The type of mismatch repair deficiency shapes dinucleotide repeat expansion and WRN inhibitor sensitivity in colorectal cancer

Abstract Even though cancer genetics was revolutionized by the discovery of microsatellite instability (MSI) in colorectal cancer (CRC) about thirty years ago, this phenotype is yet to be fully characterized 1–3 . Here, we used long-read sequencing to uncover the landscape of repeat instability in primary CRC. We found that long TA repeats, which underlie the formation of alternative DNA structures that break upon inactivation of WRN helicase, are a common feature of MSH2-, MLH1-, PMS2-, but not MSH6-deficient primary CRCs. Dinucleotide expansion is exacerbated in PMS2-deficient tumors, where most dinucleotide motifs are prone to expand. Importantly, acquisition of resistance to WRN inhibition in MSI cells is not driven by overcoming DNA structure formation. Altogether, our data uncover the full landscape of repeat instability in CRC where dinucleotide expansions are unlikely to be overcome by acquired resistance to WRN-inhibitor therapy, defining a novel actionable genetic feature of CRC.