Genetic insights into biological mechanisms governing human ovarian ageing

Reproductive longevity is critical for fertility and impacts healthy ageing in women, yet insights into the underlying biological mechanisms and treatments to preserve it are limited. Here, we identify 290 genetic determinants of ovarian ageing, assessed using normal variation in age at natural menopause (ANM) in ~200,000 women of European ancestry. These common alleles influence clinical extremes of ANM; women in the top 1% of genetic susceptibility have an equivalent risk of premature ovarian insufficiency to those carrying monogenic FMR1 premutations. Identified loci implicate a broad range of DNA damage response (DDR) processes and include loss-of-function variants in key DDR genes. Integration with experimental models demonstrates that these DDR processes act across the life-course to shape the ovarian reserve and its rate of depletion. Furthermore, we demonstrate that experimental manipulation of DDR pathways highlighted by human genetics increase fertility and extend reproductive life in mice. Causal inference analyses using the identified genetic variants indicates that extending reproductive life in women improves bone health and reduces risk of type 2 diabetes, but increases risks of hormone-sensitive cancers. These findings provide insight into the mechanisms governing ovarian ageing, when they act across the life-course, and how they might be targeted by therapeutic approaches to extend fertility and prevent disease.

[1]  Sri V. V. Deevi,et al.  Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank , 2021, Nature Genetics.

[2]  Alexander E. Lopez,et al.  Advancing Human Genetics Research and Drug Discovery through Exome Sequencing of the UK Biobank , 2020, medRxiv.

[3]  S. Mccarroll,et al.  Chromosomal alterations among age-related haematopoietic clones in Japan , 2020, Nature.

[4]  D. Durocher,et al.  Endogenous DNA 3' Blocks Are Vulnerabilities for BRCA1 and BRCA2 Deficiency and Are Reversed by the APE2 Nuclease. , 2020, Molecular cell.

[5]  G. Livera,et al.  Homozygous hypomorphic BRCA2 variant in primary ovarian insufficiency without cancer or Fanconi anaemia trait , 2020, Journal of Medical Genetics.

[6]  J. Schimenti,et al.  Oocyte Elimination Through DNA Damage Signaling from CHK1/CHK2 to p53 and p63 , 2020, Genetics.

[7]  K. Helin,et al.  KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes , 2020, Nature Cell Biology.

[8]  A. Bortvin,et al.  Maximizing the ovarian reserve in mice by evading LINE-1 genotoxicity , 2020, Nature Communications.

[9]  M. McCarthy,et al.  Using human genetics to understand the disease impacts of testosterone in men and women , 2020, Nature Medicine.

[10]  N. Cherbuin,et al.  Lipid profile differences during menopause: a review with meta-analysis. , 2019, Menopause.

[11]  C. Andersen,et al.  Freezing of ovarian tissue and clinical opportunities. , 2019, Reproduction.

[12]  N. Panay,et al.  Premature Ovarian Insufficiency and Long-Term Health Consequences. , 2019, Current vascular pharmacology.

[13]  Robert C. Blanshard,et al.  Chromosome errors in human eggs shape natural fertility over reproductive life span , 2019, Science.

[14]  V. Beral,et al.  Type and timing of menopausal hormone therapy and breast cancer risk: individual participant meta-analysis of the worldwide epidemiological evidence , 2019, The Lancet.

[15]  G. Viglietto,et al.  The Genetics of Non-Syndromic Primary Ovarian Insufficiency: A Systematic Review , 2019, International journal of fertility & sterility.

[16]  InterLACE Study Team Variations in reproductive events across life: a pooled analysis of data from 505 147 women across 10 countries. , 2019, Human reproduction.

[17]  Wei Zhou,et al.  Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts , 2019, Nature Genetics.

[18]  J. Danesh,et al.  Association of menopausal characteristics and risk of coronary heart disease: a pan-European case–cohort analysis , 2019, International journal of epidemiology.

[19]  Hannes P. Eggertsson,et al.  Characterizing mutagenic effects of recombination through a sequence-level genetic map , 2019, Science.

[20]  Jacob C. Ulirsch,et al.  Genetic predisposition to mosaic Y chromosome loss in blood , 2019, bioRxiv.

[21]  Ping Liu,et al.  Transcriptome Landscape of Human Folliculogenesis Reveals Oocyte and Granulosa Cell Interactions. , 2018, Molecular cell.

[22]  S. Pacheco,et al.  ATR function is indispensable to allow proper mammalian follicle development , 2018, bioRxiv.

[23]  Anna Murray,et al.  Using genetics to understand the causal influence of higher BMI on depression , 2018, International journal of epidemiology.

[24]  Sina A. Gharib,et al.  Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis , 2018, bioRxiv.

[25]  S. Keeney,et al.  Shu complex SWS1-SWSAP1 promotes early steps in mouse meiotic recombination , 2018, Nature Communications.

[26]  P. Donnelly,et al.  The UK Biobank resource with deep phenotyping and genomic data , 2018, Nature.

[27]  James T. Webber,et al.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018, Nature.

[28]  Day Fr,et al.  Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk , 2018, Yearbook of Paediatric Endocrinology.

[29]  Birgit Sikkema-Raddatz,et al.  Improving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis , 2018, Nature Communications.

[30]  Jack Bowden,et al.  Improving the visualization, interpretation and analysis of two-sample summary data Mendelian randomization via the Radial plot and Radial regression , 2018, International journal of epidemiology.

[31]  Lars E. Borm,et al.  Molecular Architecture of the Mouse Nervous System , 2018, Cell.

[32]  Michael T. Zimmermann,et al.  Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas , 2018, Cell reports.

[33]  P. Andreassen,et al.  CHEK1 coordinates DNA damage signaling and meiotic progression in the male germline of mice , 2018, Human molecular genetics.

[34]  J. Manson,et al.  Cigarette Smoking and Risk of Early Natural Menopause , 2018, American journal of epidemiology.

[35]  A. Dobson,et al.  Body mass index and age at natural menopause: an international pooled analysis of 11 prospective studies , 2018, European Journal of Epidemiology.

[36]  S. Knapp,et al.  Oocyte DNA damage quality control requires consecutive interplay of CHK2 and CK1 to activate p63 , 2018, Nature Structural & Molecular Biology.

[37]  H. Kurahashi,et al.  The DNA Damage Checkpoint Eliminates Mouse Oocytes with Chromosome Synapsis Failure. , 2017, Molecular cell.

[38]  C. A. Toro,et al.  Elucidating the genetic architecture of reproductive ageing in the Japanese population , 2018, Nature Communications.

[39]  Yang I Li,et al.  An Expanded View of Complex Traits: From Polygenic to Omnigenic , 2017, Cell.

[40]  Rong Li,et al.  Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. , 2017, Cell stem cell.

[41]  Julian Lange,et al.  ATR is required to complete meiotic recombination in mice , 2017, Nature Communications.

[42]  S. Thompson,et al.  Interpreting findings from Mendelian randomization using the MR-Egger method , 2017, European Journal of Epidemiology.

[43]  R. Lobo Hormone-replacement therapy: current thinking , 2017, Nature Reviews Endocrinology.

[44]  Yue Han,et al.  AfterQC: automatic filtering, trimming, error removing and quality control for fastq data , 2017, BMC Bioinformatics.

[45]  Evan Z. Macosko,et al.  Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types , 2017, Nature Genetics.

[46]  H. Adami,et al.  Early menarche, nulliparity and the risk for premature and early natural menopause , 2017, Human reproduction.

[47]  M. Eijkemans,et al.  Unraveling the associations of age and menopause with cardiovascular risk factors in a large population-based study , 2017, BMC Medicine.

[48]  C. Pike Sex and the development of Alzheimer's disease , 2017, Journal of neuroscience research.

[49]  A. LaCroix,et al.  Ages at menarche and menopause and reproductive lifespan as predictors of exceptional longevity in women: the Women's Health Initiative , 2017, Menopause.

[50]  Samuel L. Wolock,et al.  A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. , 2016, Cell systems.

[51]  P. Kaldis,et al.  Inhibitory phosphorylation of Cdk1 mediates prolonged prophase I arrest in female germ cells and is essential for female reproductive lifespan , 2016, Cell Research.

[52]  Jeffrey T Leek,et al.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown , 2016, Nature Protocols.

[53]  Nicola K. Wilson,et al.  A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. , 2016, Blood.

[54]  J. Harper,et al.  Oocyte cryopreservation: where are we now? , 2016, Human reproduction update.

[55]  P. Visscher,et al.  Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets , 2016, Nature Genetics.

[56]  D. Melzer,et al.  Events in Early Life are Associated with Female Reproductive Ageing: A UK Biobank Study , 2016, Scientific Reports.

[57]  G. Davey Smith,et al.  Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator , 2016, Genetic epidemiology.

[58]  Anna Murray,et al.  Variants in the FTO and CDKAL1 loci have recessive effects on risk of obesity and type 2 diabetes, respectively , 2015, bioRxiv.

[59]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[60]  Daniel Marbach,et al.  Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics , 2016, PLoS Comput. Biol..

[61]  C. Aiken,et al.  Decreased ovarian reserve, dysregulation of mitochondrial biogenesis, and increased lipid peroxidation in female mouse offspring exposed to an obesogenic maternal diet , 2015, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[62]  P. Visscher,et al.  Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores , 2015, bioRxiv.

[63]  Andrew D. Johnson,et al.  Nature Genetics Advance Online Publication Large-scale Genomic Analyses Link Reproductive Aging to Hypothalamic Signaling, Breast Cancer Susceptibility and Brca1-mediated Dna Repair , 2022 .

[64]  T. Takeo,et al.  Superovulation Using the Combined Administration of Inhibin Antiserum and Equine Chorionic Gonadotropin Increases the Number of Ovulated Oocytes in C57BL/6 Female Mice , 2015, PloS one.

[65]  G. Kempermann Faculty Opinions recommendation of Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. , 2015 .

[66]  Joris M. Mooij,et al.  MAGMA: Generalized Gene-Set Analysis of GWAS Data , 2015, PLoS Comput. Biol..

[67]  Frances M. G. Pearl,et al.  Therapeutic opportunities within the DNA damage response , 2015, Nature Reviews Cancer.

[68]  C. Wijmenga,et al.  Gene expression analysis identifies global gene dosage sensitivity in cancer , 2015, Nature Genetics.

[69]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[70]  J. Hirschhorn,et al.  Biological interpretation of genome-wide association studies using predicted gene functions , 2015, Nature Communications.

[71]  B. Berger,et al.  Efficient Bayesian mixed model analysis increases association power in large cohorts , 2014, Nature Genetics.

[72]  Joris M. Mooij,et al.  MAGMA: Generalized Gene-Set Analysis of GWAS Data , 2015, PLoS Comput. Biol..

[73]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[74]  R. Veitia,et al.  Mutant cohesin in premature ovarian failure. , 2014, The New England journal of medicine.

[75]  Ewelina Bolcun-Filas,et al.  Reversal of Female Infertility by Chk2 Ablation Reveals the Oocyte DNA Damage Checkpoint Pathway , 2014, Science.

[76]  A. Ashworth,et al.  Population-based estimates of the prevalence of FMR1 expansion mutations in women with early menopause and primary ovarian insufficiency , 2013, Genetics in Medicine.

[77]  J. Donnez,et al.  Fertility preservation in women , 2013, Nature Reviews Endocrinology.

[78]  Lewis H Kuller,et al.  Menopausal hormone therapy and health outcomes during the intervention and extended poststopping phases of the Women's Health Initiative randomized trials. , 2013, JAMA.

[79]  A. Butterworth,et al.  Mendelian Randomization Analysis With Multiple Genetic Variants Using Summarized Data , 2013, Genetic epidemiology.

[80]  M. Robson,et al.  Impairment of BRCA1-Related DNA Double-Strand Break Repair Leads to Ovarian Aging in Mice and Humans , 2013, Science Translational Medicine.

[81]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[82]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[83]  Zhenbo Wang,et al.  Checkpoint kinase 1 is essential for meiotic cell cycle regulation in mouse oocytes , 2012, Cell cycle.

[84]  O. Fernandez-Capetillo,et al.  An extra allele of Chk1 limits oncogene-induced replicative stress and promotes transformation , 2012, The Journal of experimental medicine.

[85]  Roger Woodgate,et al.  Y-family DNA polymerases and their role in tolerance of cellular DNA damage , 2012, Nature Reviews Molecular Cell Biology.

[86]  Yan V. Sun,et al.  Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways , 2012, Nature Genetics.

[87]  S. Knapp,et al.  DNA Damage in Oocytes Induces a Switch of the Quality Control Factor TAp63α from Dimer to Tetramer , 2011, Cell.

[88]  P. Visscher,et al.  GCTA: a tool for genome-wide complex trait analysis. , 2011, American journal of human genetics.

[89]  Ayellet V. Segrè,et al.  Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits , 2010, PLoS genetics.

[90]  P. Plevani,et al.  Overlapping mechanisms promote postsynaptic RAD-51 filament disassembly during meiotic double-strand break repair. , 2010, Molecular cell.

[91]  Thomas W. Kelsey,et al.  Human Ovarian Reserve from Conception to the Menopause , 2009, PloS one.

[92]  J. Vaupel,et al.  Ageing populations: the challenges ahead , 2009, The Lancet.

[93]  C. Lambalk,et al.  Testing ovarian reserve to predict age at menopause. , 2009, Maturitas.

[94]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[95]  A. Constantinou,et al.  Remodeling of DNA replication structures by the branch point translocase FANCM , 2008, Proceedings of the National Academy of Sciences.

[96]  A. Cooney,et al.  Oocyte-Specific Deletion of Pten Causes Premature Activation of the Primordial Follicle Pool , 2008, Science.

[97]  P. Taylor,et al.  Diet-Induced Obesity in Female Mice Leads to Offspring Hyperphagia, Adiposity, Hypertension, and Insulin Resistance: A Novel Murine Model of Developmental Programming , 2008, Hypertension.

[98]  Andrzej Stasiak,et al.  The Fanconi anemia protein FANCM can promote branch migration of Holliday junctions and replication forks. , 2008, Molecular cell.

[99]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[100]  A. Yang,et al.  p63 protects the female germ line during meiotic arrest , 2006, Nature.

[101]  E. Salpeter,et al.  Meta‐analysis: effect of hormone‐replacement therapy on components of the metabolic syndrome in postmenopausal women , 2006, Diabetes, obesity & metabolism.

[102]  D. Grobbee,et al.  Postmenopausal status and early menopause as independent risk factors for cardiovascular disease: a meta-analysis , 2006, Menopause.

[103]  C. Mathew,et al.  A human ortholog of archaeal DNA repair protein Hef is defective in Fanconi anemia complementation group M , 2005, Nature Genetics.

[104]  P. Cohen,et al.  Extreme heterogeneity in the molecular events leading to the establishment of chiasmata during meiosis i in human oocytes. , 2005, American journal of human genetics.

[105]  J. Rosen,et al.  Chk1 is haploinsufficient for multiple functions critical to tumor suppression. , 2004, Cancer cell.

[106]  E. Revenkova,et al.  Cohesin SMC1β is required for meiotic chromosome dynamics, sister chromatid cohesion and DNA recombination , 2004, Nature Cell Biology.

[107]  T. Kunkel,et al.  Inactivation of Exonuclease 1 in mice results in DNA mismatch repair defects, increased cancer susceptibility, and male and female sterility. , 2003, Genes & development.

[108]  E. Appella,et al.  Chk2‐deficient mice exhibit radioresistance and defective p53‐mediated transcription , 2002, The EMBO journal.

[109]  S. Elledge,et al.  Chk1 is an essential kinase that is regulated by Atr and required for the G(2)/M DNA damage checkpoint. , 2000, Genes & development.

[110]  S. Ueno,et al.  Absence of Wee1 ensures the meiotic cell cycle in Xenopus oocytes. , 2000, Genes & development.

[111]  D. G. Rooij,et al.  Mouse MutS-like protein Msh5 is required for proper chromosome synapsis in male and female meiosis. , 1999, Genes & development.

[112]  Y. Matsuda,et al.  The mouse RecA-like gene Dmc1 is required for homologous chromosome synapsis during meiosis. , 1998, Molecular cell.

[113]  M. Handel,et al.  Meiotic prophase arrest with failure of chromosome synapsis in mice deficient for Dmc1, a germline-specific RecA homolog. , 1998, Molecular cell.

[114]  K. Wassarman,et al.  Zp3–cre, a transgenic mouse line for the activation or inactivation of loxP-flanked target genes specifically in the female germ line , 1997, Current Biology.