Journal Article

Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

Yesilyurt, Betül Tuba, Aerts, Stein, Metcalf, Alex, Spurdle, Amanda, Sagaert, Xavier, Smeets, Dominiek, Zhao, Hui, Coenegrachts, Lieve, Reumers, Joke, Amant, Frederic, Thienpont, Bernard, Matthijs, Gert, Cools, Jan, Lambrechts, Diether, Schrauwen, Stefanie, Moisse, Matthieu

2014

Overview

DNA replication errors that persist as mismatch mutations make up the molecular fingerprint of mismatch repair (MMR)-deficient tumors and convey them with resistance to standard therapy. Using whole-genome and whole-exome sequencing, we here confirm an MMR-deficient mutation signature that is distinct from other tumor genomes, but surprisingly similar to germ-line DNA, indicating that a substantial fraction of human genetic variation arises through mutations escaping MMR. Moreover, we identify a large set of recurrent indels that may serve to detect microsatellite instability (MSI). Indeed, using endometrial tumors with immunohistochemically proven MMR deficiency, we optimize a novel marker set capable of detecting MSI and show it to have greater specificity and selectivity than standard MSI tests. Additionally, we show that recurrent indels are enriched for the ‘DNA double-strand break repair by homologous recombination’ pathway. Consequently, DSB repair is reduced in MMR-deficient tumors, triggering a dose-dependent sensitivity of MMR-deficient tumor cultures to DSB inducers. Before a cell divides, it must first copy all of its genetic material. Any mistakes that are made during this process are called mutations. Mutations can give rise to new traits but are mostly harmful to the cells, or cause cancer; therefore, cells have evolved tools that can efficiently spot these mistakes and repair them. One of the main tools is called mismatch repair (MMR). Defects in the cell's mismatch repair tools can wreak havoc as this allows many mutations to accumulate. Zhao et al. looked at the genomes of tumors where mismatch repair was not working properly to see what makes these ‘MMR-deficient tumors’ different from other tumors. This revealed that MMR-deficient tumors have similar patterns of mutations to those seen in egg and sperm cells. This was unexpected and suggests that mutations that are not corrected by mismatch repair are an important source of the genetic differences found between different humans, and between humans and their ancestors. Identifying cancerous tumors that are MMR-deficient is vital, as these tumors tend not to respond to commonly used cancer treatments. However, current clinical methods to identify MMR-deficient tumors often fail or produce results that are difficult to interpret. MMR-deficient tumors commonly contain mutations called indels, where short fragments of DNA are inserted or deleted into longer DNA sequences. Zhao et al. have found 59 indels that can be used to detect MMR-deficient tumors, where each indel had been identified in several tumors taken from different tissues. This new approach allowed MMR-deficiency to be identified in several types of tumor, including colon and ovarian cancers, with greater sensitivity and accuracy than the existing methods. Zhao et al. also found that the indels in MMR-deficient tumors reduce the ability of the tumors to repair a type of DNA damage called double-strand breaks. In these, both strands of DNA that make up the double helix are broken and the DNA chain is severed. As this kind of damage is very harmful to a cell, making more double-strand breaks could therefore form part of a more effective treatment against MMR-deficient tumors; further research is needed to investigate this possibility.

• Publisher: eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Base Pair Mismatch / Biomarkers, Tumor - genetics / Cancer / Chemotherapy / Cytotoxicity / Deoxyribonucleic acid / Diagnostic tests / DNA / DNA biosynthesis / DNA Breaks, Double-Stranded / DNA damage / DNA double-strand break / DNA Fingerprinting / DNA methylation / DNA Mismatch Repair / DNA repair / Double-strand break repair / DSB inducer / Endometrial cancer / Endometrial Neoplasms - diagnosis / Endometrial Neoplasms - genetics / Endometrial Neoplasms - pathology / Endometrium / Epigenetics / Female / Gene expression / Genetic diversity / Genomes / Genomics / Genomics and Evolutionary Biology / Homologous Recombination / Human Biology and Medicine / Humans / INDEL Mutation / Microsatellite Instability / Microsatellite Repeats / Mismatch repair / mismatch repair deficiency / MSI / Mutation / mutation pattern / Neoplasm Staging / Ovarian Neoplasms - diagnosis / Ovarian Neoplasms - genetics / Ovarian Neoplasms - pathology / Polyclonal antibodies / Sensitivity and Specificity / Tumors / whole-genome sequencing