 expression, disrupted CCNE1 topologically associating domain (TAD) boundaries, and novel TAD interactions in CCNE1-rearranged primary tumours. We also observed IGF2 enhancer-based SVs, previously noted in colorectal cancer, highlighting a common non-coding genetic driver alteration in gastric and colorectal malignancies.ConclusionIntegrated 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.

DNA Methylation and Genetic Aberrations in Gastric Cancer

“…Aberrant chromatin structures are associated with the regulation of gene expression, and these chromatin structures are detected in cancer [14, 15]. Recent studies revealed long-range chromatin interaction in regions related to genomic rearrangements [16]. Genomic rearrangements are involved in “enhancer hijacking,” promoting the expression of CCNE1 and IGF2 .…”

Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis

“…Super-enhancers tend to be preferentially insulated by strong boundaries to keep away from genes in adjacent TADs [ 38 ]. Enhancer-hijacking is considered a rare event and a mechanism exploited by genomic rearrangements [ 125 , 127 ]. For many genes, structural variants are remarkably related to elevated numbers or greater proximity of enhancer regulatory elements near the gene [ 3 , 127 ].…”

“…Enhancer-hijacking is considered a rare event and a mechanism exploited by genomic rearrangements [ 125 , 127 ]. For many genes, structural variants are remarkably related to elevated numbers or greater proximity of enhancer regulatory elements near the gene [ 3 , 127 ]. In medulloblastoma, enhancer-hijacking resulting from somatic structural variants has been demonstrated to activate the proto-oncogenes GFI1 and GFI1B [ 128 ].…”

<p>Monoamine Oxidase A is a Major Mediator of Mitochondrial Homeostasis and Glycolysis in Gastric Cancer Progression</p>

“…Although numerous improvements have been made in gastric cancer (GC) diagnosis and treatment, GC still is the third most deadly cancer worldwide, especially in East Asia. [1][2][3][4] Thus, the further identification and validation of GC-associated genes, new pathways and therapeutic targets, drugs and strategies for combination therapy are urgently needed.…”