Multiregional transcriptomics identifies congruent consensus molecular subtypes with prognostic value beyond tumor heterogeneity in colorectal cancer.

Abstract Intra-tumor heterogeneity compromises the clinical value of transcriptomic classifications of colorectal cancer. We investigated the prognostic effect of transcriptomic heterogeneity and the potential for a classification less vulnerable to heterogeneity in a single-hospital series of 1,093 primary and metastatic tumor samples from 692 patients, including 2–4 multiregional samples from 98 primary tumors and primary-metastasis sets from 35 patients. Intra-tumor heterogeneity of the consensus molecular subtypes (CMS) was frequent (40%) and associated with poor patient survival independently of tumor microenvironment markers. Multiregional transcriptomics uncovered cancer cell-intrinsic and low-heterogeneity signals that recapitulated the two intrinsic subtypes (iCMS2/iCMS3) proposed by single-cell sequencing. Further subclassification resulted in four congruent CMSs defining good-prognostic and poor-prognostic subtypes. Congruent CMS explained a larger proportion of variation in patient survival than intra-tumor CMS heterogeneity. Evidence of plasticity was found by discordant phenotypes of matched primary and metastatic tumors (28%), even according to the two-state intrinsic classification. In conclusion, multiregional sampling reconciled the prognostic power of tumor classifications from single-cell and bulk transcriptomics in the context of intra-tumor heterogeneity, and phenotypic plasticity challenges the reconciliation of primary and metastatic subtypes.