Inhibition of colorectal cancer genomic copy number alterations and chromosomal fragile site tumor suppressor FHIT and WWOX deletions by DNA mismatch repair

// Sohail Jahid 1, * , Jian Sun 1, * , Ozkan Gelincik 1 , Pedro Blecua 8 , Winfried Edelmann 2 , Raju Kucherlapati 3 , Kathy Zhou 4 , Maria Jasin 5 , Zeynep H. Gumus 6, 7 and Steven M. Lipkin 1 1 Departments of Medicine and Genetic Medicine, Weill Cornell Medicine, 10021, NY, USA 2 Department of Cell Biology and Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, 10461, NY, USA 3 Department of Genetics, Harvard Medical School, 02115, Boston, MA, USA 4 Department of Biostatistics and Epidemiology, Weill Cornell Medical College, 10021, NY, USA 5 Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 10065, NY, USA 6 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 10029, NY, USA 7 Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 10029, NY, USA 8 Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, 10065, NY, USA * These authors contributed equally to this work Correspondence to: Steven M. Lipkin, email: stl2012@med.cornell.edu Zeynep H. Gumus, email: zeynep.gumus@mssm.edu Keywords: mismatch repair, homologous recombination, homeologous recombination, colorectal cancer Received: January 16, 2017 Accepted: April 24, 2017 Published: May 10, 2017 ABSTRACT Homologous recombination (HR) enables precise DNA repair after DNA double strand breaks (DSBs) using identical sequence templates, whereas homeologous recombination (HeR) uses only partially homologous sequences. Homeologous recombination introduces mutations through gene conversion and genomic deletions through single-strand annealing (SSA). DNA mismatch repair (MMR) inhibits HeR, but the roles of mammalian MMR MutL homologues (MLH1, PMS2 and MLH3) proteins in HeR suppression are poorly characterized. Here, we demonstrate that mouse embryonic fibroblasts (MEFs) carrying Mlh1 , Pms2 , and Mlh3 mutations have higher HeR rates, by using 7,863 uniquely mapping paired direct repeat sequences (DRs) in the mouse genome as endogenous gene conversion and SSA reporters. Additionally, when DSBs are induced by gamma-radiation, Mlh1 , Pms2 and Mlh3 mutant MEFs have higher DR copy number alterations (CNAs), including DR CNA hotspots previously identified in mouse MMR-deficient colorectal cancer (dMMR CRC). Analysis of The Cancer Genome Atlas CRC data revealed that dMMR CRCs have higher genome-wide DR HeR rates than MMR proficient CRCs, and that dMMR CRCs have deletion hotspots in tumor suppressors FHIT/WWOX at chromosomal fragile sites FRA3B and FRA16D (which have elevated DSB rates) flanked by paired homologous DRs and inverted repeats (IR). Overall, these data provide novel insights into the MMR-dependent HeR inhibition mechanism and its role in tumor suppression.