Human longevity and variation in DNA damage response and repair: study of the contribution of sub-processes using competitive gene-set analysis

Birgit Debrabant*,1,8, Mette Soerensen*,1,2,8, Friederike Flachsbart3, Serena Dato4, Jonas Mengel-From1,2, Tinna Stevnsner5, Vilhelm A Bohr5,6, Torben A Kruse2, Stefan Schreiber3, Almut Nebel3, Kaare Christensen1,2,7, Qihua Tan1,2 and Lene Christiansen1,2

DNA-damage response and repair are crucial to maintain genetic stability, and are consequently considered central to aging and longevity. Here, we investigate whether this pathway overall associates to longevity, and whether specific sub-processes are more strongly associated with longevity than others. Data were applied on 592 SNPs from 77 genes involved in nine sub-processes: DNA-damage response, base excision repair (BER), nucleotide excision repair, mismatch repair, non-homologous end-joining,

DNA-damage response and repair are crucial to maintain genetic stability, and are consequently considered central to aging longevity. Here, we investigate whether this pathway overall associates to longevity, and whether specific sub-processes are strongly associated with longevity than others. Data were applied on 592 SNPs from 77 genes involved in nine sub-processes: DNA-damage response, base excision repair (BER), nucleotide excision repair, mismatch repair, non-homologous end-joining, homologous recombinational repair (HRR), RecQ helicase activities (RECQ), telomere functioning and mitochondrial DNA processes. The study population was 1089 long-lived and 736 middle-aged Danes. A self-contained set-based test of all SNPs displayed association with longevity (P-value ¼9.9 (cid:2)10(cid:3)5), supporting that the overall pathway could affect longevity. Investigation of the nine sub-processes using the competitive gene-set analysis by Wang et al indicated that BER, HRR and RECQ associated stronger with longevity than the respective remaining genes of the pathway (P-values¼0.004–0.048). For HRR and RECQ, only one gene contributed to the significance, whereas for BER several genes contributed. These associations did, however, generally not pass correction for multiple testing. Still, these findings indicate that, of the entire pathway, variation in BER might influence longevity the most. These modest sized P-values were not replicated in a German sample. might, though, be due to differences in genotyping procedures and investigated SNPs, potentially inducing differences in the coverage of gene regions. Specifically, five genes were not covered at all in the German data. Therefore, investigations in additional study populations are needed before final conclusion can be drawn. European Journal of Human Genetics advance online publication, 12 February 2014; doi:10.1038/ejhg.2013.299

Keywords: competitive gene-set analysis; human longevity; SNPs; case-control data; DNA-damage response and DNA

INTRODUCTION

lesions (eg induced by UV light); mismatch repair among other repair errors arising during DNA replication, while double-strand break repair (DSB) removes DSB breaks and complex lesions (eg induced by ionizing radiation or chemotherapeutics). DSB is divided into homologous recombinational repair and non-homologous end- joining. The RecQ helicases are among the other things important for ensuring the proper structure of the DNA helix during DNA repair.8 Severe mutations in two of the RecQ helicase genes, WRN and RECQL4, can cause Werner and Rothmund–Thomson premature aging syndromes, respectively.9,10 Additional mechanisms affect the stability of the chromosomes’ ends, the telomeres. Telomeres undergo shortening with every replication cycle in cells lacking telomerase until the telomeres reach a critical length at which the cell enters cellular senescence.11,12 Telomere shortening is associated with organismal aging; in humans, leukocyte telomere length is inversely related to age13,14 and is associated with an increased risk of age-

It has been estimated that about 25% of the variation in human life span is caused by genetic factors,1 a contribution which is likely to be minimal before age 60 years and most pronounced from age 85 years onwards.2 Candidate longevity genes encode proteins involved in several biological processes including DNA-damage response and DNA repair,3 which are essential for cellular function due to the constant exposure of living cells to various kinds of endogenous and exogenous agents. Such agents can damage diverse cellular components, including the DNA, and potentially induce genomic instability or mutagenesis. To maintain the integrity of the genome, DNA-damage response processes detect the DNA lesions and activate cell cycle arrest and DNA repair processes.4 The DNA repair processes each repair a certain subset of DNA lesions:5–7 base excision repair removes single-base lesions (eg oxidative lesions induced by reactive oxygen species (ROS)); nucleotide excision repair operates on bulky