Nunes, L.; Eilertsen, I. A.; Pinto, R.; Vedeld, H. M.; Bolstad, I. M.; Saeed, U.; Sjo, O. H.; Yaqub, S.; Nesbakken, A.; Kryeziu, K.; Lind, G. E.; Lothe, R. A.; Sveen, A.

Colorectal cancer (CRC) has high phenotypic plasticity, but regulatory mechanisms of aberrant cell states are not well described. We investigated DNA methylation-based regulation of cancer cell-intrinsic transcriptomic heterogeneity in 1,183 multiregional primary tumor samples, liver metastases and tumor organoids. Most genes with strong methylation-transcriptomic association reflected canonical promoter hypermethylation and expression repression related to the CpG island methylator phenotype (CIMP). However, promoter hypomethylation and overexpression of APOLD1 and ELF5 identified two largely non-overlapping subgroups of canonical CIMP-negative CRCs enriched with stem-like and transit-amplifying cell states. APOLD1 tumors were further highly proliferative while ELF5 tumors were slow-cycling and associated with good survival in early-stage disease. Target genes showed patient-specific expression changes in matched primary-metastasis samples, and ELF5 aberrant metastases showed ex vivo sensitivity to putative targeting of stem cells by PI3K/mTOR inhibition, fetal de-differentiation and transition into non-canonical intestinal states. This implicates focal promoter hypomethylation in phenotypic plasticity in CRC metastasis.