DNA polymerase and mismatch repair deficient cancers exert distinct and clinically-useful genome-wide microsatellite signatures

Tumors with a deficiency in the DNA mismatch repair mechanism (MMRD) or in the DNA polymerase proofreading have elevated mutation rates with characteristic mutational signatures. We showed that the two mechanisms overlap in repairing certain specific single nucleotide variants (SNV), and thus when both are inactivated they generate a unique mutational SNV-signature¹.

However, only MMRD is considered to cause microsatellite instability (MSI) but not the loss of polymerase proofreading. Using a tool for calling indels in microsatellite loci (MS-indels) that we recently developed (MSMuTetct²), [REF] we checked the effect of the loss of polymerase proofreading on indels in microsatellite loci. We applied MSMuTect on next generation sequencing data from a cohort of tumors with germline and somatic deficiencies in MMR, polymerase proofreading or both. We revealed a novel association between loss of polymerase proofreading and MSI, especially when both components are lost.

Analysis of MS-indels identified five distinct signatures (MS-sigs). MMRD MS-sigs are dominated by multi-base losses, while mutant-polymerase MS-sigs contain primarily single-base gains. Strikingly, MS-deletions in MMRD tumors depend on the original size of the microsatellite and converge to a preferred length.

Finally, we demonstrate that MS-sigs can be a powerful clinical tool for managing individuals with germline MMRD and replication repair deficient cancers, as they can detect the replication repair deficiency even in normal cells, and thus directly detect cases (mainly pediatric) with germline MMRD before tumors develop.

In addition we show that MS-sigs activity can predict responsiveness to immunotherapy better than tumor mutational burden.