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Park J, Peña-Tauber A, Talozzi L, Greicius MD, Guen YL. Genetic associations with human longevity are enriched for oncogenic genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.30.24311226. [PMID: 39132489 PMCID: PMC11312667 DOI: 10.1101/2024.07.30.24311226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Human lifespan is shaped by both genetic and environmental exposures and their interaction. To enable precision health, it is essential to understand how genetic variants contribute to earlier death or prolonged survival. In this study, we tested the association of common genetic variants and the burden of rare non-synonymous variants in a survival analysis, using age-at-death (N = 35,551, median [min, max] = 72.4 [40.9, 85.2]), and last-known-age (N = 358,282, median [min, max] = 71.9 [52.6, 88.7]), in European ancestry participants of the UK Biobank. The associations we identified seemed predominantly driven by cancer, likely due to the age range of the cohort. Common variant analysis highlighted three longevity-associated loci: APOE, ZSCAN23, and MUC5B. We identified six genes whose burden of loss-of-function variants is significantly associated with reduced lifespan: TET2, ATM, BRCA2, CKMT1B, BRCA1 and ASXL1. Additionally, in eight genes, the burden of pathogenic missense variants was associated with reduced lifespan: DNMT3A, SF3B1, CHL1, TET2, PTEN, SOX21, TP53 and SRSF2. Most of these genes have previously been linked to oncogenic-related pathways and some are linked to and are known to harbor somatic variants that predispose to clonal hematopoiesis. A direction-agnostic (SKAT-O) approach additionally identified significant associations with C1orf52, TERT, IDH2, and RLIM, highlighting a link between telomerase function and longevity as well as identifying additional oncogenic genes. Our results emphasize the importance of understanding genetic factors driving the most prevalent causes of mortality at a population level, highlighting the potential of early genetic testing to identify germline and somatic variants increasing one's susceptibility to cancer and/or early death.
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Affiliation(s)
- Junyoung Park
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Andrés Peña-Tauber
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Lia Talozzi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Michael D. Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Yann Le Guen
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, 94304, USA
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Bian Z, Wang L, Fan R, Sun J, Yu L, Xu M, Timmers PRHJ, Shen X, Wilson JF, Theodoratou E, Wu X, Li X. Genetic predisposition, modifiable lifestyles, and their joint effects on human lifespan: evidence from multiple cohort studies. BMJ Evid Based Med 2024; 29:255-263. [PMID: 38684374 DOI: 10.1136/bmjebm-2023-112583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 05/02/2024]
Abstract
OBJECTIVE To investigate the associations across genetic and lifestyle factors with lifespan. DESIGN A longitudinal cohort study. SETTING UK Biobank. PARTICIPANTS 353 742 adults of European ancestry, who were recruited from 2006 to 2010 and were followed up until 2021. EXPOSURES A polygenic risk score for lifespan with long (highest quintile) risk categories and a weighted healthy lifestyle score, including no current smoking, moderate alcohol consumption, regular physical activity, healthy body shape, adequate sleep duration, and a healthy diet, categorised into favourable, intermediate, and unfavourable lifestyles. MAIN OUTCOME MEASURES Lifespan defined as the date of death or the censor date minus the date of birth. RESULTS Of the included 353 742 participants of European ancestry with a median follow-up of 12.86 years, 24 239 death cases were identified. Participants were grouped into three genetically determined lifespan categories including long (20.1%), intermediate (60.1%), and short (19.8%), and into three lifestyle score categories including favourable (23.1%), intermediate (55.6%), and unfavourable (21.3%). The hazard ratio (HR) of death for individuals with a genetic predisposition to a short lifespan was 1.21 (95% CI 1.16 to 1.26) compared to those with a genetic predisposition to a long lifespan. The HR of death for individuals in the unfavourable lifestyle category was 1.78 (95% CI 1.71 to 1.85), compared with those in the favourable lifestyle category. Participants with a genetic predisposition to a short lifespan and an unfavourable lifestyle had 2.04 times (95% CI 1.87 to 2.22) higher rates of death compared with those with a genetic predisposition to a long lifespan and a favourable lifestyle. No multiplicative interaction was detected between the polygenic risk score of lifespan and the weighted healthy lifestyle score (p=0.10). The optimal combination of healthy lifestyles, including never smoking, regular physical activity, adequate sleep duration, and a healthy diet, was derived to decrease risk of premature death (death before 75 years). CONCLUSION Genetic and lifestyle factors were independently associated with lifespan. Adherence to healthy lifestyles could largely attenuate the genetic risk of a shorter lifespan or premature death. The optimal combination of healthy lifestyles could convey better benefits for a longer lifespan, regardless of genetic background.
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Affiliation(s)
- Zilong Bian
- Department of Big Data in Health Science, School of Public Health and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lijuan Wang
- Department of Big Data in Health Science, School of Public Health and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Rong Fan
- Department of Big Data in Health Science, School of Public Health and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jing Sun
- Department of Big Data in Health Science, School of Public Health and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lili Yu
- Department of Big Data in Health Science, School of Public Health and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meihong Xu
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Paul R H J Timmers
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xia Shen
- Department of Biostatistics, School of Public Health and The Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - James F Wilson
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xifeng Wu
- Department of Big Data in Health Science, School of Public Health and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Xue Li
- Department of Big Data in Health Science, School of Public Health and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
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Venkatesh SS, Ganjgahi H, Palmer DS, Coley K, Linchangco GV, Hui Q, Wilson P, Ho YL, Cho K, Arumäe K, Wittemans LBL, Nellåker C, Vainik U, Sun YV, Holmes C, Lindgren CM, Nicholson G. Characterising the genetic architecture of changes in adiposity during adulthood using electronic health records. Nat Commun 2024; 15:5801. [PMID: 38987242 PMCID: PMC11237142 DOI: 10.1038/s41467-024-49998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
Obesity is a heritable disease, characterised by excess adiposity that is measured by body mass index (BMI). While over 1,000 genetic loci are associated with BMI, less is known about the genetic contribution to adiposity trajectories over adulthood. We derive adiposity-change phenotypes from 24.5 million primary-care health records in over 740,000 individuals in the UK Biobank, Million Veteran Program USA, and Estonian Biobank, to discover and validate the genetic architecture of adiposity trajectories. Using multiple BMI measurements over time increases power to identify genetic factors affecting baseline BMI by 14%. In the largest reported genome-wide study of adiposity-change in adulthood, we identify novel associations with BMI-change at six independent loci, including rs429358 (APOE missense variant). The SNP-based heritability of BMI-change (1.98%) is 9-fold lower than that of BMI. The modest genetic correlation between BMI-change and BMI (45.2%) indicates that genetic studies of longitudinal trajectories could uncover novel biology of quantitative traits in adulthood.
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Affiliation(s)
- Samvida S Venkatesh
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Habib Ganjgahi
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Duncan S Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Kayesha Coley
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Gregorio V Linchangco
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Peter Wilson
- Atlanta VA Health Care System, Decatur, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kadri Arumäe
- Institute of Psychology, Faculty of Social Sciences, University of Tartu, Tartu, Estonia
| | - Laura B L Wittemans
- Novo Nordisk Research Centre Oxford, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Christoffer Nellåker
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Uku Vainik
- Institute of Psychology, Faculty of Social Sciences, University of Tartu, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
- Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, University of McGill, Montreal, Canada
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Chris Holmes
- Department of Statistics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, UK
- The Alan Turing Institute, London, UK
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Nuffield Department of Women's and Reproductive Health, Medical Sciences Division, University of Oxford, Oxford, UK.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Peng K, Liu Q, Wang N, Wang L, Duan X, Ding D. Association between smoking and alcohol drinking and benign adrenal tumors: a Mendelian randomization study. Endocrine 2024; 84:1206-1215. [PMID: 38409624 DOI: 10.1007/s12020-024-03714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND In recent years, the detection rate of adrenal tumors has increased, but it is unclear whether smoking and alcohol drinking are risk factors for benign adrenal tumors. The objective of this study is to employ Mendelian randomization (MR) analysis to explore the causal relationship between smoking, alcohol drinking and susceptibility to benign adrenal tumors. METHODS We acquired large-scale data from publicly accessible databases on genome-wide association studies (GWAS) pertaining to smoking, alcohol drinking and benign adrenal tumors. A total of 11 sets of instrumental variables (IVs) and 281 associated single nucleotide polymorphic (SNP) loci were identified. The Mendelian randomization analyses were conducted using inverse variance weighting (IVW), MR-Egger regression and weighted median estimation (WME) methods, in addition to sensitivity analyses. RESULTS There is no causal relationship between smoking status, alcohol drinking status, alcohol intake frequency, alcohol taken with meals, alcohol consumption and benign adrenal tumors, while pack years of smoking and cigarettes per day are risk factors for benign adrenal tumors. The IVW analysis revealed that both the pack years of smoking and cigarettes per day were positively associated with an increased risk of benign adrenal tumors (OR = 2.853, 95%CI = 1.384-5.878, p = 0.004; OR = 1.543, 95%CI = 1.147-2.076, p = 0.004). Two SNPs (rs8042849 in the analysis of pack years of smoking and rs8034191 in the analysis of cigarettes per day) significantly drove the observed causal effects. CONCLUSION Two-sample Mendelian randomization analysis showed a causal effect between smoking but not alcohol consumption and benign adrenal tumors.
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Affiliation(s)
- Kun Peng
- Department of Urology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, 450003, China
| | - Qingyuan Liu
- Department of Urology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, 450003, China
| | - Ning Wang
- Department of Urology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, 450003, China
| | - Lingdian Wang
- Department of Urology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, 450003, China
| | - Xiaoyu Duan
- Department of Urology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, 450003, China
| | - Degang Ding
- Department of Urology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, 450003, China.
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Capalbo A, de Wert G, Mertes H, Klausner L, Coonen E, Spinella F, Van de Velde H, Viville S, Sermon K, Vermeulen N, Lencz T, Carmi S. Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations. Hum Reprod Update 2024:dmae012. [PMID: 38805697 DOI: 10.1093/humupd/dmae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The genetic composition of embryos generated by in vitro fertilization (IVF) can be examined with preimplantation genetic testing (PGT). Until recently, PGT was limited to detecting single-gene, high-risk pathogenic variants, large structural variants, and aneuploidy. Recent advances have made genome-wide genotyping of IVF embryos feasible and affordable, raising the possibility of screening embryos for their risk of polygenic diseases such as breast cancer, hypertension, diabetes, or schizophrenia. Despite a heated debate around this new technology, called polygenic embryo screening (PES; also PGT-P), it is already available to IVF patients in some countries. Several articles have studied epidemiological, clinical, and ethical perspectives on PES; however, a comprehensive, principled review of this emerging field is missing. OBJECTIVE AND RATIONALE This review has four main goals. First, given the interdisciplinary nature of PES studies, we aim to provide a self-contained educational background about PES to reproductive specialists interested in the subject. Second, we provide a comprehensive and critical review of arguments for and against the introduction of PES, crystallizing and prioritizing the key issues. We also cover the attitudes of IVF patients, clinicians, and the public towards PES. Third, we distinguish between possible future groups of PES patients, highlighting the benefits and harms pertaining to each group. Finally, our review, which is supported by ESHRE, is intended to aid healthcare professionals and policymakers in decision-making regarding whether to introduce PES in the clinic, and if so, how, and to whom. SEARCH METHODS We searched for PubMed-indexed articles published between 1/1/2003 and 1/3/2024 using the terms 'polygenic embryo screening', 'polygenic preimplantation', and 'PGT-P'. We limited the review to primary research papers in English whose main focus was PES for medical conditions. We also included papers that did not appear in the search but were deemed relevant. OUTCOMES The main theoretical benefit of PES is a reduction in lifetime polygenic disease risk for children born after screening. The magnitude of the risk reduction has been predicted based on statistical modelling, simulations, and sibling pair analyses. Results based on all methods suggest that under the best-case scenario, large relative risk reductions are possible for one or more diseases. However, as these models abstract several practical limitations, the realized benefits may be smaller, particularly due to a limited number of embryos and unclear future accuracy of the risk estimates. PES may negatively impact patients and their future children, as well as society. The main personal harms are an unindicated IVF treatment, a possible reduction in IVF success rates, and patient confusion, incomplete counselling, and choice overload. The main possible societal harms include discarded embryos, an increasing demand for 'designer babies', overemphasis of the genetic determinants of disease, unequal access, and lower utility in people of non-European ancestries. Benefits and harms will vary across the main potential patient groups, comprising patients already requiring IVF, fertile people with a history of a severe polygenic disease, and fertile healthy people. In the United States, the attitudes of IVF patients and the public towards PES seem positive, while healthcare professionals are cautious, sceptical about clinical utility, and concerned about patient counselling. WIDER IMPLICATIONS The theoretical potential of PES to reduce risk across multiple polygenic diseases requires further research into its benefits and harms. Given the large number of practical limitations and possible harms, particularly unnecessary IVF treatments and discarded viable embryos, PES should be offered only within a research context before further clarity is achieved regarding its balance of benefits and harms. The gap in attitudes between healthcare professionals and the public needs to be narrowed by expanding public and patient education and providing resources for informative and unbiased genetic counselling.
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Affiliation(s)
- Antonio Capalbo
- Juno Genetics, Department of Reproductive Genetics, Rome, Italy
- Center for Advanced Studies and Technology (CAST), Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics & Society, CAPHRI-School for Public Health and Primary Care and GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Ghent University, Ghent, Belgium
- Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
| | - Liraz Klausner
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edith Coonen
- Departments of Clinical Genetics and Reproductive Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - Francesca Spinella
- Eurofins GENOMA Group Srl, Molecular Genetics Laboratories, Department of Scientific Communication, Rome, Italy
| | - Hilde Van de Velde
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
- Brussels IVF, UZ Brussel, Brussel, Belgium
| | - Stephane Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, France
- Laboratoire de Diagnostic Génétique, Unité de Génétique de l'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Karen Sermon
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
| | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Pisanu C, Congiu D, Meloni A, Paribello P, Patrinos GP, Severino G, Ardau R, Chillotti C, Manchia M, Squassina A. Dissecting the genetic overlap between severe mental disorders and markers of cellular aging: Identification of pleiotropic genes and druggable targets. Neuropsychopharmacology 2024; 49:1033-1041. [PMID: 38402365 PMCID: PMC11039620 DOI: 10.1038/s41386-024-01822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/17/2024] [Accepted: 02/04/2024] [Indexed: 02/26/2024]
Abstract
Patients with severe mental disorders such as bipolar disorder (BD), schizophrenia (SCZ) and major depressive disorder (MDD) show a substantial reduction in life expectancy, increased incidence of comorbid medical conditions commonly observed with advanced age and alterations of aging hallmarks. While severe mental disorders are heritable, the extent to which genetic predisposition might contribute to accelerated cellular aging is not known. We used bivariate causal mixture models to quantify the trait-specific and shared architecture of mental disorders and 2 aging hallmarks (leukocyte telomere length [LTL] and mitochondrial DNA copy number), and the conjunctional false discovery rate method to detect shared genetic loci. We integrated gene expression data from brain regions from GTEx and used different tools to functionally annotate identified loci and investigate their druggability. Aging hallmarks showed low polygenicity compared with severe mental disorders. We observed a significant negative global genetic correlation between MDD and LTL (rg = -0.14, p = 6.5E-10), and no significant results for other severe mental disorders or for mtDNA-cn. However, conditional QQ plots and bivariate causal mixture models pointed to significant pleiotropy among all severe mental disorders and aging hallmarks. We identified genetic variants significantly shared between LTL and BD (n = 17), SCZ (n = 55) or MDD (n = 19), or mtDNA-cn and BD (n = 4), SCZ (n = 12) or MDD (n = 1), with mixed direction of effects. The exonic rs7909129 variant in the SORCS3 gene, encoding a member of the retromer complex involved in protein trafficking and intracellular/intercellular signaling, was associated with shorter LTL and increased predisposition to all severe mental disorders. Genetic variants underlying risk of SCZ or MDD and shorter LTL modulate expression of several druggable genes in different brain regions. Genistein, a phytoestrogen with anti-inflammatory and antioxidant effects, was an upstream regulator of 2 genes modulated by variants associated with risk of MDD and shorter LTL. While our results suggest that shared heritability might play a limited role in contributing to accelerated cellular aging in severe mental disorders, we identified shared genetic determinants and prioritized different druggable targets and compounds.
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Affiliation(s)
- Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy.
| | - Donatella Congiu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Anna Meloni
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Pasquale Paribello
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Unit of Clinical Psychiatry, University Hospital Agency of Cagliari, Cagliari, Italy
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, School of Health Sciences, Department of Pharmacy, University of Patras, Patras, Greece
- College of Medicine and Health Sciences, Department of Genetics and Genomics, United Arab Emirates University, Al‑Ain, Abu Dhabi, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al‑Ain, Abu Dhabi, UAE
| | - Giovanni Severino
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Raffaella Ardau
- Unit of Clinical Pharmacology, University Hospital Agency of Cagliari, Cagliari, Italy
| | - Caterina Chillotti
- Unit of Clinical Pharmacology, University Hospital Agency of Cagliari, Cagliari, Italy
| | - Mirko Manchia
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Unit of Clinical Psychiatry, University Hospital Agency of Cagliari, Cagliari, Italy
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy.
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Thalén A, Ledberg A. Consequences of heterogeneity in aging: parental age at death predicts midlife all-cause mortality and hospitalization in a Swedish national birth cohort. BMC Geriatr 2024; 24:207. [PMID: 38424528 PMCID: PMC10903026 DOI: 10.1186/s12877-024-04786-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The processes that underlie aging may advance at different rates in different individuals and an advanced biological age, relative to the chronological age, is associated with increased risk of disease and death. Here we set out to quantify the extent to which heterogeneous aging shapes health outcomes in midlife by following a Swedish birth-cohort and using parental age at death as a proxy for biological age in the offspring. METHODS We followed a nationwide Swedish birth cohort (N = 89,688) between the ages of 39 and 66 years with respect to hospitalizations and death. Cox regressions were used to quantify the association, in the offspring, between parental age at death and all-cause mortality, as well as hospitalization for conditions belonging to the 10 most common ICD-10 chapters. RESULTS Longer parental lifespan was consistently associated with reduced risks of hospitalization and all-cause mortality. Differences in risk were mostly evident from before the age of 50 and persisted throughout the follow-up. Each additional decade of parental survival decreased the risk of offspring all-cause mortality by 22% and risks of hospitalizations by 9 to 20% across the 10 diseases categories considered. The number of deaths and hospitalizations attributable to having parents not living until old age were 1500 (22%) and 11,000 (11%) respectively. CONCLUSIONS Our findings highlight that increased parental lifespan is consistently associated with health benefits in the offspring across multiple outcomes and suggests that heterogeneous aging processes have clinical implications already in midlife.
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Affiliation(s)
- Anna Thalén
- Department of Public Health Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Anders Ledberg
- Department of Public Health Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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Qureshi D, Collister J, Allen NE, Kuźma E, Littlejohns T. Association between metabolic syndrome and risk of incident dementia in UK Biobank. Alzheimers Dement 2024; 20:447-458. [PMID: 37675869 PMCID: PMC10916994 DOI: 10.1002/alz.13439] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/05/2023] [Accepted: 07/29/2023] [Indexed: 09/08/2023]
Abstract
INTRODUCTION The association between metabolic syndrome (MetS) and incident dementia remains inconclusive. METHODS In 176,249 dementia-free UK Biobank participants aged ≥60 years at baseline, Cox proportional-hazards models were used to investigate the association between MetS and incident dementia. MetS was defined as the presence of ≥3 of the following: elevated waist circumference, triglycerides, blood pressure, blood glucose, and reduced high-density lipoprotein cholesterol. RESULTS Over 15 years of follow-up (median = 12.3), 5255 participants developed dementia. MetS was associated with an increased risk of incident dementia (hazard ratio [HR]: 1.12, 95% confidence interval [CI]: 1.06, 1.18). The association remained consistent when restricting to longer follow-up intervals: >5 to 10 years (HR: 1.17, 95% CI: 1.07, 1.27) and >10 years (HR: 1.22, 95% CI: 1.12, 1.32). Stronger associations were observed in those with ≥4 MetS components and in apolipoprotein-E (APOE)-ε4 non-carriers. DISCUSSION In this large population-based prospective cohort, MetS was associated with an increased risk of dementia. HIGHLIGHTS MetS was associated with a 12% increased risk of incident all-cause dementia. Associations remained similar after restricting the analysis to those with longer follow-up. The presence of four or five MetS components was significantly associated with dementia. Stronger associations were observed in those with a low genetic risk for dementia.
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Affiliation(s)
- Danial Qureshi
- Nuffield Department of Population HealthUniversity of OxfordOxfordUK
| | | | - Naomi E. Allen
- Nuffield Department of Population HealthUniversity of OxfordOxfordUK
- UK Biobank LtdStockportUK
| | - Elżbieta Kuźma
- Albertinen Haus Centre for Geriatrics and GerontologyUniversity of HamburgHamburgGermany
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Chen H, Zhou X, Hu J, Li S, Wang Z, Zhu T, Cheng H, Zhang G. Genetic insights into the association of statin and newer nonstatin drug target genes with human longevity: a Mendelian randomization analysis. Lipids Health Dis 2023; 22:220. [PMID: 38082436 PMCID: PMC10714481 DOI: 10.1186/s12944-023-01983-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND It remains controversial whether the long-term use of statins or newer nonstatin drugs has a positive effect on human longevity. Therefore, this study aimed to investigate the genetic associations between different lipid-lowering therapeutic gene targets and human longevity. METHODS Two-sample Mendelian randomization analyses were conducted. The exposures comprised genetic variants that proxy nine drug target genes mimicking lipid-lowering effects (LDLR, HMGCR, PCKS9, NPC1L1, APOB, CETP, LPL, APOC3, and ANGPTL3). Two large-scale genome-wide association study (GWAS) summary datasets of human lifespan, including up to 500,193 European individuals, were used as outcomes. The inverse-variance weighting method was applied as the main approach. Sensitivity tests were conducted to evaluate the robustness, heterogeneity, and pleiotropy of the results. Causal effects were further validated using expression quantitative trait locus (eQTL) data. RESULTS Genetically proxied LDLR variants, which mimic the effects of lowering low-density lipoprotein cholesterol (LDL-C), were associated with extended lifespan. This association was replicated in the validation set and was further confirmed in the eQTL summary data of blood and liver tissues. Mediation analysis revealed that the genetic mimicry of LDLR enhancement extended lifespan by reducing the risk of major coronary heart disease, accounting for 22.8% of the mediation effect. The genetically proxied CETP and APOC3 inhibitions also showed causal effects on increased life expectancy in both outcome datasets. The lipid-lowering variants of HMGCR, PCKS9, LPL, and APOB were associated with longer lifespans but did not causally increase extreme longevity. No statistical evidence was detected to support an association between NPC1L1 and lifespan. CONCLUSION This study suggests that LDLR is a promising genetic target for human longevity. Lipid-related gene targets, such as PCSK9, CETP, and APOC3, might potentially regulate human lifespan, thus offering promising prospects for developing newer nonstatin therapies.
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Affiliation(s)
- Han Chen
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029, People's Republic of China.
- Branch of Health Promotion and Education, Jiangsu Anti-aging Association, Nanjing, People's Republic of China.
| | - Xiaoying Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Jingwen Hu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Shuo Li
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Zi Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Tong Zhu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Hong Cheng
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Guoxin Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029, People's Republic of China.
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10
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von Berg J, McArdle PF, Häppölä P, Haessler J, Kooperberg C, Lemmens R, Pezzini A, Thijs V, Pulit SL, Kittner SJ, Mitchell BD, de Ridder J, van der Laan SW. Evidence of survival bias in the association between APOE-ϵ4 and age of ischemic stroke onset. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.01.23294385. [PMID: 38076909 PMCID: PMC10705635 DOI: 10.1101/2023.12.01.23294385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Large genome-wide association studies (GWAS) employing case-control study designs have now identified tens of loci associated with ischemic stroke (IS). As a complement to these studies, we performed GWAS in a case-only design to identify loci influencing age at onset (AAO) of ischemic stroke. Analyses were conducted in a Discovery cohort of 10,857 ischemic stroke cases using a linear regression framework. We meta-analyzed all SNPs with p-value < 1×10-5 in a sex-combined or sex-stratified analysis using summary data from two additional replication cohorts. In the women-only meta-analysis, we detected significant evidence for association of AAO with rs429358, an exonic variant in APOE that encodes for the APOE-ϵ4 allele. Each copy of the rs429358:T>C allele was associated with a 1.29 years earlier stroke AOO (meta p-value = 2.48×10-11). This APOE variant has previously been associated with increased mortality and ischemic stroke AAO. We hypothesized that the association with AAO may reflect a survival bias attributable to an age-related decline in mortality among APOE-ϵ4 carriers and have no association to stroke AAO per se. Using a simulation study, we found that a variant associated with overall mortality might indeed be detected with an AAO analysis. A variant with a two-fold increase on mortality risk would lead to an observed effect of AAO that is comparable to what we found. In conclusion, we detected a robust association of the APOE locus with stroke AAO and provided simulations to suggest that this association may be unrelated to ischemic stroke per se but related to a general survival bias.
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Affiliation(s)
- Joanna von Berg
- Center for Molecular Medicine, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Patrick F. McArdle
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Paavo Häppölä
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seatle, WA, USA
| | - Robin Lemmens
- University Hospitals Leuven, Department of Neurology, Leuven, Belgium
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, Leuven, Belgium
| | - Alessandro Pezzini
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Stroke Care Program, Department of Emergency, Parma University Hospital, Parma, Italy
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Vincent Thijs
- Stroke Theme, The Florey, Heidelberg, Victoria, Australia
- Department of Medicine, University of Melbourne, Victoria, Australia
- Department of Neurology, Austin Health, Heidelberg, Victoria, Australia
| | | | - Sara L. Pulit
- Center for Molecular Medicine, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Steven J. Kittner
- Geriatric Research and Education Clinical Center, VA Maryland Health Care System, Baltimore, MD, USA
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Braxton D. Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatric Research and Education Clinical Center, VA Maryland Health Care System, Baltimore, MD, USA
| | - Jeroen de Ridder
- Center for Molecular Medicine, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Center of Population Health and Genomics, University of Virginia, Charlottesville, VA, USA
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11
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Gebski V, Silva SSM, Byth K, Jenkins A, Keech A. Improving efficiency of fitting Cox proportional hazards models for time-to-event outcomes in genome-wide association studies (GWAS). BIOINFORMATICS ADVANCES 2023; 3:vbad148. [PMID: 37928342 PMCID: PMC10625458 DOI: 10.1093/bioadv/vbad148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
Summary Technologies identifying single nucleotide polymorphisms (SNPs) in DNA sequencing yield an avalanche of data requiring analysis and interpretation. Standard methods may require many weeks of processing time. The use of statistical methods requiring data sorting, matrix inversions of a high-dimension and replication in subsets of the data on multiple outcomes exacerbate these times.A method which reduces the computational time in problems with time-to-event outcomes and hundreds of thousands/millions of SNPs using Cox-Snell residuals after fitting the Cox proportional hazards model (PH) to a fixed set of concomitant variables is proposed. This yields coefficients for SNP effect from a Cox-Snell adjusted Poisson model and shows a high concordance to the adjusted PH model.The method is illustrated with a sample of 10 000 SNPs from a genome-wide association study in a diabetic population. The gain in processing efficiency using the proposed method based on Poisson modelling can be as high as 62%. This could result in saving of over three weeks processing time if 5 million SNPs require analysis. The method involves only a single predictor variable (SNP), offering a simpler, computationally more stable approach to examining and identifying SNP patterns associated with the outcome(s) allowing for a faster development of genetic signatures. Use of deviance residuals from the PH model to screen SNPs demonstrates a large discordance rate at a 0.2% threshold of concordance. This rate is 15 times larger than that based on the Cox-Snell residuals from the Cox-Snell adjusted Poisson model. Availability and implementation The method is simple to implement as the procedures are available in most statistical packges. The approach involves obtaining Cox-Snell residuals from a PH model, to a binary time-to-event outcome, for factors which need to be common when assessing each SNP. Each SNP is then fitted as a predictor to the outcome of interest using a Poisson model with the Cox-Snell as the exposure variable.
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Affiliation(s)
- Val Gebski
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, NSW 1450, Australia
| | - S Sandun M Silva
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, NSW 1450, Australia
| | - Karen Byth
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, NSW 1450, Australia
| | - Alicia Jenkins
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, NSW 1450, Australia
| | - Anthony Keech
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, NSW 1450, Australia
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Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson MR. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. Am J Hum Genet 2023; 110:1549-1563. [PMID: 37543033 PMCID: PMC10502738 DOI: 10.1016/j.ajhg.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 08/07/2023] Open
Abstract
There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data.
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Affiliation(s)
- Sven E Ojavee
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Liza Darrous
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia; Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Zoltan Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
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Zhou J, Chen C, Wang J, Liu S, Li X, Wei Y, Ye L, Ye J, Kraus VB, Lv Y, Shi X. Development and Validation of a Lifespan Prediction Model in Chinese Adults Aged 65 Years or Older. J Am Med Dir Assoc 2023; 24:1068-1073.e6. [PMID: 36965505 PMCID: PMC10335838 DOI: 10.1016/j.jamda.2023.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/01/2023] [Accepted: 02/15/2023] [Indexed: 03/27/2023]
Abstract
OBJECTIVES Previous studies investigated factors associated with mortality. Nevertheless, evidence is limited regarding the determinants of lifespan. We aimed to develop and validate a lifespan prediction model based on the most important predictors. DESIGN A prospective cohort study. SETTING AND PARTICIPANTS A total of 23,892 community-living adults aged 65 years or older with confirmed death records between 1998 and 2018 from 23 provinces in China. METHODS Information including demographic characteristics, lifestyle, functional health, and prevalence of diseases was collected. The risk prediction model was generated using multivariate linear regression, incorporating the most important predictors identified by the Lasso selection method. We used 1000 bootstrap resampling for the internal validation. The model performance was assessed by adjusted R2, root mean square error (RMSE), mean absolute error (MAE), and intraclass correlation coefficient (ICC). RESULTS Twenty-one predictors were included in the final lifespan prediction model. Older adults with longer lifespans were characterized by older age at baseline, female, minority race, living in rural areas, married, with healthier lifestyles and more leisure engagement, better functional status, and absence of diseases. The predicted lifespans were highly consistent with observed lifespans, with an adjusted R2 of 0.893. RMSE was 2.86 (95% CI 2.84-2.88) and MAE was 2.18 (95% CI 2.16-2.20) years. The ICC between observed and predicted lifespans was 0.971 (95% CI 0.971-0.971). CONCLUSIONS AND IMPLICATIONS The lifespan prediction model was validated with good performance, the web-based prediction tool can be easily applied in practical use as it relies on all easily accessible variables.
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Affiliation(s)
- Jinhui Zhou
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chen Chen
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Wang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sixin Liu
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China; Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xinwei Li
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China; Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Yuan Wei
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China; Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Lihong Ye
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China; School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaming Ye
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China; Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Virginia Byers Kraus
- Duke Molecular Physiology Institute and Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Yuebin Lv
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoming Shi
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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14
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Barry CJ, Carslake D, Wade KH, Sanderson E, Davey Smith G. Comparison of intergenerational instrumental variable analyses of body mass index and mortality in UK Biobank. Int J Epidemiol 2023; 52:545-561. [PMID: 35947758 PMCID: PMC10114047 DOI: 10.1093/ije/dyac159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/25/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND An increasing proportion of people have a body mass index (BMI) classified as overweight or obese and published studies disagree whether this will be beneficial or detrimental to health. We applied and evaluated two intergenerational instrumental variable methods to estimate the average causal effect of BMI on mortality in a cohort with many deaths: the parents of UK Biobank participants. METHODS In Cox regression models, parental BMI was instrumented by offspring BMI using an 'offspring as instrument' (OAI) estimation and by offspring BMI-related genetic variants in a 'proxy-genotype Mendelian randomization' (PGMR) estimation. RESULTS Complete-case analyses were performed in parents of 233 361 UK Biobank participants with full phenotypic, genotypic and covariate data. The PGMR method suggested that higher BMI increased mortality with hazard ratios per kg/m2 of 1.02 (95% CI: 1.01, 1.04) for mothers and 1.04 (95% CI: 1.02, 1.05) for fathers. The OAI method gave considerably higher estimates, which varied according to the parent-offspring pairing between 1.08 (95% CI: 1.06, 1.10; mother-son) and 1.23 (95% CI: 1.16, 1.29; father-daughter). CONCLUSION Both methods supported a causal role of higher BMI increasing mortality, although caution is required regarding the immediate causal interpretation of these exact values. Evidence of instrument invalidity from measured covariates was limited for the OAI method and minimal for the PGMR method. The methods are complementary for interrogating the average putative causal effects because the biases are expected to differ between them.
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Affiliation(s)
- Ciarrah-Jane Barry
- Medical Research Council (MRC) Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
- Department of Mathematical Sciences, University of Bath, Bath, UK
| | - David Carslake
- Medical Research Council (MRC) Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Kaitlin H Wade
- Medical Research Council (MRC) Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Eleanor Sanderson
- Medical Research Council (MRC) Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council (MRC) Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
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15
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Genetic scores for predicting longevity in the Croatian oldest-old population. PLoS One 2023; 18:e0279971. [PMID: 36735720 PMCID: PMC9897585 DOI: 10.1371/journal.pone.0279971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 02/04/2023] Open
Abstract
Longevity is a hallmark of successful ageing and a complex trait with a significant genetic component. In this study, 43 single nucleotide polymorphisms (SNPs) were chosen from the literature and genotyped in a Croatian oldest-old sample (85+ years, sample size (N) = 314), in order to determine whether any of these SNPs have a significant effect on reaching the age thresholds for longevity (90+ years, N = 212) and extreme longevity (95+ years, N = 84). The best models were selected for both survival ages using multivariate logistic regression. In the model for reaching age 90, nine SNPs explained 20% of variance for survival to that age, while the 95-year model included five SNPs accounting for 9.3% of variance. The two SNPs that showed the most significant association (p ≤ 0.01) with longevity were TERC rs16847897 and GHRHR rs2267723. Unweighted and weighted Genetic Longevity Scores (uGLS and wGLS) were calculated and their predictive power was tested. All four scores showed significant correlation with age at death (p ≤ 0.01). They also passed the ROC curve test with at least 50% predictive ability, but wGLS90 stood out as the most accurate score, with a 69% chance of accurately predicting survival to the age of 90.
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Iannuzzi V, Bacalini MG, Franceschi C, Giuliani C. The role of genetics and epigenetics in sex differences in human survival. GENUS 2023. [DOI: 10.1186/s41118-023-00181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AbstractSex differences in human survival have been extensively investigated in many studies that have in part uncovered the biological determinants that promote a longer life in females with respect to males. Moreover, researches performed in the past years have prompted increased awareness about the biological effects of environmental factors that can modulate the magnitude of the sex gap in survival. Besides the genetic background, epigenetic modifications like DNA methylation, that can modulate cell function, have been particularly studied in this framework. In this review, we aim to summarize the role of the genetic and epigenetic mechanisms in promoting female advantage from the early in life (“INNATE” features), and in influencing the magnitude of the gap in sex differences in survival and ageing (“VARIABLE” features). After briefly discussing the biological bases of sex determination in humans, we will provide much evidence showing that (i) “innate” mechanisms common to all males and to all females (both genetic and epigenetic) play a major role in sex differences in lifespan; (ii) “variable” genetic and epigenetic patterns, that vary according to context, populations and exposures to different environments, can affect the magnitude of the gap in sex differences in survival. Then we will describe recent findings in the use of epigenetic clocks to uncover sex differences in biological age and thus potentially in mortality. In conclusion, we will discuss how environmental factors cannot be kept apart from the biological factors providing evidence from the field of human ecology.
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Venkatesh SS, Ganjgahi H, Palmer DS, Coley K, Wittemans LBL, Nellaker C, Holmes C, Lindgren CM, Nicholson G. The genetic architecture of changes in adiposity during adulthood. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.09.23284364. [PMID: 36711652 PMCID: PMC9882550 DOI: 10.1101/2023.01.09.23284364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Obesity is a heritable disease, characterised by excess adiposity that is measured by body mass index (BMI). While over 1,000 genetic loci are associated with BMI, less is known about the genetic contribution to adiposity trajectories over adulthood. We derive adiposity-change phenotypes from 1.5 million primary-care health records in over 177,000 individuals in UK Biobank to study the genetic architecture of weight-change. Using multiple BMI measurements over time increases power to identify genetic factors affecting baseline BMI. In the largest reported genome-wide study of adiposity-change in adulthood, we identify novel associations with BMI-change at six independent loci, including rs429358 (a missense variant in APOE). The SNP-based heritability of BMI-change (1.98%) is 9-fold lower than that of BMI, and higher in women than in men. The modest genetic correlation between BMI-change and BMI (45.2%) indicates that genetic studies of longitudinal trajectories could uncover novel biology driving quantitative trait values in adulthood.
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Affiliation(s)
- Samvida S. Venkatesh
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, UK
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
| | | | - Duncan S. Palmer
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Sciences Division, University of Oxford, UK
| | - Kayesha Coley
- Department of Population Health Sciences, University of Leicester, UK
| | - Laura B. L. Wittemans
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Sciences Division, University of Oxford, UK
| | - Christoffer Nellaker
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Sciences Division, University of Oxford, UK
| | - Chris Holmes
- Department of Statistics, University of Oxford, UK
- Nuffield Department of Medicine, Medical Sciences Division, University of Oxford, UK
- The Alan Turing Institute, London, UK
| | - Cecilia M. Lindgren
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, UK
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Sciences Division, University of Oxford, UK
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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18
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Pallares LF, Lea AJ, Han C, Filippova EV, Andolfatto P, Ayroles JF. Dietary stress remodels the genetic architecture of lifespan variation in outbred Drosophila. Nat Genet 2023; 55:123-129. [PMID: 36550361 DOI: 10.1038/s41588-022-01246-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Evolutionary theory suggests that lifespan-reducing alleles should be purged from the gene pool, and yet decades of genome-wide association and model organism studies have shown that they persist. One potential explanation is that alleles that regulate lifespan do so only in certain environmental contexts. We exposed outbred Drosophila to control and high-sugar diets and genotyped more than 10,000 adult flies to track allele frequency changes over the course of a single adult lifespan. We identified thousands of lifespan-associated alleles associated with early versus late-life trade-offs, late-onset effects and genotype-by-environment interactions. Remarkably, a third of lifespan-associated genetic variation had environmentally dependent effects on lifespan. We find that lifespan-reducing alleles are often recently derived, have stronger effects on a high-sugar diet and show signatures of selection in wild Drosophila populations, consistent with the evolutionary mismatch hypothesis. Our results provide insight into the highly polygenic and context-dependent genetic architecture of lifespan variation and the evolutionary processes that shape this key trait.
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Affiliation(s)
- Luisa F Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Amanda J Lea
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Clair Han
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Elena V Filippova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | - Julien F Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA.
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19
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Genetic risk factors have a substantial impact on healthy life years. Nat Med 2022; 28:1893-1901. [PMID: 36097220 PMCID: PMC9499866 DOI: 10.1038/s41591-022-01957-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/19/2022] [Indexed: 12/15/2022]
Abstract
The impact of genetic variation on overall disease burden has not been comprehensively evaluated. We introduce an approach to estimate the effect of genetic risk factors on disability-adjusted life years (DALYs; 'lost healthy life years'). We use genetic information from 735,748 individuals and consider 80 diseases. Rare variants had the highest effect on DALYs at the individual level. Among common variants, rs3798220 (LPA) had the strongest individual-level effect, with 1.18 DALYs from carrying 1 versus 0 copies. Being in the top 10% versus the bottom 90% of a polygenic score for multisite chronic pain had an effect of 3.63 DALYs. Some common variants had a population-level effect comparable to modifiable risk factors such as high sodium intake and low physical activity. Attributable DALYs vary between males and females for some genetic exposures. Genetic risk factors can explain a sizable number of healthy life years lost both at the individual and population level.
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20
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Bin-Jumah MN, Nadeem MS, Gilani SJ, Al-Abbasi FA, Ullah I, Alzarea SI, Ghoneim MM, Alshehri S, Uddin A, Murtaza BN, Kazmi I. Genes and Longevity of Lifespan. Int J Mol Sci 2022; 23:ijms23031499. [PMID: 35163422 PMCID: PMC8836117 DOI: 10.3390/ijms23031499] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/04/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
Aging is a complex process indicated by low energy levels, declined physiological activity, stress induced loss of homeostasis leading to the risk of diseases and mortality. Recent developments in medical sciences and an increased availability of nutritional requirements has significantly increased the average human lifespan worldwide. Several environmental and physiological factors contribute to the aging process. However, about 40% human life expectancy is inherited among generations, many lifespan associated genes, genetic mechanisms and pathways have been demonstrated during last decades. In the present review, we have evaluated many human genes and their non-human orthologs established for their role in the regulation of lifespan. The study has included more than fifty genes reported in the literature for their contributions to the longevity of life. Intact genomic DNA is essential for the life activities at the level of cell, tissue, and organ. Nucleic acids are vulnerable to oxidative stress, chemotherapies, and exposure to radiations. Efficient DNA repair mechanisms are essential for the maintenance of genomic integrity, damaged DNA is not replicated and transferred to next generations rather the presence of deleterious DNA initiates signaling cascades leading to the cell cycle arrest or apoptosis. DNA modifications, DNA methylation, histone methylation, histone acetylation and DNA damage can eventually lead towards apoptosis. The importance of calorie restriction therapy in the extension of lifespan has also been discussed. The role of pathways involved in the regulation of lifespan such as DAF-16/FOXO (forkhead box protein O1), TOR and JNK pathways has also been particularized. The study provides an updated account of genetic factors associated with the extended lifespan and their interactive contributory role with cellular pathways.
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Affiliation(s)
- May Nasser Bin-Jumah
- Biology Department, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
- Environment and Biomaterial Unit, Health Sciences Research Center, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence: (M.S.N.); (I.K.)
| | - Sadaf Jamal Gilani
- Department of Basic Health Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Inam Ullah
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan;
| | - Sami I. Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Aziz Uddin
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 21300, Pakistan;
| | - Bibi Nazia Murtaza
- Department of Zoology, Abbottabad University of Science and Technology (AUST), Abbottabad 22310, Pakistan;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence: (M.S.N.); (I.K.)
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21
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Matta JA, Gu S, Davini WB, Bredt DS. Nicotinic acetylcholine receptor redux: Discovery of accessories opens therapeutic vistas. Science 2021; 373:373/6556/eabg6539. [PMID: 34385370 DOI: 10.1126/science.abg6539] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The neurotransmitter acetylcholine (ACh) acts in part through a family of nicotinic ACh receptors (nAChRs), which mediate diverse physiological processes including muscle contraction, neurotransmission, and sensory transduction. Pharmacologically, nAChRs are responsible for tobacco addiction and are targeted by medicines for hypertension and dementia. Nicotinic AChRs were the first ion channels to be isolated. Recent studies have identified molecules that control nAChR biogenesis, trafficking, and function. These nAChR accessories include protein and chemical chaperones as well as auxiliary subunits. Whereas some factors act on many nAChRs, others are receptor specific. Discovery of these regulatory mechanisms is transforming nAChR research in cells and tissues ranging from central neurons to spinal ganglia to cochlear hair cells. Nicotinic AChR-specific accessories also enable drug discovery on high-confidence targets for psychiatric, neurological, and auditory disorders.
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Affiliation(s)
| | | | - Weston B Davini
- Neuroscience Discovery, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA 92121, USA
| | - David S Bredt
- Neuroscience Discovery, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA 92121, USA.
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22
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Ojavee SE, Kousathanas A, Trejo Banos D, Orliac EJ, Patxot M, Läll K, Mägi R, Fischer K, Kutalik Z, Robinson MR. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. Nat Commun 2021; 12:2337. [PMID: 33879782 PMCID: PMC8058085 DOI: 10.1038/s41467-021-22538-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/17/2021] [Indexed: 01/18/2023] Open
Abstract
While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches.
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Affiliation(s)
- Sven E Ojavee
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
| | | | - Daniel Trejo Banos
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Etienne J Orliac
- Scientific Computing and Research Support Unit, University of Lausanne, Lausanne, Switzerland
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Kristi Läll
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Krista Fischer
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Zoltan Kutalik
- University Center for Primary Care and Public Health, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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23
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Gutman D, Lidzbarsky G, Milman S, Gao T, Sin-Chan P, Gonzaga‐Jauregui C, Deelen J, Shuldiner AR, Barzilai N, Atzmon G. Similar burden of pathogenic coding variants in exceptionally long-lived individuals and individuals without exceptional longevity. Aging Cell 2020; 19:e13216. [PMID: 32860726 PMCID: PMC7576295 DOI: 10.1111/acel.13216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/22/2020] [Accepted: 07/12/2020] [Indexed: 12/13/2022] Open
Abstract
Centenarians (exceptionally long‐lived individuals—ELLI) are a unique segment of the population, exhibiting long human lifespan and healthspan, despite generally practicing similar lifestyle habits as their peers. We tested disease‐associated mutation burden in ELLI genomes by determining the burden of pathogenic variants reported in the ClinVar and HGMD databases using data from whole exome sequencing (WES) conducted in a cohort of ELLI, their offspring, and control individuals without antecedents of familial longevity (n = 1879), all descendent from the founder population of Ashkenazi Jews. The burden of pathogenic variants did not differ between the three groups. Additional analyses of variants subtypes and variant effect predictor (VEP) biotype frequencies did not reveal a decrease of pathogenic or loss‐of‐function (LoF) variants in ELLI and offspring compared to the control group. Case–control pathogenic variants enrichment analyses conducted in ELLI and controls also did not identify significant differences in any of the variants between the groups and polygenic risk scores failed to provide a predictive model. Interestingly, cancer and Alzheimer's disease‐associated variants were significantly depleted in ELLI compared to controls, suggesting slower accumulation of mutation. That said, polygenic risk score analysis failed to find any predictive variants among the functional variants tested. The high similarity in the burden of pathogenic variation between ELLI and individuals without familial longevity supports the notion that extension of lifespan and healthspan in ELLI is not a consequence of pathogenic variant depletion but rather a result of other genomic, epigenomic, or potentially nongenomic properties.
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Affiliation(s)
- Danielle Gutman
- Faculty of Natural Sciences University of Haifa Haifa Israel
| | | | - Sofiya Milman
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
| | - Tina Gao
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
| | | | | | - Joris Deelen
- Max Planck Institute for Biology of Ageing Cologne Germany
- Molecular Epidemiology Department of Biochemical Data Sciences Leiden University Medical Center Leiden The Netherlands
| | | | - Nir Barzilai
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
- Genetic, Institute for Aging Research and the Diabetes Research Center Albert Einstein College of Medicine Bronx New York USA
| | - Gil Atzmon
- Faculty of Natural Sciences University of Haifa Haifa Israel
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
- Genetic, Institute for Aging Research and the Diabetes Research Center Albert Einstein College of Medicine Bronx New York USA
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24
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Zhang Q, Sidorenko J, Couvy-Duchesne B, Marioni RE, Wright MJ, Goate AM, Marcora E, Huang KL, Porter T, Laws SM, Sachdev PS, Mather KA, Armstrong NJ, Thalamuthu A, Brodaty H, Yengo L, Yang J, Wray NR, McRae AF, Visscher PM. Risk prediction of late-onset Alzheimer's disease implies an oligogenic architecture. Nat Commun 2020; 11:4799. [PMID: 32968074 PMCID: PMC7511365 DOI: 10.1038/s41467-020-18534-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/25/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic association studies have identified 44 common genome-wide significant risk loci for late-onset Alzheimer's disease (LOAD). However, LOAD genetic architecture and prediction are unclear. Here we estimate the optimal P-threshold (Poptimal) of a genetic risk score (GRS) for prediction of LOAD in three independent datasets comprising 676 cases and 35,675 family history proxy cases. We show that the discriminative ability of GRS in LOAD prediction is maximised when selecting a small number of SNPs. Both simulation results and direct estimation indicate that the number of causal common SNPs for LOAD may be less than 100, suggesting LOAD is more oligogenic than polygenic. The best GRS explains approximately 75% of SNP-heritability, and individuals in the top decile of GRS have ten-fold increased odds when compared to those in the bottom decile. In addition, 14 variants are identified that contribute to both LOAD risk and age at onset of LOAD.
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Affiliation(s)
- Qian Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Baptiste Couvy-Duchesne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edoardo Marcora
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kuan-Lin Huang
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tenielle Porter
- Collaborative Genomics Group, Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Simon M Laws
- Collaborative Genomics Group, Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Neuroscience Research Australia, Sydney, NSW, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Murdoch University, Perth, WA, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Neuroscience Research Australia, Sydney, NSW, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Dementia Centre for Research Collaboration, University of New South Wales, Sydney, NSW, Australia
| | - Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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25
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Meisner A, Kundu P, Zhang YD, Lan LV, Kim S, Ghandwani D, Pal Choudhury P, Berndt SI, Freedman ND, Garcia-Closas M, Chatterjee N. Combined Utility of 25 Disease and Risk Factor Polygenic Risk Scores for Stratifying Risk of All-Cause Mortality. Am J Hum Genet 2020; 107:418-431. [PMID: 32758451 DOI: 10.1016/j.ajhg.2020.07.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
While genome-wide association studies have identified susceptibility variants for numerous traits, their combined utility for predicting broad measures of health, such as mortality, remains poorly understood. We used data from the UK Biobank to combine polygenic risk scores (PRS) for 13 diseases and 12 mortality risk factors into sex-specific composite PRS (cPRS). These cPRS were moderately associated with all-cause mortality in independent data within the UK Biobank: the estimated hazard ratios per standard deviation were 1.10 (95% confidence interval: 1.05, 1.16) and 1.15 (1.10, 1.19) for women and men, respectively. Differences in life expectancy between the top and bottom 5% of the cPRS were estimated to be 4.79 (1.76, 7.81) years and 6.75 (4.16, 9.35) years for women and men, respectively. These associations were substantially attenuated after adjusting for non-genetic mortality risk factors measured at study entry (i.e., middle age for most participants). The cPRS may be useful in counseling younger individuals at higher genetic risk of mortality on modification of non-genetic factors.
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Affiliation(s)
- Allison Meisner
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Prosenjit Kundu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Yan Dora Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Statistics, University of Hong Kong, 999077, Hong Kong
| | - Lauren V Lan
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sungwon Kim
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Disha Ghandwani
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Indian Statistical Institute, Kolkata, West Bengal 700108, India
| | - Parichoy Pal Choudhury
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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26
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Lee MA, McMahon G, Karhunen V, Wade KH, Corbin LJ, Hughes DA, Smith GD, Lawlor DA, Jarvelin MR, Timpson NJ. Common variation at 16p11.2 is associated with glycosuria in pregnancy: findings from a genome-wide association study in European women. Hum Mol Genet 2020; 29:2098-2106. [PMID: 32227112 PMCID: PMC7390941 DOI: 10.1093/hmg/ddaa054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 02/28/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023] Open
Abstract
Glycosuria is a condition where glucose is detected in urine at higher concentrations than normal (i.e. not detectable). Glycosuria at some point during pregnancy has an estimated prevalence of 50% and is associated with adverse outcomes in both mothers and offspring. Little is currently known about the genetic contribution to this trait or the extent to which it overlaps with other seemingly related traits, e.g. diabetes. We performed a genome-wide association study (GWAS) for self-reported glycosuria in pregnant mothers from the Avon Longitudinal Study of Parents and Children (cases/controls = 1249/5140). We identified two loci, one of which (lead SNP = rs13337037; chromosome 16; odds ratio of glycosuria per effect allele: 1.42; 95% CI: 1.30, 1.56; P = 1.97 × 10-13) was then validated using an obstetric measure of glycosuria measured in the same cohort (227/6639). We performed a secondary GWAS in the 1986 Northern Finland Birth Cohort (NFBC1986; 747/2991) using midwife-reported glycosuria and offspring genotype as a proxy for maternal genotype. The combined results revealed evidence for a consistent effect on glycosuria at the chromosome 16 locus. In follow-up analyses, we saw little evidence of shared genetic underpinnings with the exception of urinary albumin-to-creatinine ratio (Rg = 0.64; SE = 0.22; P = 0.0042), a biomarker of kidney disease. In conclusion, we identified a genetic association with self-reported glycosuria during pregnancy, with the lead SNP located 15kB upstream of SLC5A2, a target of antidiabetic drugs. The lack of strong genetic correlation with seemingly related traits such as type 2 diabetes suggests different genetic risk factors exist for glycosuria during pregnancy.
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Affiliation(s)
- Matthew A Lee
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - George McMahon
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Ville Karhunen
- Faculty of Medicine, School of Public Health, Imperial College London, 156 Norfolk Place, St Mary’s Campus, London W2 1PG, UK
- Faculty of Medicine, Northern Finland Birth Cohort Studies and Center for Life Course Health Research, University of Oulu, Aapistie 5 B, Oulu Fin-902200, Finland
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Laura J Corbin
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Marjo-Riitta Jarvelin
- Faculty of Medicine, School of Public Health, Imperial College London, 156 Norfolk Place, St Mary’s Campus, London W2 1PG, UK
- Faculty of Medicine, Northern Finland Birth Cohort Studies and Center for Life Course Health Research, University of Oulu, Aapistie 5 B, Oulu Fin-902200, Finland
| | - Nicholas J Timpson
- Medical Research Council Integrative Epidemiology Unit, Avon Longitudinal Study of Parents and Children, Population Health Science, Bristol Medical School, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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27
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Shindyapina AV, Zenin AA, Tarkhov AE, Santesmasses D, Fedichev PO, Gladyshev VN. Germline burden of rare damaging variants negatively affects human healthspan and lifespan. eLife 2020; 9:e53449. [PMID: 32254024 PMCID: PMC7314550 DOI: 10.7554/elife.53449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Heritability of human lifespan is 23-33% as evident from twin studies. Genome-wide association studies explored this question by linking particular alleles to lifespan traits. However, genetic variants identified so far can explain only a small fraction of lifespan heritability in humans. Here, we report that the burden of rarest protein-truncating variants (PTVs) in two large cohorts is negatively associated with human healthspan and lifespan, accounting for 0.4 and 1.3 years of their variability, respectively. In addition, longer-living individuals possess both fewer rarest PTVs and less damaging PTVs. We further estimated that somatic accumulation of PTVs accounts for only a small fraction of mortality and morbidity acceleration and hence is unlikely to be causal in aging. We conclude that rare damaging mutations, both inherited and accumulated throughout life, contribute to the aging process, and that burden of ultra-rare variants in combination with common alleles better explain apparent heritability of human lifespan.
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Affiliation(s)
| | - Aleksandr A Zenin
- Gero LLCMoscowRussian Federation
- The Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State UniversityMoscowRussian Federation
| | - Andrei E Tarkhov
- Gero LLCMoscowRussian Federation
- Skolkovo Institute of Science and Technology, Skolkovo Innovation CenterMoscowRussian Federation
| | | | - Peter O Fedichev
- Gero LLCMoscowRussian Federation
- Moscow Institute of Physics and TechnologyMoscowRussian Federation
| | - Vadim N Gladyshev
- Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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Iacono D, Feltis GC. Impact of Apolipoprotein E gene polymorphism during normal and pathological conditions of the brain across the lifespan. Aging (Albany NY) 2020; 11:787-816. [PMID: 30677746 PMCID: PMC6366964 DOI: 10.18632/aging.101757] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 01/05/2019] [Indexed: 12/12/2022]
Abstract
The central nervous system (CNS) is the cellular substrate for the integration of complex, dynamic, constant, and simultaneous interactions among endogenous and exogenous stimuli across the entire human lifespan. Numerous studies on aging-related brain diseases show that some genes identified as risk factors for some of the most common neurodegenerative diseases - such as the allele 4 of APOE gene (APOE4) for Alzheimer's disease (AD) - have a much earlier neuro-anatomical and neuro-physiological impact. The impact of APOE polymorphism appears in fact to start as early as youth and early-adult life. Intriguingly, though, those same genes associated with aging-related brain diseases seem to influence different aspects of the brain functioning much earlier actually, that is, even from the neonatal periods and earlier. The APOE4, an allele classically associated with later-life neurodegenerative disorders as AD, seems in fact to exert a series of very early effects on phenomena of neuroplasticity and synaptogenesis that begin from the earliest periods of life such as the fetal ones.We reviewed some of the findings supporting the hypothesis that APOE polymorphism is an early modifier of various neurobiological aspects across the entire human lifespan - from the in-utero to the centenarian life - during both normal and pathological conditions of the brain.
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Affiliation(s)
- Diego Iacono
- Neuropathology Research, Biomedical Research Institute of New Jersey (BRInj), Cedar Knolls, NJ 07927, USA.,MidAtlantic Neonatology Associates (MANA), Morristown, NJ 07960, USA.,Atlantic Neuroscience Institute, Atlantic Health System (AHS), Overlook Medical Center, Summit, NJ 07901, USA
| | - Gloria C Feltis
- Neuropathology Research, Biomedical Research Institute of New Jersey (BRInj), Cedar Knolls, NJ 07927, USA
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29
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Maskos U. The nicotinic receptor alpha5 coding polymorphism rs16969968 as a major target in disease: Functional dissection and remaining challenges. J Neurochem 2020; 154:241-250. [PMID: 32078158 DOI: 10.1111/jnc.14989] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are major signalling molecules in the central and peripheral nervous system. Over the last decade, they have been linked to a number of major human psychiatric and neurological conditions, like smoking, schizophrenia, Alzheimer's disease and many others. Human Genome-Wide Association Studies (GWAS) have robustly identified genetic alterations at a locus of chromosome 15q to several of these diseases. In this review, we discuss a major coding polymorphism in the alpha5 subunit, referred to as α5SNP, and its functional dissection in vitro and in vivo. Its presence at high frequency in many human populations lends itself to pharmaceutical intervention in the context of 'positive allosteric modulators' (PAMs). We will present the prospects of this novel treatment, and the remaining challenges to identify suitable molecules.
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Affiliation(s)
- Uwe Maskos
- Department of Neuroscience, Institut Pasteur, Paris, France
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30
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Bierut LJ. 2018 Langley Award for Basic Research on Nicotine and Tobacco: Bringing Precision Medicine to Smoking Cessation. Nicotine Tob Res 2020; 22:147-151. [PMID: 30855677 PMCID: PMC7161927 DOI: 10.1093/ntr/ntz036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/05/2019] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Large segments of the world population use combustible cigarettes, and our society pays a high price for smoking, through increased healthcare expenditures, morbidity and mortality. The development of combustible cigarette smoking requires the initiation of smoking and a subsequent chain of behavioral transitions from experimental use, to established regular use, to the conversion to addiction. Each transition is influenced by both environmental and genetic factors, and our increasing knowledge about genetic contributions to smoking behaviors opens new potential interventions. METHODS This review describes the journey from genetic discovery to the potential implementation of genetic knowledge for the treatment of tobacco use disorder. RESULTS AND CONCLUSIONS The field of genetics applied to smoking behaviors has rapidly progressed with the identification of highly validated genetic variants that are associated with different smoking behaviors. The large scale implementation of this genetic knowledge to accelerate smoking cessation represents an important clinical challenge in precision medicine.
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Affiliation(s)
- Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
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31
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Choi CK, Kweon SS, Lee YH, Nam HS, Park KS, Ryu SY, Choi SW, Kim HY, Shin MH. The Association between the Apolipoprotein E Gene Polymorphism and All-cause Mortality in the Korean Population. J Korean Med Sci 2019; 34:e269. [PMID: 31625294 PMCID: PMC6801224 DOI: 10.3346/jkms.2019.34.e269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/03/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Apolipoprotein E (APOE) gene polymorphism is associated with neurodegenerative and cardiovascular diseases. Although the effects of the gene differ by ethnic group, few studies have examined Asians. Therefore, the association between APOE polymorphism and mortality in Koreans was evaluated in this study. METHODS This study population included participants from the Dong-gu and Namwon Studies. APOE genotypes were categorized as E2 (E2/E2 and E2/E3), E3 (E3/E3), and E4 (E3/E4 and E4/E4). Multivariate Cox proportional hazard models were constructed using the E3 allele as a reference. RESULTS In the model adjusting for study site, age, gender, and lifestyle, the hazard ratio (HR) of mortality for those with the E4 allele was 1.08 (95% confidence interval [CI], 0.97-1.20), while that for those with the E2 allele was 0.84 (95% CI, 0.74-0.96). After adjusting for blood lipids to evaluate their mediating effects, the HRs of mortality for those with E4 and E2 alleles were 1.08 (95% CI, 0.97-1.20) and 0.80 (95% CI, 0.70-0.92), respectively. These associations were more evident in younger groups, with HRs of 0.70 (95% CI, 0.52-0.92) for the E2 allele and 1.25 (95% CI, 1.03-1.53) for the E4 allele. CONCLUSION In two large population-based cohort studies, the E2 allele was associated with a lower risk of mortality compared with the E3 allele, whereas the E4 genotype was not associated with mortality in Koreans.
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Affiliation(s)
- Chang Kyun Choi
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea
| | - Sun Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea
| | - Young Hoon Lee
- Department of Preventive Medicine, Institute of Wonkwang Medical Science, Wonkwang University College of Medicine, Iksan, Korea
| | - Hae Sung Nam
- Department of Preventive Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Kyeong Soo Park
- Cardiocerebrovascular Center, Mokpo Jung-Ang Hospital, Mokpo, Korea
| | - So Yeon Ryu
- Department of Preventive Medicine, Chosun University College of Medicine, Gwangju, Korea
| | - Seong Woo Choi
- Department of Preventive Medicine, Chosun University College of Medicine, Gwangju, Korea
| | - Hye Yeon Kim
- Gwangju-Jeonnam Regional Cardiocerebrovascular Center, Chonnam National University Hospital, Gwangju, Korea
| | - Min Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea.
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32
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Giuliani C, Garagnani P, Franceschi C. Genetics of Human Longevity Within an Eco-Evolutionary Nature-Nurture Framework. Circ Res 2019; 123:745-772. [PMID: 30355083 DOI: 10.1161/circresaha.118.312562] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human longevity is a complex trait, and to disentangle its basis has a great theoretical and practical consequences for biomedicine. The genetics of human longevity is still poorly understood despite several investigations that used different strategies and protocols. Here, we argue that such rather disappointing harvest is largely because of the extraordinary complexity of the longevity phenotype in humans. The capability to reach the extreme decades of human lifespan seems to be the result of an intriguing mixture of gene-environment interactions. Accordingly, the genetics of human longevity is here described as a highly context-dependent phenomenon, within a new integrated, ecological, and evolutionary perspective, and is presented as a dynamic process, both historically and individually. The available literature has been scrutinized within this perspective, paying particular attention to factors (sex, individual biography, family, population ancestry, social structure, economic status, and education, among others) that have been relatively neglected. The strength and limitations of the most powerful and used tools, such as genome-wide association study and whole-genome sequencing, have been discussed, focusing on prominently emerged genes and regions, such as apolipoprotein E, Forkhead box O3, interleukin 6, insulin-like growth factor-1, chromosome 9p21, 5q33.3, and somatic mutations among others. The major results of this approach suggest that (1) the genetics of longevity is highly population specific; (2) small-effect alleles, pleiotropy, and the complex allele timing likely play a major role; (3) genetic risk factors are age specific and need to be integrated in the light of the geroscience perspective; (4) a close relationship between genetics of longevity and genetics of age-related diseases (especially cardiovascular diseases) do exist. Finally, the urgent need of a global approach to the largely unexplored interactions between the 3 genetics of human body, that is, nuclear, mitochondrial, and microbiomes, is stressed. We surmise that the comprehensive approach here presented will help in increasing the above-mentioned harvest.
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Affiliation(s)
- Cristina Giuliani
- From the Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology (C.G.), University of Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, United Kingdom (C.G.).,Interdepartmental Centre 'L. Galvani' (CIG), University of Bologna, Italy (C.G.)
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES) (P.G.), University of Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden (P.G.)
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33
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A Prospective Analysis of Genetic Variants Associated with Human Lifespan. G3-GENES GENOMES GENETICS 2019; 9:2863-2878. [PMID: 31484785 PMCID: PMC6723124 DOI: 10.1534/g3.119.400448] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a massive investigation into the genetic basis of human lifespan. Beginning with a genome-wide association (GWA) study using a de-identified snapshot of the unique AncestryDNA database – more than 300,000 genotyped individuals linked to pedigrees of over 400,000,000 people – we mapped six genome-wide significant loci associated with parental lifespan. We compared these results to a GWA analysis of the traditional lifespan proxy trait, age, and found only one locus, APOE, to be associated with both age and lifespan. By combining the AncestryDNA results with those of an independent UK Biobank dataset, we conducted a meta-analysis of more than 650,000 individuals and identified fifteen parental lifespan-associated loci. Beyond just those significant loci, our genome-wide set of polymorphisms accounts for up to 8% of the variance in human lifespan; this value represents a large fraction of the heritability estimated from phenotypic correlations between relatives.
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34
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Morris BJ, Willcox BJ, Donlon TA. Genetic and epigenetic regulation of human aging and longevity. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1718-1744. [PMID: 31109447 PMCID: PMC7295568 DOI: 10.1016/j.bbadis.2018.08.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023]
Abstract
Here we summarize the latest data on genetic and epigenetic contributions to human aging and longevity. Whereas environmental and lifestyle factors are important at younger ages, the contribution of genetics appears more important in reaching extreme old age. Genome-wide studies have implicated ~57 gene loci in lifespan. Epigenomic changes during aging profoundly affect cellular function and stress resistance. Dysregulation of transcriptional and chromatin networks is likely a crucial component of aging. Large-scale bioinformatic analyses have revealed involvement of numerous interaction networks. As the young well-differentiated cell replicates into eventual senescence there is drift in the highly regulated chromatin marks towards an entropic middle-ground between repressed and active, such that genes that were previously inactive "leak". There is a breakdown in chromatin connectivity such that topologically associated domains and their insulators weaken, and well-defined blocks of constitutive heterochromatin give way to generalized, senescence-associated heterochromatin, foci. Together, these phenomena contribute to aging.
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Affiliation(s)
- Brian J Morris
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales 2006, Australia; Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Bradley J Willcox
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Timothy A Donlon
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Departments of Cell & Molecular Biology and Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, United States.
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35
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Hõrak P, Valge M, Fischer K, Mägi R, Kaart T. Parents of early-maturing girls die younger. Evol Appl 2019; 12:1050-1061. [PMID: 31080514 PMCID: PMC6503892 DOI: 10.1111/eva.12780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 02/05/2023] Open
Abstract
According to the life-history theory, rates of sexual maturation have coevolved with mortality rates so that individuals who mature faster tend to die younger. We used two data sets, providing different markers for the speed of pubertal development to test whether rates of sexual maturation of women predict the age at death of their parents. In the data set of Estonian schoolgirls born between 1936 and 1961, the rate of breast development predicted lifespan of both mothers and fathers (irrespectively of their socio-economic position), so that parents of rapidly maturing girls died at younger age. This finding supports the view that fast maturation rates in humans have coevolved with short lifespans and that such trade-offs can be detected as intergenerational phenotypic correlations in modern populations. Menarcheal age of participants of Estonian Biobank (born between 1925 and 1996) did not predict the age of death of their mothers; however, it did predict survival of their fathers, but only in environment where the genetic variation is exposed (families where at least one parent had tertiary education). In such families (where girls also matured 0.2-0.4 years earlier than in poorly educated families), 1-year delay in daughter's menarche corresponded to 9% lower hazard of father's death. Heritability of menarcheal age was also highest in well-educated families. The latter findings are consistent with the idea that genetic differences in the rate of pubertal maturation may be expressed most clearly in well-off families because in such families, the contribution of environmental variance to total phenotypic variance in menarcheal age is smallest. Our findings suggest that with global improvement and equalization of growth conditions, reductions of environmental variation in the rate of maturation increasingly expose the genetic differences in menarcheal age to selection. Under such conditions, selection on menarcheal age has a potential to affect the evolution of lifespan.
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Affiliation(s)
- Peeter Hõrak
- Department of ZoologyUniversity of TartuTartuEstonia
| | - Markus Valge
- Department of ZoologyUniversity of TartuTartuEstonia
| | | | - Reedik Mägi
- Estonian Genome CenterUniversity of TartuTartuEstonia
| | - Tanel Kaart
- Institute of Veterinary Medicine and Animal SciencesEstonian University of Life SciencesTartuEstonia
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36
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Singh PP, Demmitt BA, Nath RD, Brunet A. The Genetics of Aging: A Vertebrate Perspective. Cell 2019; 177:200-220. [PMID: 30901541 PMCID: PMC7592626 DOI: 10.1016/j.cell.2019.02.038] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
Abstract
Aging negatively impacts vitality and health. Many genetic pathways that regulate aging were discovered in invertebrates. However, the genetics of aging is more complex in vertebrates because of their specialized systems. This Review discusses advances in the genetic regulation of aging in vertebrates from work in mice, humans, and organisms with exceptional lifespans. We highlight challenges for the future, including sex-dependent differences in lifespan and the interplay between genes and environment. We also discuss how the identification of reliable biomarkers of age and development of new vertebrate models can be leveraged for personalized interventions to counter aging and age-related diseases.
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Affiliation(s)
- Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford, CA 94305, USA.
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37
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Belloy ME, Napolioni V, Greicius MD. A Quarter Century of APOE and Alzheimer's Disease: Progress to Date and the Path Forward. Neuron 2019; 101:820-838. [PMID: 30844401 PMCID: PMC6407643 DOI: 10.1016/j.neuron.2019.01.056] [Citation(s) in RCA: 314] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/08/2019] [Accepted: 01/27/2019] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is considered a polygenic disorder. This view is clouded, however, by lingering uncertainty over how to treat the quasi "monogenic" role of apolipoprotein E (APOE). The APOE4 allele is not only the strongest genetic risk factor for AD, it also affects risk for cardiovascular disease, stroke, and other neurodegenerative disorders. This review, based mostly on data from human studies, ranges across a variety of APOE-related pathologies, touching on evolutionary genetics and risk mitigation by ethnicity and sex. The authors also address one of the most fundamental question pertaining to APOE4 and AD: does APOE4 increase AD risk via a loss or gain of function? The answer will be of the utmost importance in guiding future research in AD.
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Affiliation(s)
- Michaël E Belloy
- Department of Neurology and Neurological Sciences, FIND Lab, Stanford University, Stanford, CA 94304, USA
| | - Valerio Napolioni
- Department of Neurology and Neurological Sciences, FIND Lab, Stanford University, Stanford, CA 94304, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, FIND Lab, Stanford University, Stanford, CA 94304, USA.
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38
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Dobewall H, Savelieva K, Seppälä I, Knafo-Noam A, Hakulinen C, Elovainio M, Keltikangas-Järvinen L, Pulkki-Råback L, Raitakari OT, Lehtimäki T, Hintsanen M. Gene-environment correlations in parental emotional warmth and intolerance: genome-wide analysis over two generations of the Young Finns Study. J Child Psychol Psychiatry 2019; 60:277-285. [PMID: 30357825 DOI: 10.1111/jcpp.12995] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Genomic analysis of the child might offer new potential to illuminate human parenting. We examined whether offspring (G2) genome-wide genotype variation (SNPs) is associated with their mother's (G1) emotional warmth and intolerance, indicating a gene-environment correlation. If this association is stronger than between G2's genes and their emotional warmth and intolerance toward their own children, then this would indicate the presence of an evocative gene-environment correlation. To further understand how G1 mother's parenting has been evoked by genetically influenced characteristics of the child (G2), we examined whether child (G2) temperament partially accounted for the association between offspring genes and parental responses. METHODS Participants were from the Young Finns Study. G1 mothers (N = 2,349; mean age 39 years) self-reported the emotional warmth and intolerance toward G2 in 1980 when the participants were from 3 to 18 years old. G2 participants answered the same parenting scales in 2007/2012 (N = 1,378; mean age = 38 years in 2007; 59% female) when their children were on average 11 years old. Offspring temperament traits were self-reported in 1992 (G2 age range 15-30 years). Estimation of the phenotypic variance explained by the SNPs of G2 was done by genome-wide complex trait analysis with restricted maximum likelihood (GCTA-GREML). RESULTS Results showed that the SNPs of a child (G2) explained 22.6% of the phenotypic variance of maternal intolerance (G1; p-value = .039). G2 temperament trait negative emotionality explained only 2.4% points of this association. G2 genes did not explain G1 emotional warmth or G2's own emotional warmth and intolerance. However, further analyses of a combined measure of both G1 parenting scales found genetic effects. Parent or child gender did not moderate the observed associations. CONCLUSIONS Presented genome-wide evidence is pointing to the important role a child plays in affecting and shaping his/her family environment, though the underlying mechanisms remain unclear.
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Affiliation(s)
- Henrik Dobewall
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Faculty of Social Sciences, Health Sciences, University of Tampere, Tampere, Finland
| | - Kateryna Savelieva
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ariel Knafo-Noam
- Department of Psychology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christian Hakulinen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Marko Elovainio
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Laura Pulkki-Råback
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Olli T Raitakari
- Research Collegium for Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
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39
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Indirect assortative mating for human disease and longevity. Heredity (Edinb) 2019; 123:106-116. [PMID: 30723306 DOI: 10.1038/s41437-019-0185-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 01/03/2019] [Accepted: 01/05/2019] [Indexed: 02/07/2023] Open
Abstract
Phenotypic correlations among partners for traits such as longevity or late-onset disease have been found to be comparable to phenotypic correlations in first-degree relatives. How these correlations arise in late life is poorly understood. Here we introduce a novel paradigm to establish the presence of indirect assortment on factors correlated across generations, by examining correlations between parents of couples, i.e., in-laws. Using correlations in additive genetic values we further corroborate the presence of indirect assortment on heritable factors. Specifically, using couples from the UK Biobank cohort, we show that longevity and disease history of the parents of White British couples are correlated, with correlations of up to 0.09. The correlations in parental longevity are replicated in the FamiLinx cohort, a larger and geographically more diverse historical ancestry dataset spanning a broader time frame. These correlations in parental longevity significantly (pval < 0.0093 for all pairs of parents) exceed what would be expected due to variations in lifespan based on year and location of birth. For cardiovascular diseases, in particular hypertension, we find significant correlations (r = 0.028, pval = 0.005) in genetic values among partners, supporting a model where partners assort for risk factors to some extent genetically correlated with cardiovascular disease. Partitioning the relative importance of indirect assortative mating and shared common environment will require large, well-characterized longitudinal cohorts aimed at understanding phenotypic correlations among none-blood relatives. Identifying the factors that mediate indirect assortment on longevity and human disease risk will help to unravel factors affecting human disease and ultimately longevity.
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40
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Kulminski AM, Loika Y, Culminskaya I, Huang J, Arbeev KG, Bagley O, Feitosa MF, Zmuda JM, Christensen K, Yashin AI. Independent associations of TOMM40 and APOE variants with body mass index. Aging Cell 2019; 18:e12869. [PMID: 30462377 PMCID: PMC6351823 DOI: 10.1111/acel.12869] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/13/2018] [Accepted: 10/04/2018] [Indexed: 02/04/2023] Open
Abstract
The TOMM40-APOE variants are known for their strong, antagonistic associations with Alzheimer's disease and body weight. While a stronger role of the APOE than TOMM40 variants in Alzheimer's disease was suggested, comparative contribution of the TOMM40-APOE variants in the regulation of body weight remains elusive. We examined additive effects of rs2075650 and rs157580 TOMM40 variants and rs429358 and rs7412 APOE variants coding the ε2/ε3/ε4 polymorphism on body mass index (BMI) in age-aggregated and age-stratified cohort-specific and cohort-pooled analysis of 27,863 Caucasians aged 20-100 years from seven longitudinal studies. Minor alleles of rs2075650, rs429358, and rs7412 were individually associated with BMI (β = -1.29, p = 3.97 × 10-9 ; β = -1.38, p = 2.78 × 10-10 ; and β = 0.58, p = 3.04 × 10-2 , respectively). Conditional analysis with rs2075650 and rs429358 identified independent BMI-lowering associations for minor alleles (β = -0.63, p = 3.99 × 10-2 and β = -0.94, p = 2.17 × 10-3 , respectively). Polygenic mega-analysis identified additive effects of the rs2075650 and rs429358 heterozygotes (β = -1.68, p = 3.00 × 10-9 ), and the strongest BMI-lowering association for the rs2075650 heterozygous and rs429358 minor allele homozygous carriers (β = -4.11, p = 2.78 × 10-3 ). Conditional analysis with four polymorphisms identified independent BMI-lowering (rs2075650, rs157580, and rs429358) and BMI-increasing (rs7412) associations of heterozygous genotypes with BMI. Age-stratified conditional analysis revealed well-powered support for a differential and independent association of the rs429358 heterozygote with BMI in younger and older individuals, β = 0.58, 95% confidence interval (CI) = -1.18, 2.35, p = 5.18 × 10-1 for 3,068 individuals aged ≤30 years and β = -4.28, CI = -5.65, -2.92, p = 7.71 × 10-10 for 6,052 individuals aged >80 years. TOMM40 and APOE variants are independently and additively associated with BMI. The APOE ε4-coding rs429358 polymorphism is associated with BMI in older individuals but not in younger individuals.
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Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth California
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth California
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth California
| | - Jian Huang
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth California
| | - Konstantin G. Arbeev
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth California
| | - Olivia Bagley
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth California
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of GeneticsWashington University School of MedicineSt LouisMissouri
| | - Joseph M. Zmuda
- Department of Epidemiology, Graduate School of Public HealthUniversity of PittsburghPittsburghPennsylvania
| | - Kaare Christensen
- The Danish Aging Research CenterUniversity of Southern DenmarkOdense CDenmark
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth California
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41
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Zenin A, Tsepilov Y, Sharapov S, Getmantsev E, Menshikov LI, Fedichev PO, Aulchenko Y. Identification of 12 genetic loci associated with human healthspan. Commun Biol 2019; 2:41. [PMID: 30729179 PMCID: PMC6353874 DOI: 10.1038/s42003-019-0290-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 01/08/2019] [Indexed: 02/06/2023] Open
Abstract
Aging populations face diminishing quality of life due to increased disease and morbidity. These challenges call for longevity research to focus on understanding the pathways controlling healthspan. We use the data from the UK Biobank (UKB) cohort and observe that the risks of major chronic diseases increased exponentially and double every eight years, i.e., at a rate compatible with the Gompertz mortality law. Assuming that aging drives the acceleration in morbidity rates, we build a risk model to predict the age at the end of healthspan depending on age, gender, and genetic background. Using the sub-population of 300,447 British individuals as a discovery cohort, we identify 12 loci associated with healthspan at the whole-genome significance level. We find strong genetic correlations between healthspan and all-cause mortality, life-history, and lifestyle traits. We thereby conclude that the healthspan offers a promising new way to interrogate the genetics of human longevity.
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Affiliation(s)
- Aleksandr Zenin
- Gero LLC, Novokuznetskaya street 24/2, Moscow, Russia 119017
| | - Yakov Tsepilov
- Novosibirsk State University, Pirogova 2, Novosibirsk, Russia 630090
- Institute of Cytology and Genetics SB RAS, Lavrentyeva ave. 10, Novosibirsk, Russia 630090
| | - Sodbo Sharapov
- Novosibirsk State University, Pirogova 2, Novosibirsk, Russia 630090
- Institute of Cytology and Genetics SB RAS, Lavrentyeva ave. 10, Novosibirsk, Russia 630090
| | | | - L. I. Menshikov
- Gero LLC, Novokuznetskaya street 24/2, Moscow, Russia 119017
- National Research Center “Kurchatov Institute”, 1, Akademika Kurchatova pl., Moscow, Russia 123182
| | - Peter O. Fedichev
- Gero LLC, Novokuznetskaya street 24/2, Moscow, Russia 119017
- Moscow Institute of Physics and Technology, Institutskii per. 9, Dolgoprudny, Moscow Russia 141700
| | - Yurii Aulchenko
- Novosibirsk State University, Pirogova 2, Novosibirsk, Russia 630090
- Institute of Cytology and Genetics SB RAS, Lavrentyeva ave. 10, Novosibirsk, Russia 630090
- PolyOmica, Het Vlaggeschip 61, 5237PA ‘s-Hertogenbosch, The Netherlands
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, Scotland EH8 9AG UK
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42
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Timmers PR, Mounier N, Lall K, Fischer K, Ning Z, Feng X, Bretherick AD, Clark DW, Shen X, Esko T, Kutalik Z, Wilson JF, Joshi PK. Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances. eLife 2019; 8:39856. [PMID: 30642433 PMCID: PMC6333444 DOI: 10.7554/elife.39856] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/20/2018] [Indexed: 12/31/2022] Open
Abstract
We use a genome-wide association of 1 million parental lifespans of genotyped subjects and data on mortality risk factors to validate previously unreplicated findings near CDKN2B-AS1, ATXN2/BRAP, FURIN/FES, ZW10, PSORS1C3, and 13q21.31, and identify and replicate novel findings near ABO, ZC3HC1, and IGF2R. We also validate previous findings near 5q33.3/EBF1 and FOXO3, whilst finding contradictory evidence at other loci. Gene set and cell-specific analyses show that expression in foetal brain cells and adult dorsolateral prefrontal cortex is enriched for lifespan variation, as are gene pathways involving lipid proteins and homeostasis, vesicle-mediated transport, and synaptic function. Individual genetic variants that increase dementia, cardiovascular disease, and lung cancer - but not other cancers - explain the most variance. Resulting polygenic scores show a mean lifespan difference of around five years of life across the deciles. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Paul Rhj Timmers
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Ninon Mounier
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kristi Lall
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Krista Fischer
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Zheng Ning
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xiao Feng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Xia Shen
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom.,Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland
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43
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van den Berg N, Rodríguez-Girondo M, van Dijk IK, Mourits RJ, Mandemakers K, Janssens AAPO, Beekman M, Smith KR, Slagboom PE. Longevity defined as top 10% survivors and beyond is transmitted as a quantitative genetic trait. Nat Commun 2019; 10:35. [PMID: 30617297 PMCID: PMC6323124 DOI: 10.1038/s41467-018-07925-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/04/2018] [Indexed: 11/30/2022] Open
Abstract
Survival to extreme ages clusters within families. However, identifying genetic loci conferring longevity and low morbidity in such longevous families is challenging. There is debate concerning the survival percentile that best isolates the genetic component in longevity. Here, we use three-generational mortality data from two large datasets, UPDB (US) and LINKS (Netherlands). We study 20,360 unselected families containing index persons, their parents, siblings, spouses, and children, comprising 314,819 individuals. Our analyses provide strong evidence that longevity is transmitted as a quantitative genetic trait among survivors up to the top 10% of their birth cohort. We subsequently show a survival advantage, mounting to 31%, for individuals with top 10% surviving first and second-degree relatives in both databases and across generations, even in the presence of non-longevous parents. To guide future genetic studies, we suggest to base case selection on top 10% survivors of their birth cohort with equally long-lived family members.
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Affiliation(s)
- Niels van den Berg
- Department of Biomedical Data Sciences, Section of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
- Department of Family and Consumer Studies, Population Sciences, Huntsman Cancer Institute, University of Utah, 225 S. 1400 E. Rm 228, Salt Lake City, UT, USA.
- Radboud Group for Historical Demography and Family History, Radboud University, Erasmusplein 1, 6525 HT, Nijmegen, The Netherlands.
| | - Mar Rodríguez-Girondo
- Department of Biomedical Data Sciences, Section of Medical Statistics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Ingrid K van Dijk
- Radboud Group for Historical Demography and Family History, Radboud University, Erasmusplein 1, 6525 HT, Nijmegen, The Netherlands
| | - Rick J Mourits
- Radboud Group for Historical Demography and Family History, Radboud University, Erasmusplein 1, 6525 HT, Nijmegen, The Netherlands
| | - Kees Mandemakers
- International Institute of Social History, Cruquiusweg 31, 1019 AT, Amsterdam, The Netherlands
| | - Angelique A P O Janssens
- Radboud Group for Historical Demography and Family History, Radboud University, Erasmusplein 1, 6525 HT, Nijmegen, The Netherlands
| | - Marian Beekman
- Department of Biomedical Data Sciences, Section of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Ken R Smith
- Department of Family and Consumer Studies, Population Sciences, Huntsman Cancer Institute, University of Utah, 225 S. 1400 E. Rm 228, Salt Lake City, UT, USA
| | - P Eline Slagboom
- Department of Biomedical Data Sciences, Section of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
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44
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Schork NJ, Raghavachari N. Report: NIA workshop on translating genetic variants associated with longevity into drug targets. GeroScience 2018; 40:523-538. [PMID: 30374935 PMCID: PMC6294726 DOI: 10.1007/s11357-018-0046-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/03/2018] [Indexed: 12/16/2022] Open
Abstract
To date, candidate gene and genome-wide association studies (GWAS) have led to the discovery of longevity-associated variants (LAVs) in genes such as FOXO3A and APOE. Unfortunately, translating variants into drug targets is challenging for any trait, and longevity is no exception. Interdisciplinary and integrative multi-omics approaches are needed to understand how LAVs affect longevity-related phenotypes at the molecular physiologic level in order to leverage their discovery to identify new drug targets. The NIA convened a workshop in August 2017 on emerging and novel in silico (i.e., bioinformatics and computational) approaches to the translation of LAVs into drug targets. The goal of the workshop was to identify ways of enabling, enhancing, and facilitating interactions among researchers from different disciplines whose research considers either the identification of LAVs or the mechanistic or causal pathway(s) and protective factors they influence for discovering drug targets. Discussions among the workshop participants resulted in the identification of critical needs for enabling the translation of LAVs into drug targets in several areas. These included (1) the initiation and better use of cohorts with multi-omics profiling on the participants; (2) the generation of longitudinal information on multiple individuals; (3) the collection of data from non-human species (both long and short-lived) for comparative biology studies; (4) the refinement of computational tools for integrative analyses; (5) the development of novel computational and statistical inference techniques for assessing the potential of a drug target; (6) the identification of available drugs that could modulate a target in a way that could potentially provide protection against age-related diseases and/or enhance longevity; and (7) the development or enhancement of databases and repositories of relevant information, such as the Longevity Genomics website ( https://www.longevitygenomics.org ), to enhance and help motivate future interdisciplinary studies. Integrative approaches that examine the influence of LAVs on molecular physiologic phenotypes that might be amenable to pharmacological modulation are necessary for translating LAVs into drugs to enhance health and life span.
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Affiliation(s)
- Nicholas J. Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute, Phoenix, AZ USA
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45
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Fedichev PO. Hacking Aging: A Strategy to Use Big Data From Medical Studies to Extend Human Life. Front Genet 2018; 9:483. [PMID: 30405692 PMCID: PMC6206166 DOI: 10.3389/fgene.2018.00483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/28/2018] [Indexed: 12/26/2022] Open
Abstract
Age is the most important single factor associated with chronic diseases and ultimately, death. The mortality rate in humans doubles approximately every eight years, as described by the Gompertz law of mortality. The incidence of specific diseases, such as cancer or stroke, also accelerates after the age of about 40 and doubles at a rate that mirrors the mortality-rate doubling time. It is therefore, entirely plausible to think that there is a single underlying process, the driving force behind the progressive reduction of the organism's health leading to the increased susceptibility to diseases and death; aging. There is, however, no fundamental law of nature requiring exponential morbidity and mortality risk trajectories. The acceleration of mortality is thus the most important characteristics of the aging process. It varies dramatically even among closely related mammalian species and hence appears to be a tunable phenotype. Here, we follow how big data from large human medical studies, and analytical approaches borrowed from physics of complex dynamic systems can help to reverse engineer the underlying biology behind Gompertz mortality law. With such an approach we hope to generate predictive models of aging for systematic discovery of biomarkers of aging followed by identification of novel therapeutic targets for future anti-aging interventions.
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Affiliation(s)
- Peter O. Fedichev
- Gero LLC, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
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46
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Hook M, Roy S, Williams EG, Bou Sleiman M, Mozhui K, Nelson JF, Lu L, Auwerx J, Williams RW. Genetic cartography of longevity in humans and mice: Current landscape and horizons. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2718-2732. [PMID: 29410319 PMCID: PMC6066442 DOI: 10.1016/j.bbadis.2018.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 12/14/2022]
Abstract
Aging is a complex and highly variable process. Heritability of longevity among humans and other species is low, and this finding has given rise to the idea that it may be futile to search for DNA variants that modulate aging. We argue that the problem in mapping longevity genes is mainly one of low power and the genetic and environmental complexity of aging. In this review we highlight progress made in mapping genes and molecular networks associated with longevity, paying special attention to work in mice and humans. We summarize 40 years of linkage studies using murine cohorts and 15 years of studies in human populations that have exploited candidate gene and genome-wide association methods. A small but growing number of gene variants contribute to known longevity mechanisms, but a much larger set have unknown functions. We outline these and other challenges and suggest some possible solutions, including more intense collaboration between research communities that use model organisms and human cohorts. Once hundreds of gene variants have been linked to differences in longevity in mammals, it will become feasible to systematically explore gene-by-environmental interactions, dissect mechanisms with more assurance, and evaluate the roles of epistasis and epigenetics in aging. A deeper understanding of complex networks-genetic, cellular, physiological, and social-should position us well to improve healthspan.
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Affiliation(s)
- Michael Hook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
| | - Maroun Bou Sleiman
- Interfaculty Institute of Bioengineering, Laboratory of Integrative and Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - James F Nelson
- Department of Cellular and Integrative Physiology and Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Johan Auwerx
- Interfaculty Institute of Bioengineering, Laboratory of Integrative and Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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47
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Halaschek-Wiener J, Tindale LC, Collins JA, Leach S, McManus B, Madden K, Meneilly G, Le ND, Connors JM, Brooks-Wilson AR. The Super-Seniors Study: Phenotypic characterization of a healthy 85+ population. PLoS One 2018; 13:e0197578. [PMID: 29795606 PMCID: PMC5967696 DOI: 10.1371/journal.pone.0197578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 05/06/2018] [Indexed: 11/18/2022] Open
Abstract
Background To understand why some people live to advanced age in good health and others do not, it is important to study not only disease, but also long-term good health. The Super-Seniors Study aims to identify factors associated with healthy aging. Methods 480 healthy oldest-old ‘Super-Seniors’ aged 85 to 105 years and never diagnosed with cancer, cardiovascular disease, diabetes, dementia, or major pulmonary disease, were compared to 545 mid-life controls aged 41–54, who represent a group that is unselected for survival from late-life diseases. Health and lifestyle information, personal and family medical history, and blood samples were collected from all participants. Super-Seniors also underwent four geriatric tests. Results Super-Seniors showed high cognitive (Mini-Mental State Exam mean = 28.3) and functional capacity (Instrumental Activities of Daily Living Scale mean = 21.4), as well as high physical function (Timed Up and Go mean = 12.3 seconds) and low levels of depression (Geriatric Depression Scale mean = 1.5). Super-Seniors were less likely to be current smokers than controls, but the frequency of drinking alcohol was the same in both groups. Super-Seniors were more likely to have 4 or more offspring; controls were more likely to have no children. Female Super-Seniors had a mean age of last fertility 1.9 years older than controls, and were 2.3 times more likely to have had a child at ≥ 40 years. The parents of Super-Seniors had mean ages of deaths of 79.3 years for mothers, and 74.5 years for fathers, each exceeding the life expectancy for their era by a decade. Conclusions Super-Seniors are cognitively and physically high functioning individuals who have evaded major age-related chronic diseases into old age, representing the approximately top 1% for healthspan. The familiality of long lifespan of the parents of Super-Seniors supports the hypothesis that heritable factors contribute to this desirable phenotype.
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Affiliation(s)
- Julius Halaschek-Wiener
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Lauren C. Tindale
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jennifer A. Collins
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Stephen Leach
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Bruce McManus
- PROOF Centre of Excellence, University of British Columbia, Providence Health Care, Vancouver, British Columbia, Canada
| | - Kenneth Madden
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Graydon Meneilly
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nhu D. Le
- Cancer Control Research, BCCA, Vancouver, British Columbia, Canada
| | - Joseph M. Connors
- Centre for Lymphoid Cancer, BCCA, Vancouver, British Columbia, Canada
| | - Angela R. Brooks-Wilson
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
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48
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Wolford BN, Willer CJ, Surakka I. Electronic health records: the next wave of complex disease genetics. Hum Mol Genet 2018; 27:R14-R21. [PMID: 29547983 PMCID: PMC5946915 DOI: 10.1093/hmg/ddy081] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 12/29/2022] Open
Abstract
The combination of electronic health records (EHRs) with genetic data has ushered in the next wave of complex disease genetics. Population-based biobanks and other large cohorts provide sufficient sample sizes to identify novel genetic associations across the hundreds to thousands of phenotypes gleaned from EHRs. In this review, we summarize the current state of these EHR-linked biobanks, explore ongoing methods development in the field and highlight recent discoveries of genetic associations. We enumerate the many existing biobanks with EHRs linked to genetic data, many of which are available to researchers via application and contain sample sizes >50 000. We also discuss the computational and statistical considerations for analysis of such large datasets including mixed models, phenotype curation and cloud computing. Finally, we demonstrate how genome-wide association studies and phenome-wide association studies have identified novel genetic findings for complex diseases, specifically cardiometabolic traits. As more researchers employ innovative hypotheses and analysis approaches to study EHR-linked biobanks, we anticipate a richer understanding of the genetic etiology of complex diseases.
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Affiliation(s)
- Brooke N Wolford
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
- Center for Statistical Genetics, Ann Arbor, MI, USA
| | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
- Center for Statistical Genetics, Ann Arbor, MI, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ida Surakka
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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49
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Bierut LJ, Tyndale RF. Preparing the Way: Exploiting Genomic Medicine to Stop Smoking. Trends Mol Med 2018; 24:187-196. [PMID: 29307500 DOI: 10.1016/j.molmed.2017.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 12/10/2017] [Indexed: 12/15/2022]
Abstract
Clinical medicine of the future is poised to use an individual's genomic data to predict disease risk and guide clinical care. The treatment of cigarette smoking and tobacco use disorder represents a prime area for genomics implementation. The genes CHRNA5 and CYP2A6 are strong genomic contributors that alter the risk of heaviness of smoking, tobacco use disorder, and smoking-related diseases in humans. These biomarkers have proven analytical and clinical validity, and evidence for their clinical utility continues to grow. We propose that these biomarkers harbor the potential of enabling the identification of elevated disease risk in smokers, personalizing smoking cessation treatments, and motivating behavioral changes. We must prepare for the integration of genomic applications into clinical care of patients who smoke.
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Affiliation(s)
- Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH) and Departments of Psychiatry, Pharmacology and Toxicology, University of Toronto, Toronto, M5S 1A8, Ontario, Canada
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Ray A, Ahalawat N, Mondal J. Atomistic Insights into Structural Differences between E3 and E4 Isoforms of Apolipoprotein E. Biophys J 2018; 113:2682-2694. [PMID: 29262361 DOI: 10.1016/j.bpj.2017.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 12/23/2022] Open
Abstract
Among various isoforms of Apolipoprotein E (ApoE), the E4 isoform (ApoE4) is considered to be the strongest risk factor for Alzheimer's disease, whereas the E3 isoform (ApoE3) is neutral to the disease. Interestingly, the sequence of ApoE4 differs from its wild-type ApoE3 by a single amino acid C112R in the 299-amino-acid-long sequence. Hence, the puzzle remains: how a single-amino-acid difference between the ApoE3 and ApoE4 sequences can give rise to structural dissimilarities between the two isoforms, which can potentially lead to functional differences with significant pathological consequences. The major obstacle in addressing this question has been the lack of a 3D atomistic structure of ApoE4 to date. In this work, we resolve the issue by computationally modeling a plausible atomistic 3D structure of ApoE4. Our microsecond-long atomistic simulations elucidate key structural differences between monomeric ApoE3 and ApoE4, which renders ApoE4 thermodynamically less stable, less structured, and topologically less rigid compared to ApoE3. Consistent with an experimental report of the molten globule state of ApoE4, simulations identify multiple partially folded intermediates for ApoE4, which are implicated in the stronger aggregation propensity of ApoE4.
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Affiliation(s)
- Angana Ray
- Tata Institute of Fundamental Research, Hyderabad, Telangana, India
| | - Navjeet Ahalawat
- Tata Institute of Fundamental Research, Hyderabad, Telangana, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Hyderabad, Telangana, India.
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