A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues

Consensus Molecular Subtype (CMS) classi fication of colorectal cancer (CRC) tissues is complicated by RNA degradation upon formalin- fixed paraf fin -embedded (FFPE) preservation. Here, we present an FFPE-curated CMS classi fier. The CMSFFPE classi fier was developed using genes with a high transcript integrity in FFPE-derived RNA. We evaluated the classi fication accuracy in two FFPE-RNA datasets with matched fresh -frozen (FF) RNA data, and an FF-derived RNA set. An FFPE-RNA application cohort of metastatic CRC patients was established, partly treated with antiEGFR therapy. Key characteristics per CMS were assessed. Crossreferenced with matched benchmark FF CMS calls, the CMSFFPE classi fier strongly improved classi fication accuracy in two FFPE datasets compared with the original CMSClassi fier (63.6% versus 40.9% and 83.3% versus 66.7%, respectively). We recovered CMSspeci fic recurrence -free survival patterns (CMS4 versus CMS2: hazard ratio 1.75, 95% CI 1.24 -2.46). Key molecular and clinical associations of the CMSs were con firmed. In particular, we demonstrated the predictive value of CMS2 and CMS3 for antiEGFR therapy response (CMS2&3: odds ratio 5.48, 95% CI 1.10 -27.27). The CMSFFPE classi fier is an optimized FFPE-curated research tool for CMS classi fication of clinical CRC samples.