The impact of germline variants in DNA repair pathways on survival and temozolomide toxicity in adults with glioma

Gliomas are highly fatal malignant brain tumors with prognostically relevant molecular subtypes. Genomic instability is a hallmark of cancer, including glioma, and DNA repair mechanisms are crucial to maintaining cell integrity. Temozolomide (TMZ), which utilizes specific DNA repair pathways in its mechanism of action, is one of the few standard-of-care drugs with a meaningful impact on IDH wildtype glioblastoma survival. However, its utility in non-glioblastomas is complicated by temozolomide-induced hypermutation. This study aims to identify if germline polymorphisms in DNA repair genes are associated with overall survival within glioma subtypes and if the polymorphisms modify survival in subjects treated with temozolomide. We utilized genotype data of 2078 adults with glioma collected through the UCSF Adult Glioma Study, Mayo Clinic, and TCGA, to study 1393 SNPs within 22 specific DNA repair genes on overall survival for all cases and for those with/without temozolomide exposure during first course of treatment. All models were fit separately for individuals grouped by major molecular subtypes. We identified four germline SNPs (within MLH1 , MSH4 , MSH3 , and MUTYH ) with a significant (p<0.00019) polygenic effect on survival, where the presence of at least one SNP decreased overall survival among grade 2 and 3 glioma cases with IDH mutated tumors (Hazard ratio per unit increase in number of present polymorphic sites, HR-PS=1.52, 95% confidence interval, CI: 1.26-1.83, p=1.3×10-5). In IDH mutant gliomas without somatic 1p/19q chromosomal arm codeletion, we identified a group of SNPs (in MSH4 , ERCC2 , and ERCC1 ) which showed a stepwise significant improvement on overall survival for each present germline polymorphism (HR-PS=0.67, 95% CI: 0.56-0.80, p=8.9×10-6). Within IDH mutant glioma cases, we also identified two mutations (rs1540354-T in MLH1 , rs71636247-G in MSH3 ) which were significantly associated with decreased overall survival only amongst those with known temozolomide usage (HR-PS=2.23, 95% CI: 1.55-3.20, p=1.56×10-5), with no survival effect observed in the non-temozolomide group (HR=0.90, 95% CI: 0.63-1.28, p=0.56). One SNP in MSH2 was suggestively associated (p<0.005) with altered IDH wildtype glioblastoma response to temozolomide (rs149630102-T, HR=1.74, 95% CI: 1.27-2.39, p=0.00052). Suggestive associations for other glioma subtypes are also reported. We found evidence that germline polygenic alterations within DNA repair pathways may alter prognosis and potentially modulate temozolomide toxicity in adults with glioma. Further validation and functional work are warranted to assess if these markers can assist clinicians in individually tailoring therapeutic treatments for adults with glioma tumors. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Work at the University of California, San Francisco, was supported by the National Institutes of Health (grant numbers T32CA112355, R01CA52689, P50CA097257, R01CA126831, R01CA139020, and R01CA266676), as well as the loglio Collective, the National Brain Tumor Foundation, the Stanley D. Lewis and Virginia S. Lewis Endowed Chair in Brain Tumor Research, the Robert Magnin Newman Endowed Chair in Neuro-oncology, and by donations from families and friends of John Berardi, Helen Glaser, Elvera Olsen, Raymond E. Cooper, and William Martinusen. The work at Mayo was supported by National Cancer Institute (NCI) grants CA230712, P50 CA108961, and CA139020; the National Brain Tumor Society; the loglio Collective; the Mayo Clinic; and the Ting Tsung and Wei Fong Chao Foundation. This publication was supported by the National Center for Research Resources and the National Center for Advancing Translational Sciences, National Institutes of Health, through UCSF-CTSI Grant Number UL1 RR024131. Its contents are solely the authors responsibility and do not necessarily represent the official views of the NIH. The authors wish to acknowledge study participants, the clinicians, and the research staff at the participating medical centers, the UCSF Cancer Registry, and the UCSF Neurosurgery Tissue Bank. The collection of cancer incidence data used in this study was supported by the California Department of Public Health pursuant to California Health and Safety Code Section 103885; Centers for Disease Control and Preventions (CDC) National Program of Cancer Registries, under cooperative agreement 5NU58DP006344; the National Cancer Institutes Surveillance, Epidemiology and End Results Program under contract HHSN261201800032I awarded to the University of California, San Francisco, contract HHSN261201800015I awarded to the University of Southern California, and contract HHSN261201800009I awarded to the Public Health Institute, Cancer Registry of Greater California. The ideas and opinions expressed herein are those of the author(s) and do not necessarily reflect the opinions of the State of California, Department of Public Health, the National Cancer Institute, and the Centers for Disease Control and Prevention or their Contractors and Subcontractors. All analyses, interpretations, and conclusions reached in this manuscript from the mortality data are those of the author(s) and not the State of California Department of Public Health. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The data used for the analyses described in this manuscript were obtained from the GTEx Portal on 04/26/23. The results published here are in whole or part based upon data generated by The Cancer Genome Atlas managed by the NCI and NHGRI. Information about TCGA can be found at http://cancergenome.nih.gov. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Collection of patient samples and associated clinicopathological information was undertaken with written informed consent and relevant ethical review board approval at the respective study centers in accordance with the tenets of the Declaration of Helsinki. Specifically informed consent and ethical board approval was obtained from the UCSF Committee on Human Research (USA) and the Mayo Clinic Office for Human Research Protection (USA). The diagnosis of glioma (ICDO-3 codes 9380-9480 or equivalent) was established through histology and somatic molecular markers in all cases in accordance with World Health Organization guidelines. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors. TCGA data is available at http://cancergenome.nih.gov. Data from the GTEx study is available at https://gtexportal.org/home/