RAS pathway mutations orchestrate chromatin reconfiguration and transcriptional rewiring in colorectal cancer

RAS pathway mutations occur in ~ 40% of colorectal cancers (CRCs), with KRAS- and BRAF- mutant tumors exhibiting distinct mutational, transcriptional, and epigenetic landscapes. Advances in next-generation sequencing enable integrated analyses of multi-omics data, providing insight into their regulatory relationships. To define the molecular programs driven by RAS pathway mutations, we generated isogenic CRC cell models and profiled chromatin accessibility using ATAC-seq.

We performed ATAC-seq in isogenic HCT116 and RKO models. Mutation-associated changes in genes, regulatory elements, and signaling pathways were identified, together with inferred transcription factor (TF) binding activity. Clinical datasets were analyzed to assess whether features identified in the cell models were recapitulated in patient tumors and whether they were associated with clinical outcomes.

Isogenic CRC models segregated by RAS pathway mutation status at both epigenetic and transcriptomic levels. Mutation alterations modulated WNT signaling, accompanied by changes in RUNX2 and TCF7L2 expression and binding activity. Comparison between the HCT116 and RKO models identified 85 genes, eight of which displayed reproducible expression patterns across three independent clinical cohorts. TCF7L2 were associated with RAS pathway mutations in patient tumors, with elevated expression level predicting worse overall survival independent of cofactors.

We identified RAS pathway mutation-driven regulatory reprogramming with convergent effects on WNT signaling. TCF7L2 emerged as a key TF, with elevated expression in BRAF-mutant tumors independently associated with poor clinical outcomes. These findings highlight a clinically relevant epigenetic mechanism linking RAS pathway mutations to CRC cell survival maintenance.