Integrative Clinical and DNA Methylation Analyses in a Population-Based Cohort Identifies CDH17 and LRP2 as Risk Recurrence Factors in Stage II Colon Cancer

SIMPLE SUMMARY: Stage II colon cancer, although manageable by surgical resection with or without adjuvant chemotherapy, still accounts for 16% of colorectal cancer deaths. Prognostic biomarkers are keys to the risk stratification of patients and the decision to recommend adjuvant chemotherapy, but these are currently lacking. Here, by using a French stage II CC population-based cohort to perform DNA methylation and clinical screens (383 patients), we uncovered a methylation classifier that separates stage II CC into four disease subclasses. Survival analysis revealed two methylation sites localised at the CDH17 and LRP2 genes, respectively, to be able to predict risk of cancer recurrence. Hypermethylated CDH17 conferred high risk of disease recurrence and was associated with over-activity of oncogene signalling pathways, such as KRAS and low anti-tumour immune activity. Conversely, hypermethylation of the LRP2 gene identified relatively good prognosis stage II CC tumours characterised by intact DNA repair pathways and active anti-tumour immunity. ABSTRACT: Stage II colon cancer (CC), although diagnosed early, accounts for 16% of CC deaths. Predictors of recurrence risk could mitigate this but are currently lacking. By using a DNA methylation-based clinical screening in real-world (n = 383) and in TCGA-derived cohorts of stage II CC (n = 134), we have devised a novel 40 CpG site-based classifier that can segregate stage II CC into four previously undescribed disease sub-classes that are characterised by distinct molecular features, including activation of MYC/E2F-dependant proliferation signatures. By multivariate analyses, hypermethylation of 2 CpG sites at genes CDH17 and LRP2, respectively, was found to independently confer either significantly increased (CDH17; p-value, 0.0203) or reduced (LRP2; p-value, 0.0047) risk of CC recurrence. Functional enrichment and immune cell infiltration analyses, on RNAseq data from the TCGA cohort, revealed cases with hypermethylation at CDH17 to be enriched for KRAS, epithelial-mesenchymal transition and inflammatory functions (via IL2/STAT5), associated with infiltration by ‘exhausted’ T cells. By contrast, LRP2 hypermethylated cases showed enrichment for mTORC1, DNA repair pathways and activated B cell signatures. These findings will be of value for improving personalised care paths and treatment in stage II CC patients.