# Systematic analysis of functional genetic and epigenetic variants in colorectal cancer

## TL;DR

This study identifies genetic and epigenetic variants that influence enhancer activity in colorectal cancer, offering new insights into disease progression and potential biomarkers for early detection.

## Contribution

The study introduces a comprehensive platform for evaluating noncoding SNPs and CpG sites in CRC, revealing metastasis-specific regulatory elements and diagnostic biomarkers.

## Key findings

- 922 SNPs and 487 CpG-containing elements modulate enhancer activity in primary CRC cells.
- 3136 SNPs and 3008 methylation-sensitive elements show metastasis-specific regulatory effects.
- Two CRC-specific hypomethylated loci (cg08640619 and cg25982657) serve as effective early detection biomarkers with AUROC > 0.96.

## Abstract

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, yet the functional impact of noncoding variants on enhancer activity remains largely unexplored. In this study, we adapted and applied two high-throughput techniques, SNP-STARR-seq and Methyl-STARR-seq, to systematically evaluate the influence of 30,790 noncoding SNPs and more than 134,000 CpG sites on enhancer activity in primary and metastatic CRC cells. We identified 922 SNPs and 487 CpG-containing elements modulating enhancer activity in primary cells and found 3136 SNPs and 3008 methylation-sensitive elements with metastasis-specific regulatory effects. Multi-omics integration linked these variants to target genes, and CRISPR editing validated their roles in driving tumorigenic and metastatic phenotypes. Furthermore, we identified two CRC-specific hypomethylated loci, cg08640619 and cg25982657, as exceptional tissue-based early detection biomarkers (AUROC > 0.96). Mechanistically, hypermethylation at cg08640619 disrupts RUNX2 binding, leading to inhibition of KIRREL1 and ETV3. Our study provides a comprehensive platform for understanding how genetic and epigenetic variants disrupt transcriptional programs in CRC, offering insights into disease susceptibility and identifying potential diagnostic and therapeutic targets.

Functional screening pinpoints genetic and epigenetic drivers of colorectal cancer progression and diagnosis.