Complex Mutation Profiles in Mismatch Repair and Ribonucleotide Reductase Mutants Reveal Novel Repair Substrate Specificity of MutS Homolog (MSH) Complexes
Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate (dNTP) pools by ribonucleotide reductase (RNR) and repair of replication errors by the mismatch repair (MMR) system. We identified genetic interactions between rnr1 alleles that elevate dNTP levels and MMR. We then utilized a targeted deep-sequencing approach to determine mutational signatures associated with MMR pathway defects. By combining rnr1 and msh mutations to increase dNTP levels and alter the mutational load, we uncovered previously unreported specificities of Msh2-Msh3 and Msh2-Msh6. Msh2-Msh3 is uniquely able to direct repair of G/C single base deletions in GC runs, while Msh2-Msh6 specifically directs repair of substitutions at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when MMR is defective.
Authors: Natalie A. Lamb, Jonathan E. Bard, Raphael Loll-Krippleber, Grant W. Brown, Jennifer A. Surtees
https://www.biorxiv.org/content/10.1101/2021.06.30.450577v3
Included is example code for applying a filter based on permissive variants. Also included is how variant frequencies were determined, both based on counts of unique variants and total frequency. Lastly, an example for performing cluser analysis on COSMIC SBS signatures combined with our own SNV trinucleotide signatures is included. CAN1ManuscriptVariants.txt was generated by combining 198 VCF files with associated metadata in Excel.COSMIC_CAN1.csv was generated by combining single base substitutions (SBS) COSMIC signatures from GRCh38 (v3.2- March 2021, https://cancer.sanger.ac.uk/signatures/downloads/) with variants in trinucleotide context.