Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy

Abstract

Genome sequencing can be used to detect DNA repair failures in tumors and learn about underlying mechanisms. Here, we synthesize findings from genomic studies that examined deficiencies of the DNA mismatch repair (MMR) pathway. The impairment of MMR results in genome-wide hypermutation and in the 'microsatellite instability' (MSI) phenotype-occurrence of indel mutations at short tandem repeat (microsatellite) loci. The MSI status of tumors was traditionally assessed by molecular testing of a selected set of MS loci or by measuring MMR protein expression levels. Today, genomic data can provide a more complete picture of the consequences on genomic instability. Multiple computational studies examined somatic mutation distributions that result from failed DNA repair pathways in tumors. These include analyzing the commonly studied trinucleotide mutational spectra of single-nucleotide variants (SNVs), as well as of other features such as indels, structural variants, mutation clusters and regional mutation rate redistribution. The identified mutation patterns can be used to rigorously measure prevalence of MMR failures across cancer types, and potentially to subcategorize the MMR deficiencies. Diverse data sources, genomic and pre-genomic, from human and from experimental models, suggest there are different ways in which MMR can fail, and/or that the cell-type or genetic background may result in different types of MMR mutational patterns. The spectrum of MMR failures may direct cancer evolution, generating particular sets of driver mutations. Moreover, MMR affects outcomes of therapy by DNA damaging drugs, antimetabolites, nonsense-mediated mRNA decay (NMD) inhibitors, and immunotherapy by promoting either resistance or sensitivity, depending on the type of therapy.

Keywords: DNA synthesis and repair; chemotherapy resistance; genome integrity; immunomodulation; mutagenesis; oncogenesis.

Figure 1. Genomic signatures of MMR failures, and possible subtypes thereof

(A) Methods for detecting MMR deficiencies (left) are based on assaying the instability of MS loci across the genome (middle). This can be done either by a PCR+electrophoresis experimental assay of various MS panels such as the commonly employed Bethesda panel (middle, above), or more recently by a statistical analysis of WGS/WES data across many MS loci simultaneously by various bioinformatics tools (middle, below). In both cases, the output is the binary-labeled MSS (stable) or MSI (instable) (right). The Bethesda panel can distinguish MSI-H (high) versus MSI-L (low), however the significance of this distinction is unclear. (B) Different molecular mechanisms are known to cause MMR failures, either through pathogenic germline variation, somatic mutations and/or copy-number alterations, or epigenetic silencing of different MMR genes or MMR-associated genes (left). All converge on a set of broadly similar genomic patterns involving a high burden of SNV and indel mutations. However recent data suggest that these mechanisms may be separable based on classifying the SNVs and indels by type, as defined in mutational signatures (middle) observed in genomes of cancers and of experimental models where MMR deficiencies were induced (right). For example, MSH6 LOF may generate similar burden of SNVs as MLH1 or MSH2 loss, however with fewer indels generated. Another example is that PMS2 loss might generate a different SNV trinucleotide spectrum than the MSH2 or MLH1 loss. Abbreviation: SNV, single-nucleotide variant.

Figure 2. MMR failures in cancers can cause resistance or sensitization to certain therapies

(A) MMR dysfunction may sensitize tumors to various therapies via different mechanisms; some of these are well established and applied in the clinic (immunotherapy), while others are proposed based on known molecular mechanisms and/or studies on experimental models, however awaiting clinical validation (in panel A). A common consequence of MMR failures are indel mutations at MS repeats, which can be in coding regions and so generate frameshifted, and usually truncated, mutant proteins (note that some indels at repeats also in introns can induce misplicing, consequently again resulting in frameshifting and truncation of coding regions). Expression of such truncated proteins is often silenced by the NMD surveillance pathway that degrades mutant mRNA. However some frameshifted mRNAs can escape NMD detection and generate neoantigens that sensitize to immunotherapy, or that generate toxic proteins (e.g. HSP110 mutant), suggesting that beneficial effects of therapy might be potentiated by NMD inhibition. Frameshifting indels also can cause LOF in DNA repair proteins e.g. MRE11 and RAD50, sensitizing to irinotecan and potentially to DNA damage-signaling drugs e.g. ATR inhibitors. Finally, expansions at repeats due to MMR failure increase reliance on the WRN DNA helicase. (B) MMR inactivation causes resistance to some commonly used cancer drugs, which can trigger MMR activity—either by methylation of nucleobases [TMZ, dacarbazine], or by incorporation of chemically modified nucleotides [6-TG, 5-FU] that can register as mismatches—potentially resulting in apoptosis via DNA damage signalling. A dysfunctional MMR results in reduced clinical utility of such drugs, as well as in increased mutation rates in the MMR-deficient tumor upon treatment, which can generate further mutations in cancer driver genes or in drug resistance genes. Abbreviations: 5-FU, 5-fluorouracil; 6-TG, 6-thioguanine.