Molecular Lineages of Sporadic Mismatch Repair–Deficient Colorectal Cancer

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PURPOSE: Mismatch repair-deficient (MMRd) colorectal cancers are classified based on MMR protein loss and BRAFV600E mutations. BRAF wild-type sporadic MMRd tumors exhibit a diverse landscape of alternative oncogenes, including gene fusions, with unclear biological and clinical significance. We evaluated mutually exclusive subtypes of sporadic MMRd tumors defined by oncogenic mitogen-activated protein kinase (MAPK) variants and gene fusions to determine the relationship among predominant genomic driver, MMR deficiency mechanism, and clinical outcomes. EXPERIMENTAL DESIGN: We assessed 6,789 patients with colorectal cancer sequenced by MSK-IMPACT to identify 518 patients with sporadic MMRd colorectal cancer. We defined mutually exclusive oncogenic alteration subtypes and then assessed differences in allele-specific MMR-inactivating events, co-occurring oncogenic variants, and patient outcomes. We validated findings in an Italian cohort (n = 69). RESULTS: We identify 4 sporadic MMRd colorectal cancer subtypes: (i) oncogenic fusion-positive, (ii) RAS-mutant (mut), (iii) BRAFV600E-mut, and (iv) MAPK/fusion driver-negative. These mutually exclusive subtypes were associated with conserved molecular lineages of MMR gene inactivation and WNT signaling variants. Oncogenic fusions were disproportionately prevalent in non-Caucasians, among nonsmokers, and in the transverse colon, compared with subtypes that were enriched in smokers (BRAF-mut) and male, younger patients (RAS-mut and MAPK/fusion-driverless). Oncogene-defined molecular lineages were strong predictors of patient outcomes and response to immunotherapy and tyrosine kinase inhibition for metastatic disease. Fusion-positive patients demonstrated improved survival compared with BRAF-mut cancers and benefited from immunotherapy and fusion inhibitors. MAPK/fusion driver-negative tumors were aneuploid, responded poorly to immunotherapy, and were sensitive to EGFR blockade. CONCLUSIONS: Overall, MAPK and fusion oncogenic drivers distinguish MMRd colorectal cancer molecular lineages that inform molecular and clinical phenotypes.

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