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Lipid-Associated Variants near ANGPTL3 and LPL Show Parent-of-Origin Specific Effects on Blood Lipid Levels and Obesity. Genes (Basel) 2021; 13:genes13010091. [PMID: 35052431 PMCID: PMC8774740 DOI: 10.3390/genes13010091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/16/2021] [Accepted: 12/25/2021] [Indexed: 11/23/2022] Open
Abstract
Parent-of-origin effects (POE) and sex-specific parental effects have been reported for plasma lipid levels, and a strong relationship exists between dyslipidemia and obesity. We aim to explore whether genetic variants previously reported to have an association to lipid traits also show POE on blood lipid levels and obesity. Families from the Botnia cohort and the Hungarian Transdanubian Biobank (HTB) were genotyped for 12 SNPs, parental origin of alleles were inferred, and generalized estimating equations were modeled to assess parental-specific associations with lipid traits and obesity. POE were observed for the variants at the TMEM57, DOCK7/ANGPTL3, LPL, and APOA on lipid traits, the latter replicated in HTB. Sex-specific parental effects were also observed; variants at ANGPTL3/DOCK7 showed POE on lipid traits and obesity in daughters only, while those at LPL and TMEM57 showed POE on lipid traits in sons. Variants at LPL and DOCK7/ANGPTL3 showed POE on obesity-related traits in Botnia and HTB, and POE effects on obesity were seen to a higher degree in daughters. This highlights the need to include analysis of POEs in genetic studies of complex traits.
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102
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Kouraki A, Doherty M, Fernandes GS, Zhang W, Walsh DA, Kelly A, Valdes AM. Different genes may be involved in distal and local sensitisation: a genome-wide gene-based association study and meta-analysis. Eur J Pain 2021; 26:740-753. [PMID: 34958702 PMCID: PMC9303629 DOI: 10.1002/ejp.1902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/11/2021] [Accepted: 12/25/2021] [Indexed: 11/22/2022]
Abstract
Background Neuropathic pain symptoms and signs of increased pain sensitization in osteoarthritis (OA) patients may explain persistent pain after total joint replacement (TJR). Therefore, identifying genetic markers associated with pain sensitization and neuropathic‐like pain phenotypes could be clinically important in identifying targets for early intervention. Methods We performed a genome‐wide gene‐based association study (GWGAS) using pressure pain detection thresholds (PPTs) from distal pain‐free sites (anterior tibia), a measure of distal sensitization, and from proximal pain‐affected sites (lateral joint line), a measure of local sensitization, in 320 knee OA participants from the Knee Pain and related health in the Community (KPIC) cohort. We next performed gene‐based fixed‐effects meta‐analysis of PPTs and a neuropathic‐like pain phenotype using genome‐wide association study (GWAS) data from KPIC and from an independent cohort of 613 post‐TJR participants, respectively. Results The most significant genes associated with distal and local sensitization were OR5B3 and BRDT, respectively. We also found previously identified neuropathic pain‐associated genes—KCNA1, MTOR, ADORA1 and SCN3B—associated with PPT at the anterior tibia and an inflammatory pain gene—PTAFR—associated with PPT at the lateral joint line. Meta‐analysis results of anterior tibia and neuropathic‐like pain phenotypes revealed genes associated with bone morphogenesis, neuro‐inflammation, obesity, type 2 diabetes, cardiovascular disease and cognitive function. Conclusions Overall, our results suggest that different biological processes might be involved in distal and local sensitization, and common genetic mechanisms might be implicated in distal sensitization and neuropathic‐like pain. Future studies are needed to replicate these findings. Significance To the best of our knowledge, this is the first GWAS for pain sensitization and the first gene‐based meta‐analysis of pain sensitization and neuropathic‐like pain. Higher pain sensitization and neuropathic pain symptoms are associated with persistent pain after surgery hence, identifying genetic biomarkers and molecular pathways associated with these traits is clinically relevant.
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Affiliation(s)
- A Kouraki
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - M Doherty
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,Versus Arthritis Centre for Sports, Exercise and Osteoarthritis, University of Nottingham, Nottingham, NG7 2UH, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - G S Fernandes
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 6EH, United Kingdom
| | - W Zhang
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,Versus Arthritis Centre for Sports, Exercise and Osteoarthritis, University of Nottingham, Nottingham, NG7 2UH, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - D A Walsh
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,Versus Arthritis Centre for Sports, Exercise and Osteoarthritis, University of Nottingham, Nottingham, NG7 2UH, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - A Kelly
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - A M Valdes
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
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103
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Becker J, Burik CAP, Goldman G, Wang N, Jayashankar H, Bennett M, Belsky DW, Karlsson Linnér R, Ahlskog R, Kleinman A, Hinds DA, Caspi A, Corcoran DL, Moffitt TE, Poulton R, Sugden K, Williams BS, Harris KM, Steptoe A, Ajnakina O, Milani L, Esko T, Iacono WG, McGue M, Magnusson PKE, Mallard TT, Harden KP, Tucker-Drob EM, Herd P, Freese J, Young A, Beauchamp JP, Koellinger PD, Oskarsson S, Johannesson M, Visscher PM, Meyer MN, Laibson D, Cesarini D, Benjamin DJ, Turley P, Okbay A. Resource profile and user guide of the Polygenic Index Repository. Nat Hum Behav 2021; 5:1744-1758. [PMID: 34140656 PMCID: PMC8678380 DOI: 10.1038/s41562-021-01119-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/16/2021] [Indexed: 02/05/2023]
Abstract
Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is growing rapidly. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs' prediction accuracies, we constructed them using genome-wide association studies-some not previously published-from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the 'additive SNP factor'. Regressions in which the true regressor is this factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available.
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Affiliation(s)
- Joel Becker
- Department of Economics, New York University, New York, NY, USA
| | - Casper A P Burik
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Grant Goldman
- National Bureau of Economic Research, Cambridge, MA, USA
| | - Nancy Wang
- National Bureau of Economic Research, Cambridge, MA, USA
| | | | | | - Daniel W Belsky
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- Robert N. Butler Columbia Aging Center, Columbia University, New York, NY, USA
| | - Richard Karlsson Linnér
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Rafael Ahlskog
- Department of Government, Uppsala University, Uppsala, Sweden
| | | | | | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, University of Otago, Dunedin, New Zealand
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | | | - Kathleen Mullan Harris
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew Steptoe
- Department of Behavioural Science and Health, University College London, London, UK
| | - Olesya Ajnakina
- Department of Behavioural Science and Health, University College London, London, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Lili Milani
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Patrik K E Magnusson
- Swedish Twin Registry, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Travis T Mallard
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - K Paige Harden
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - Elliot M Tucker-Drob
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - Pamela Herd
- McCourt School of Public Policy, Georgetown University, Washington, DC, USA
| | - Jeremy Freese
- Department of Sociology, Stanford University, Stanford, CA, USA
| | - Alexander Young
- UCLA Anderson School of Management, Los Angeles, CA, USA
- Human Genetics Department, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Beauchamp
- Interdisciplinary Center for Economic Science and Department of Economics, George Mason University, Fairfax, VA, USA
| | - Philipp D Koellinger
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Robert M. La Follette School of Public Affairs, University of Wisconsin-Madison, Madison, WI, USA
| | - Sven Oskarsson
- Department of Government, Uppsala University, Uppsala, Sweden
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Stockholm, Sweden
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Michelle N Meyer
- Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - David Laibson
- National Bureau of Economic Research, Cambridge, MA, USA
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - David Cesarini
- Department of Economics, New York University, New York, NY, USA.
- National Bureau of Economic Research, Cambridge, MA, USA.
| | - Daniel J Benjamin
- National Bureau of Economic Research, Cambridge, MA, USA.
- UCLA Anderson School of Management, Los Angeles, CA, USA.
- Human Genetics Department, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Patrick Turley
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA.
- Department of Economics, University of Southern California, Los Angeles, CA, USA.
| | - Aysu Okbay
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
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104
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Identifying causality, genetic correlation, priority and pathways of large-scale complex exposures of breast and ovarian cancers. Br J Cancer 2021; 125:1570-1581. [PMID: 34671129 PMCID: PMC8608803 DOI: 10.1038/s41416-021-01576-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 09/13/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Genetic correlations, causalities and pathways between large-scale complex exposures and ovarian and breast cancers need systematic exploration. METHODS Mendelian randomisation (MR) and genetic correlation (GC) were used to identify causal biomarkers from 95 cancer-related exposures for risk of breast cancer [BC: oestrogen receptor-positive (ER + BC) and oestrogen receptor-negative (ER - BC) subtypes] and ovarian cancer [OC: high-grade serous (HGSOC), low-grade serous, invasive mucinous (IMOC), endometrioid (EOC) and clear cell (CCOC) subtypes]. RESULTS Of 31 identified robust risk factors, 16 were new causal biomarkers for BC and OC. Body mass index (BMI), body fat mass (BFM), comparative body size at age 10 (CBS-10), waist circumference (WC) and education attainment were shared risk factors for overall BC and OC. Childhood obesity, BMI, CBS-10, WC, schizophrenia and age at menopause were significantly associated with ER + BC and ER - BC. Omega-6:omega-3 fatty acids, body fat-free mass and basal metabolic rate were positively associated with CCOC and EOC; BFM, linoleic acid, omega-6 fatty acids, CBS-10 and birth weight were significantly associated with IMOC; and body fat percentage, BFM and adiponectin were significantly associated with HGSOC. Both GC and MR identified 13 shared factors. Factors were stratified into five priority levels, and visual causal networks were constructed for future interventions. CONCLUSIONS With analysis of large-scale exposures for breast and ovarian cancers, causalities, genetic correlations, shared or specific factors, risk factor priority and causal pathways and networks were identified.
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105
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Association of phthalates and early menarche in Korean adolescent girls from Korean National Environmental Health Survey (KoNEHS) 2015-2017. Ann Occup Environ Med 2021; 33:e4. [PMID: 34754465 PMCID: PMC7952777 DOI: 10.35371/aoem.2021.33.e4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Background Phthalates are one of renowned endocrine-disrupting chemicals, although inconsistent results are present around their effect on onset of menarche. Our hypothesis is that pre-pubertal exposure to phthalates is associated with acceleration of menarche. Methods We analyzed a total of 236 middle school (7th to 9th grade) girls from Korean National Environmental Health Survey 2015-2017. We used multiple linear regression to investigate impact of eight phthalate metabolites on age of menarche. We also conducted logistic regression to evaluate association between phthalate metabolite concentrations and early onset of menarche, adjusting for grade, maternal age of menarche and body mass index (BMI). Results In linear regression analysis, no significant association was found for any phthalate metabolites. In logistic regression analysis, however, odds ratios (ORs) of early menarche were significantly increased for mono-n-butyl phthalate (MnBP) and for sum of all phthalates. When compared to group with the lowest level, high concentration group for MnBP presented significantly increased odds of early menarche (OR: 2.09; 95% confidence interval [CI]: 1.03, 4.23) after adjusting for grade, maternal age of menarche and BMI. Furthermore, high concentrations of sum of all phthalates were associated with significant increase of OR of early menarche (OR: 2.22; 95% CI: 1.10, 4.49) after adjustment, compared to the lowest concentration group. Conclusions Results of our study suggest that exposure to phthalates around puberty may be associated with increased risk of early menarche.
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106
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Vazquez MJ, Daza-Dueñas S, Tena-Sempere M. Emerging Roles of Epigenetics in the Control of Reproductive Function: Focus on Central Neuroendocrine Mechanisms. J Endocr Soc 2021; 5:bvab152. [PMID: 34703958 PMCID: PMC8533971 DOI: 10.1210/jendso/bvab152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 12/11/2022] Open
Abstract
Reproduction is an essential function for perpetuation of the species. As such, it is controlled by sophisticated regulatory mechanisms that allow a perfect match between environmental conditions and internal cues to ensure adequate pubertal maturation and achievement of reproductive capacity. Besides classical genetic regulatory events, mounting evidence has documented that different epigenetic mechanisms operate at different levels of the reproductive axis to finely tune the development and function of this complex neuroendocrine system along the lifespan. In this mini-review, we summarize recent evidence on the role of epigenetics in the control of reproduction, with special focus on the modulation of the central components of this axis. Particular attention will be paid to the epigenetic control of puberty and Kiss1 neurons because major developments have taken place in this domain recently. In addition, the putative role of central epigenetic mechanisms in mediating the influence of nutritional and environmental cues on reproductive function will be discussed.
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Affiliation(s)
- Maria Jesus Vazquez
- Instituto Maimónides de Investigación Biomédica de Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Hospital Universitario Reina Sofia, 14004 Cordoba, Spain
| | - Silvia Daza-Dueñas
- Instituto Maimónides de Investigación Biomédica de Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain
| | - Manuel Tena-Sempere
- Instituto Maimónides de Investigación Biomédica de Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Hospital Universitario Reina Sofia, 14004 Cordoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 14004 Cordoba, Spain.,Institute of Biomedicine, University of Turku, FIN-20520 Turku, Finland
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107
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Sinclair-Waters M, Piavchenko N, Ruokolainen A, Aykanat T, Erkinaro J, Primmer CR. Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus. Mol Ecol 2021; 31:562-570. [PMID: 34716945 DOI: 10.1111/mec.16256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022]
Abstract
Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation. By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity.
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Affiliation(s)
- Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Nikolai Piavchenko
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
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Louwers YV, Visser JA. Shared Genetics Between Age at Menopause, Early Menopause, POI and Other Traits. Front Genet 2021; 12:676546. [PMID: 34691139 PMCID: PMC8529948 DOI: 10.3389/fgene.2021.676546] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Reproductive ageing leading to menopause is characterized by depletion of follicles and its regulating mechanisms are only partly understood. Early age at menopause and premature ovarian insufficiency (POI) are associated with several other traits such as cardiovascular disease, dyslipidemia, osteoporosis and diabetes. In large cohorts of Northern European women hundreds of Single Nucleotide Polymorphisms (SNPs) have been identified to be associated with age at menopause. These SNPs are located in genes enriched for immune and mitochondrial function as well as DNA repair and maintenance processes. Genetic predisposition to earlier menopause might also increase the risk of other associated traits. Increased risk for cardiovascular disease in women has been associated with age at menopause lowering SNPs. Pleiotropy between early age at menopause and increased mortality from coronary artery disease has been observed, implicating that genetic variants affecting age at menopause also affect the risk for coronary deaths. This review will discuss the shared genetics of age at menopause with other traits. Mendelian Randomization studies implicate causal genetic association between age at menopause and age at menarche, breast cancer, ovarian cancer, BMD and type 2 diabetes. Although the shared biological pathways remain to be determined, mechanisms that regulate duration of estrogen exposure remain an important focus.
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Affiliation(s)
- Yvonne V Louwers
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jenny A Visser
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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Manotas MC, González DM, Céspedes C, Forero C, Rojas Moreno AP. Genetic and Epigenetic Control of Puberty. Sex Dev 2021; 16:1-10. [PMID: 34649256 DOI: 10.1159/000519039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 08/16/2021] [Indexed: 11/19/2022] Open
Abstract
Puberty is a complex transitional phase in which reproductive capacity is achieved. There is a very wide variation in the age range of the onset of puberty, which follows a familial, ethnic, and sex pattern. The hypothalamic-pituitary-gonadal axis and several genetic, environmental, and nutritional factors play an important role in the onset of and throughout puberty. Recently, there has been significant progress in identifying factors that affect normal pubertal timing. Different studies have identified single nucleotide polymorphisms (SNPs) that affect pubertal timing in both sexes and across ethnic groups. Single genes are implicated in both precocious and delayed puberty, and epigenetic mechanisms have been suggested to affect the development and function of the GnRH neuronal network and responsiveness of end organs. All these factors can influence normal puberty timing, precocious puberty, and delayed puberty. The objective of this review is to describe recent findings related to the genetic and epigenetic control of puberty and highlight the need to deepen the knowledge of the regulatory mechanisms of this process in the normal and abnormal context.
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Affiliation(s)
- María Carolina Manotas
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Daniel Mauricio González
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Camila Céspedes
- Pediatric Endocrinologist, Hospital Universitario San Ignacio, Bogotá, Colombia.,Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Catalina Forero
- Pediatric Endocrinologist, Hospital Universitario San Ignacio, Bogotá, Colombia.,Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá, Colombia
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Maione L, Bouvattier C, Kaiser UB. Central precocious puberty: Recent advances in understanding the aetiology and in the clinical approach. Clin Endocrinol (Oxf) 2021; 95:542-555. [PMID: 33797780 PMCID: PMC8586890 DOI: 10.1111/cen.14475] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
Central precocious puberty (CPP) results from early activation of the hypothalamic-pituitary-gonadal (HPG) axis. The current state of knowledge of the complex neural network acting at the level of the hypothalamus and the GnRH neuron to control puberty onset has expanded, particularly in the context of molecular interactions. Along with these advances, the knowledge of pubertal physiology and pathophysiology has also increased. This review focuses on regulatory abnormalities occurring at the hypothalamic level of the HPG axis to cause CPP. The clinical approach to diagnosis of puberty and pubertal disorders is also reviewed, with a particular focus on aetiologies of CPP. The recent identification of mutations in MKRN3 and DLK1 in familial as well sporadic forms of CPP has changed the state of the art of the approach to patients with CPP. Genetic advances have also had important repercussions beyond consideration of puberty alone. Syndromic disorders and central nervous system lesions associated with CPP are also discussed. If untreated, these conditions may lead to adverse physical, psychosocial and medical outcomes.
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Affiliation(s)
- Luigi Maione
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Inserm, Physiologie et Physiopathologie Endocriniennes, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Service d’Endocrinologie et des Maladies de la Reproduction, Centre de Référence des Maladies Rares de l’Hypophyse, Université Paris-Saclay, Paris-Saclay University, Le Kremlin-Bicêtre, France
| | - Claire Bouvattier
- Inserm, Physiologie et Physiopathologie Endocriniennes, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Service d’Endocrinologie et des Maladies de la Reproduction, Centre de Référence des Maladies Rares de l’Hypophyse, Université Paris-Saclay, Paris-Saclay University, Le Kremlin-Bicêtre, France
| | - Ursula B. Kaiser
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Neocleous V, Fanis P, Toumba M, Gorka B, Kousiappa I, Tanteles GA, Iasonides M, Nicolaides NC, Christou YP, Michailidou K, Nicolaou S, Papacostas SS, Christoforidis A, Kyriakou A, Vlachakis D, Skordis N, Phylactou LA. Pathogenic and Low-Frequency Variants in Children With Central Precocious Puberty. Front Endocrinol (Lausanne) 2021; 12:745048. [PMID: 34630334 PMCID: PMC8498594 DOI: 10.3389/fendo.2021.745048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Background Central precocious puberty (CPP) due to premature activation of GnRH secretion results in early epiphyseal fusion and to a significant compromise in the achieved final adult height. Currently, few genetic determinants of children with CPP have been described. In this translational study, rare sequence variants in MKRN3, DLK1, KISS1, and KISS1R genes were investigated in patients with CPP. Methods Fifty-four index girls and two index boys with CPP were first tested by Sanger sequencing for the MKRN3 gene. All children found negative (n = 44) for the MKRN3 gene were further investigated by whole exome sequencing (WES). In the latter analysis, the status of variants in genes known to be related with pubertal timing was compared with an in-house Cypriot control cohort (n = 43). The identified rare variants were initially examined by in silico computational algorithms and confirmed by Sanger sequencing. Additionally, a genetic network for the MKRN3 gene, mimicking a holistic regulatory depiction of the crosstalk between MKRN3 and other genes was designed. Results Three previously described pathogenic MKRN3 variants located in the coding region of the gene were identified in 12 index girls with CPP. The most prevalent pathogenic MKRN3 variant p.Gly312Asp was exclusively found among the Cypriot CPP cohort, indicating a founder effect phenomenon. Seven other CPP girls harbored rare likely pathogenic upstream variants in the MKRN3. Among the 44 CPP patients submitted to WES, nine rare DLK1 variants were identified in 11 girls, two rare KISS1 variants in six girls, and two rare MAGEL2 variants in five girls. Interestingly, the frequent variant rs10407968 (p.Gly8Ter) of the KISS1R gene appeared to be less frequent in the cohort of patients with CPP. Conclusion The results of the present study confirm the importance of the MKRN3-imprinted gene in genetics of CPP and its key role in pubertal timing. Overall, the results of the present study have emphasized the importance of an approach that aligns genetics and clinical aspects, which is necessary for the management and treatment of CPP.
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Affiliation(s)
- Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Meropi Toumba
- Child Endocrine Care, Department of Pediatrics, Aretaeio Hospital, Nicosia, Cyprus
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Barbara Gorka
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ioanna Kousiappa
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Neurobiology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George A Tanteles
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Michalis Iasonides
- Department of Pediatrics, Iliaktida Paediatric & Adolescent Medical Centre, Limassol, Cyprus
- University of Nicosia Medical School, Nicosia, Cyprus
| | - Nicolas C Nicolaides
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
- Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Yiolanda P Christou
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Neurobiology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Stella Nicolaou
- Division of Pediatric Endocrinology, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Savvas S Papacostas
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Neurobiology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- University of Nicosia Medical School, Nicosia, Cyprus
- Centre for Neuroscience and Integrative Brain Research (CENIBRE), University of Nicosia, Nicosia, Cyprus
| | - Athanasios Christoforidis
- First Pediatric Department, School of Medicine, Faculty of Medical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Kyriakou
- Division of Pediatric Endocrinology, Archbishop Makarios III Hospital, Nicosia, Cyprus
- Developmental Endocrinology Research Group, School of Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
- Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- St George's, University of London Medical School, University of Nicosia, Nicosia, Cyprus
- Division of Pediatric Endocrinology, Paedi Center for specialized Pediatrics, Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
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112
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Corre T, Ponte B, Pivin E, Pruijm M, Ackermann D, Ehret G, Spanaus K, Bochud M, Wenger RH. Heritability and association with distinct genetic loci of erythropoietin levels in the general population. Haematologica 2021; 106:2499-2501. [PMID: 33832210 PMCID: PMC8409065 DOI: 10.3324/haematol.2021.278389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 02/26/2021] [Indexed: 01/24/2023] Open
Affiliation(s)
- Tanguy Corre
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland; National Centre of Competence in Research "Kidney.CH", Switzerland; Department of Computational Biology, University of Lausanne, Lausanne
| | - Belen Ponte
- Nephrology Service, Department Medicine, Geneva University Hospital, Geneva
| | - Edward Pivin
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne
| | - Menno Pruijm
- Nephrology Service, University Hospital of Lausanne and University of Lausanne, Lausanne
| | - Daniel Ackermann
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Bern
| | - Georg Ehret
- Cardiology, Department of Medicine, Geneva University Hospital, Geneva
| | - Katharina Spanaus
- Institute of Clinical Chemistry, University Hospital of Zurich, Zurich
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland; National Centre of Competence in Research "Kidney.CH"
| | - Roland H Wenger
- National Centre of Competence in Research "Kidney.CH", Switzerland; Institute of Physiology, University of Zurich, Zurich.
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113
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Busch AS, Ljubicic ML, Upners EN, Fischer MB, Kolby N, Eckert-Lind C, Jespersen K, Andersson AM, Frederiksen H, Johannsen TH, Hegaard HK, Sharif H, Hagen CP, Juul A. Cohort profile: The COPENHAGEN Minipuberty Study-A longitudinal prospective cohort of healthy full-term infants and their parents. Paediatr Perinat Epidemiol 2021; 35:601-611. [PMID: 34156716 DOI: 10.1111/ppe.12777] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND The hypothalamic-pituitary-gonadal (HPG) axis governs sexual maturation and reproductive function in humans. In early postnatal life, it is transiently active during which circulating sex steroids reach adult levels. While this so-called minipuberty represents a universal phenomenon in infants of both sexes, its role for early maturation and growth remains incompletely understood. OBJECTIVES To provide normative data on auxology as well as serum and urinary hormone levels in healthy, full-term infants throughout the first year of life and to investigate associations of postnatal HPG axis dynamics as well as hormonal, genetic and environmental exposures with early genital development and growth. POPULATION Healthy, Danish, full-term, singleton newborns including their parents. DESIGN Single-centre, prospective, observational longitudinal pregnancy and birth cohort. METHODS Newborns were followed with six repeated clinical examinations during a one-year follow-up period. An umbilical cord blood sample was drawn at birth. At each visit, infants underwent a clinical examination focusing on auxology and genital development. Further, blood (serum, plasma, DNA) and urine samples were collected at each visit. Mothers and fathers underwent a clinical examination and provided blood samples prior to and after birth. A subset of parents provided urine samples and breast milk samples. Pregnancy and obstetrical outcomes, and detailed parental questionnaires were compiled. PRELIMINARY RESULTS Between August 2016 and August 2018, 2481 women with singleton pregnancies were invited to participate of which 298, including their partners, were enrolled (12.0%). A total of 268 healthy, full-term newborns born appropriate for gestational age (AGA) were included at birth, 233 newborns participated in the postnatal follow-up period and 186 completed the one-year follow-up period (9.4% and 7.5%, respectively). CONCLUSION The COPENHAGEN Minipuberty Study provides detailed, longitudinal data on early genital development and growth including hormonal and genetic profiles and environmental exposure in healthy infants including additional data in their parents.
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Affiliation(s)
- Alexander Siegfried Busch
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Marie Lindhardt Ljubicic
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Emmie N Upners
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Margit Bistrup Fischer
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Nanna Kolby
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Camilla Eckert-Lind
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Kirstine Jespersen
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Anna-Maria Andersson
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Hanne Frederiksen
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Trine Holm Johannsen
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Hanne Kristine Hegaard
- Department of Obstetrics, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,The Research Unit Women's and Children's Health, Juliane Marie Center for Women, Children and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Heidi Sharif
- Department of Obstetrics, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Casper P Hagen
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC, Copenhagen University Hospital - Rigshospitalet, Copenhagen O, Denmark
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114
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Võsa U, Claringbould A, Westra HJ, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Yazar S, Brugge H, Oelen R, de Vries DH, van der Wijst MGP, Kasela S, Pervjakova N, Alves I, Favé MJ, Agbessi M, Christiansen MW, Jansen R, Seppälä I, Tong L, Teumer A, Schramm K, Hemani G, Verlouw J, Yaghootkar H, Sönmez Flitman R, Brown A, Kukushkina V, Kalnapenkis A, Rüeger S, Porcu E, Kronberg J, Kettunen J, Lee B, Zhang F, Qi T, Hernandez JA, Arindrarto W, Beutner F, Dmitrieva J, Elansary M, Fairfax BP, Georges M, Heijmans BT, Hewitt AW, Kähönen M, Kim Y, Knight JC, Kovacs P, Krohn K, Li S, Loeffler M, Marigorta UM, Mei H, Momozawa Y, Müller-Nurasyid M, Nauck M, Nivard MG, Penninx BWJH, Pritchard JK, Raitakari OT, Rotzschke O, Slagboom EP, Stehouwer CDA, Stumvoll M, Sullivan P, 't Hoen PAC, Thiery J, Tönjes A, van Dongen J, van Iterson M, Veldink JH, Völker U, Warmerdam R, Wijmenga C, Swertz M, Andiappan A, Montgomery GW, Ripatti S, Perola M, Kutalik Z, Dermitzakis E, Bergmann S, Frayling T, van Meurs J, Prokisch H, Ahsan H, Pierce BL, Lehtimäki T, Boomsma DI, Psaty BM, Gharib SA, Awadalla P, Milani L, Ouwehand WH, Downes K, Stegle O, Battle A, Visscher PM, Yang J, Scholz M, Powell J, Gibson G, Esko T, Franke L. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. Nat Genet 2021; 53:1300-1310. [PMID: 34475573 PMCID: PMC8432599 DOI: 10.1038/s41588-021-00913-z] [Citation(s) in RCA: 647] [Impact Index Per Article: 215.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/12/2021] [Indexed: 12/22/2022]
Abstract
Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms on the transcriptome. To investigate the genetics of gene expression, we performed cis- and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals through the eQTLGen Consortium. We detected cis-eQTL for 88% of genes, and these were replicable in numerous tissues. Distal trans-eQTL (detected for 37% of 10,317 trait-associated variants tested) showed lower replication rates, partially due to low replication power and confounding by cell type composition. However, replication analyses in single-cell RNA-seq data prioritized intracellular trans-eQTL. Trans-eQTL exerted their effects via several mechanisms, primarily through regulation by transcription factors. Expression of 13% of the genes correlated with polygenic scores for 1,263 phenotypes, pinpointing potential drivers for those traits. In summary, this work represents a large eQTL resource, and its results serve as a starting point for in-depth interpretation of complex phenotypes.
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Affiliation(s)
- Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Oncode Institute, Amsterdam, the Netherlands.
- Structural & Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
- Genomics Coordination Center, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Biao Zeng
- School of Biological Sciences, Georgia Tech, Atlanta, GA, USA
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ashis Saha
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Roman Kreuzhuber
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seyhan Yazar
- Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, New South Wales, Australia
| | - Harm Brugge
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Roy Oelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Dylan H de Vries
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Silva Kasela
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Natalia Pervjakova
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Isabel Alves
- Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- L'institut du thorax, Université de Nantes, CHU Nantes, INSERM, CNRS, Nantes, France
| | - Marie-Julie Favé
- Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mawussé Agbessi
- Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mark W Christiansen
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Rick Jansen
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Katharina Schramm
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, University Hospital Munich, Ludwig Maximilian's University, Munich, Germany
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Joost Verlouw
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, United Kingdom
- School of Life Sciences, College of Liberal Arts and Science, University of Westminster, London, United Kingdom
- Division of Medical Sciences, Department of Health Sciences, Luleå University of Technology, Luleå, Sweden
| | - Reyhan Sönmez Flitman
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andrew Brown
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Population Health and Genomics, University of Dundee, Dundee, United Kingdom
| | - Viktorija Kukushkina
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anette Kalnapenkis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Sina Rüeger
- Lausanne University Hospital, Lausanne, Switzerland
| | | | - Jaanika Kronberg
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Futao Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Ting Qi
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jose Alquicira Hernandez
- Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, New South Wales, Australia
| | | | - Frank Beutner
- Heart Center Leipzig, Universität Leipzig, Leipzig, Germany
| | - Julia Dmitrieva
- Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Mahmoud Elansary
- Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Benjamin P Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Michel Georges
- Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | | | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Eye Research Australia, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Yungil Kim
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Genetics and Genomic Science Department, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter Kovacs
- IFB Adiposity Diseases, Universität Leipzig, Leipzig, Germany
| | - Knut Krohn
- Interdisciplinary Center for Clinical Research, Faculty of Medicine, Universität Leipzig, Leipzig, Germany
| | - Shuang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genomics Coordination Center, University Medical Centre Groningen, Groningen, the Netherlands
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Urko M Marigorta
- School of Biological Sciences, Georgia Tech, Atlanta, GA, USA
- Integrative Genomics Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Hailang Mei
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Yukihide Momozawa
- Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, University Hospital Munich, Ludwig Maximilian's University, Munich, Germany
- IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Michel G Nivard
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit, Amsterdam, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Jonathan K Pritchard
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Olaf Rotzschke
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Coen D A Stehouwer
- Department of Internal Medicine and School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | | | - Patrick Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, the Netherlands
| | - Joachim Thiery
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Laboratory Medicine, LIFE-Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Department of Medicine, Universität Leipzig, Leipzig, Germany
| | - Jenny van Dongen
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands
| | | | - Jan H Veldink
- UMC Utrecht Brain Center, University Medical Center Utrecht, Department of Neurology, Utrecht University, Utrecht, the Netherlands
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Robert Warmerdam
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Morris Swertz
- Genomics Coordination Center, University Medical Centre Groningen, Groningen, the Netherlands
| | - Anand Andiappan
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Markus Perola
- National Institute for Health and Welfare, University of Helsinki, Helsinki, Finland
| | - Zoltan Kutalik
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Emmanouil Dermitzakis
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Timothy Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Philip Awadalla
- Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Oliver Stegle
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Joseph Powell
- Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, New South Wales, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Greg Gibson
- School of Biological Sciences, Georgia Tech, Atlanta, GA, USA
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Oncode Institute, Amsterdam, the Netherlands.
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115
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Li M, Lin J, Liang S, Chen Z, Bai Y, Long X, Huang S, Mo Z. The role of age at menarche and age at menopause in Alzheimer's disease: evidence from a bidirectional mendelian randomization study. Aging (Albany NY) 2021; 13:19722-19749. [PMID: 34347623 PMCID: PMC8386554 DOI: 10.18632/aging.203384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
The association between endogenous estrogen exposure and Alzheimer's disease (AD) remains inconclusive in previous observational studies, and few Mendelian randomization (MR) studies have focused on their causality thus far. We performed a bidirectional MR study to clarify the causality and causal direction of age at menarche and age at menopause, which are indicators of endogenous estrogen exposure, on AD risk. We obtained all genetic datasets for the MR analyses using publicly available summary statistics based on individuals of European ancestry from the IEU GWAS database. The MR analyses indicated no significant causal relationship between the genetically determined age at menarche (outlier-adjusted inverse variance weighted odds ratio [IVWOR] = 0.926; 95% confidence interval [CI], 0.803-1.066) or age at menopause (outlier-adjusted IVWOR = 0.981; 95% CI, 0.941-1.022) and AD risk. Similarly, AD did not show any causal association with age at menarche or age at menopause. The sensitivity analyses yielded similar results. In contrast, an inverse association was detected between age at menarche and body mass index (BMI, outlier-adjusted IVW β = -0.043; 95% CI, -0.077 to -0.009). Our bidirectional MR study provides no evidence for a causal relationship between the genetically determined age at menarche or age at menopause and AD susceptibility, or vice versa. However, earlier menarche might be associated with higher adult BMI.
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Affiliation(s)
- Mingli Li
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,School of Public Health of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Jiali Lin
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,School of Public Health of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Shuang Liang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,School of Public Health of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Zefeng Chen
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,School of Public Health of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Yulan Bai
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,School of Public Health of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Xinyang Long
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,School of Public Health of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Shengzhu Huang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,School of Public Health of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, Guangxi, China.,Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
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116
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Nevo D, Ogino S, Wang M. Reflection on modern methods: causal inference considerations for heterogeneous disease etiology. Int J Epidemiol 2021; 50:1030-1037. [PMID: 33484125 DOI: 10.1093/ije/dyaa278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 12/19/2020] [Indexed: 11/12/2022] Open
Abstract
Molecular pathological epidemiology research provides information about pathogenic mechanisms. A common study goal is to evaluate whether the effects of risk factors on disease incidence vary between different disease subtypes. A popular approach to carrying out this type of research is to implement a multinomial regression in which each of the non-zero values corresponds to a bona fide disease subtype. Then, heterogeneity in the exposure effects across subtypes is examined by comparing the coefficients of the exposure between the different subtypes. In this paper, we explain why this common method potentially cannot recover causal effects, even when all confounders are measured, due to a particular type of selection bias. This bias can be explained by recognizing that the multinomial regression is equivalent to a series of logistic regressions; each compares cases of a certain subtype to the controls. We further explain how this bias arises using directed acyclic graphs and we demonstrate the potential magnitude of the bias by analysis of a hypothetical data set and by a simulation study.
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Affiliation(s)
- Daniel Nevo
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Departments of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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117
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Mulvey B, Dougherty JD. Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assays. Transl Psychiatry 2021; 11:403. [PMID: 34294677 PMCID: PMC8298436 DOI: 10.1038/s41398-021-01493-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/02/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023] Open
Abstract
Family and population studies indicate clear heritability of major depressive disorder (MDD), though its underlying biology remains unclear. The majority of single-nucleotide polymorphism (SNP) linkage blocks associated with MDD by genome-wide association studies (GWASes) are believed to alter transcriptional regulators (e.g., enhancers, promoters) based on enrichment of marks correlated with these functions. A key to understanding MDD pathophysiology will be elucidation of which SNPs are functional and how such functional variants biologically converge to elicit the disease. Furthermore, retinoids can elicit MDD in patients and promote depressive-like behaviors in rodent models, acting via a regulatory system of retinoid receptor transcription factors (TFs). We therefore sought to simultaneously identify functional genetic variants and assess retinoid pathway regulation of MDD risk loci. Using Massively Parallel Reporter Assays (MPRAs), we functionally screened over 1000 SNPs prioritized from 39 neuropsychiatric trait/disease GWAS loci, selecting SNPs based on overlap with predicted regulatory features-including expression quantitative trait loci (eQTL) and histone marks-from human brains and cell cultures. We identified >100 SNPs with allelic effects on expression in a retinoid-responsive model system. Functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs), with additional allelic differences unmasked by treatment with all-trans retinoic acid (ATRA). Finally, motifs overrepresented across functional SNPs corresponded to TFs highly specific to serotonergic neurons, suggesting an in vivo site of action. Our application of MPRAs to screen MDD-associated SNPs suggests a shared transcriptional-regulatory program across loci, a component of which is unmasked by retinoids.
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Affiliation(s)
- Bernard Mulvey
- Departments of Genetics and Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Joseph D Dougherty
- Departments of Genetics and Psychiatry, Washington University in St. Louis, St. Louis, MO, USA.
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118
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Barbieri F, Inzaghi E, Caruso Nicoletti M, Cassio A, Grandone A, DE Sanctis L, Bizzarri C. Biological clock and heredity in pubertal timing: what is new? Minerva Pediatr (Torino) 2021; 73:537-548. [PMID: 34264049 DOI: 10.23736/s2724-5276.21.06511-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Puberty represents a milestone during a person's life and is characterized by several physical and psychological changes which end with the achievement of sexual maturation and of fertility. Puberty onset depends on a series of sophisticated, not completely understood, mechanisms certainly involving Gonadotropin-Releasing Hormone (GnRH) and its effects on pituitary gonadotropins. As recent evidence has demonstrated that pubertal timing deeply affects future adult health life, much efforts have been performed in order to clarify the exact actors involved in the onset and progression of puberty. Genetic factors are undoubtedly essential players in the regulation of pubertal development, accounting for approximately 50-80% of its variability. Mutations in genes such as KISS1, MKRN3 and DLK1 have been associated with central precocious puberty. Interestingly, a possible involvement of epigenetic mechanisms has been proposed as additional element able to affect pubertal phase. Environmental factors have recently attracted much attention. Indeed, an overall decrease in the age of puberty has been observed in the last decades. As genetic factors require long time to exert their effect, other players, such as environmental ones, may be involved. Special focus has been posed on nutritional status, endocrine-disrupting chemicals with non-conclusive results. Pubertal timing deeply affects future life, suggesting the need to clarify mechanisms driving pubertal onset and progression, in order to identify tailored therapeutic strategies and targets.
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Affiliation(s)
- Flavia Barbieri
- Pediatric Section, Department of translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Elena Inzaghi
- Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manuela Caruso Nicoletti
- Pediatric Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alessandra Cassio
- Pediatric Unit, Department of Medical and Surgical Sciences, S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Anna Grandone
- Departement of Women's and Children's Health and General and Specialized Surgery, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Luisa DE Sanctis
- Pediatric Endocrinology Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Carla Bizzarri
- Unit of Endocrinology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy -
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119
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Kim HI, Ye B, Staples J, Marcketta A, Gao C, Shuldiner AR, Van Hout CV. Genome-wide survey of parent-of-origin-specific associations across clinical traits derived from electronic health records. HGG ADVANCES 2021; 2:100039. [PMID: 35047837 PMCID: PMC8756508 DOI: 10.1016/j.xhgg.2021.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/31/2021] [Indexed: 11/03/2022] Open
Abstract
Parent-of-origin (PoO) effects refer to the differential phenotypic impacts of genetic variants dependent on their parental inheritance due to imprinting. While PoO effects can influence complex traits, they may be poorly captured by models that do not differentiate the parental origin of the variant. The aim of this study was to conduct a genome-wide screen for PoO effects on a broad range of clinical traits derived from electronic health records (EHR) in the DiscovEHR study enriched with familial relationships. Using pairwise kinship estimates from genetic data and demographic data, we identified 22,051 offspring among 134,049 individuals in the DiscovEHR study. PoO of ~9 million variants was assigned in the offspring by comparing offspring and parental genotypes and haplotypes. We then performed genome-wide PoO association analyses across 154 quantitative and 611 binary traits extracted from EHR. Of the 732 significant PoO associations identified (p < 5 × 10-8), we attempted to replicate 274 PoO associations in the UK Biobank study with 5,015 offspring and replicated 9 PoO associations (p < 0.05). In summary, our study implements a bioinformatic and statistical approach to examine PoO effects genome-wide in a large population study enriched with familial relationships and systematically characterizes PoO effects on hundreds of clinical traits derived from EHR. Our results suggest that, while the statistical power to detect PoO effects remains modest yet, accurately modeling PoO effects has the potential to find new associations that may have been missed by the standard additive model, further enhancing the mechanistic understanding of genetic influence on complex traits.
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Affiliation(s)
- Hye In Kim
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - Bin Ye
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | | | | | - Chuan Gao
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
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120
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Endocrine-Disrupting Chemicals and Early Puberty in Girls. CHILDREN-BASEL 2021; 8:children8060492. [PMID: 34200537 PMCID: PMC8226958 DOI: 10.3390/children8060492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/27/2022]
Abstract
In recent decades, pubertal onset in girls has been considered to occur at an earlier age than previously. Exposure to endocrine-disrupting chemicals (EDCs) has been associated with alterations in pubertal timing, with several reports suggesting that EDCs may have a role in the secular trend in pubertal maturation, at least in girls. However, relevant studies give inconsistent results. On the other hand, the majority of girls with idiopathic precocious or early puberty present the growth pattern of constitutional advancement of growth (CAG), i.e., growth acceleration soon after birth. Herein, we show that the growth pattern of CAG is unrelated to exposure to endocrine-disrupting chemicals and is the major determinant of precocious or early puberty. Presented data suggest that EDCs, at most, have a minor effect on the timing of pubertal onset in girls.
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121
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Effect of longevity genetic variants on the molecular aging rate. GeroScience 2021; 43:1237-1251. [PMID: 33948810 DOI: 10.1007/s11357-021-00376-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
We conducted a genome-wide association study of 1320 centenarians from the New England Centenarian Study (median age = 104 years) and 2899 unrelated controls using >9 M genetic variants imputed to the HRC panel of ~65,000 haplotypes. The genetic variants with the most significant associations were correlated to 4131 proteins that were profiled in the serum of a subset of 224 study participants using a SOMAscan array. The genetic associations were replicated in a genome-wide association study of 480 centenarians and ~800 controls of Ashkenazi Jewish descent. The proteomic associations were replicated in a proteomic scan of approximately 1000 Ashkenazi Jewish participants from a third cohort. The analysis replicated a protein signature associated with APOE genotypes and confirmed strong overexpression of BIRC2 (p < 5E-16) and under-expression of APOB in carriers of the APOE2 allele (p < 0.05). The analysis also discovered and replicated associations between longevity variants and slower changes of protein biomarkers of aging, including a novel protein signature of rs2184061 (CDKN2A/CDKN2B in chromosome 9) that suggests a genetic regulation of GDF15. The analyses showed that longevity variants correlate with proteome signatures that could be manipulated to discover healthy-aging targets.
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122
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Scagliotti V, Esse R, Willis TL, Howard M, Carrus I, Lodge E, Andoniadou CL, Charalambous M. Dynamic Expression of Imprinted Genes in the Developing and Postnatal Pituitary Gland. Genes (Basel) 2021; 12:genes12040509. [PMID: 33808370 PMCID: PMC8066104 DOI: 10.3390/genes12040509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
In mammals, imprinted genes regulate many critical endocrine processes such as growth, the onset of puberty and maternal reproductive behaviour. Human imprinting disorders (IDs) are caused by genetic and epigenetic mechanisms that alter the expression dosage of imprinted genes. Due to improvements in diagnosis, increasing numbers of patients with IDs are now identified and monitored across their lifetimes. Seminal work has revealed that IDs have a strong endocrine component, yet the contribution of imprinted gene products in the development and function of the hypothalamo-pituitary axis are not well defined. Postnatal endocrine processes are dependent upon the production of hormones from the pituitary gland. While the actions of a few imprinted genes in pituitary development and function have been described, to date there has been no attempt to link the expression of these genes as a class to the formation and function of this essential organ. This is important because IDs show considerable overlap, and imprinted genes are known to define a transcriptional network related to organ growth. This knowledge deficit is partly due to technical difficulties in obtaining useful transcriptomic data from the pituitary gland, namely, its small size during development and cellular complexity in maturity. Here we utilise high-sensitivity RNA sequencing at the embryonic stages, and single-cell RNA sequencing data to describe the imprinted transcriptome of the pituitary gland. In concert, we provide a comprehensive literature review of the current knowledge of the role of imprinted genes in pituitary hormonal pathways and how these relate to IDs. We present new data that implicate imprinted gene networks in the development of the gland and in the stem cell compartment. Furthermore, we suggest novel roles for individual imprinted genes in the aetiology of IDs. Finally, we describe the dynamic regulation of imprinted genes in the pituitary gland of the pregnant mother, with implications for the regulation of maternal metabolic adaptations to pregnancy.
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Affiliation(s)
- Valeria Scagliotti
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Ruben Esse
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Thea L. Willis
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
| | - Mark Howard
- MRC Centre for Transplantation, Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London SE19RT, UK;
| | - Isabella Carrus
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Emily Lodge
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
| | - Cynthia L. Andoniadou
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Marika Charalambous
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
- Correspondence:
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123
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Waters CD, Clemento A, Aykanat T, Garza JC, Naish KA, Narum S, Primmer CR. Heterogeneous genetic basis of age at maturity in salmonid fishes. Mol Ecol 2021; 30:1435-1456. [PMID: 33527498 DOI: 10.1111/mec.15822] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/07/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 × 10-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Anthony Clemento
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA.,Santa Cruz Laboratory, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, USA
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - John Carlos Garza
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA.,Santa Cruz Laboratory, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Shawn Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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124
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McGrath IM, Mortlock S, Montgomery GW. Genetic Regulation of Physiological Reproductive Lifespan and Female Fertility. Int J Mol Sci 2021; 22:2556. [PMID: 33806348 PMCID: PMC7961500 DOI: 10.3390/ijms22052556] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
There is substantial genetic variation for common traits associated with reproductive lifespan and for common diseases influencing female fertility. Progress in high-throughput sequencing and genome-wide association studies (GWAS) have transformed our understanding of common genetic risk factors for complex traits and diseases influencing reproductive lifespan and fertility. The data emerging from GWAS demonstrate the utility of genetics to explain epidemiological observations, revealing shared biological pathways linking puberty timing, fertility, reproductive ageing and health outcomes. The observations also identify unique genetic risk factors specific to different reproductive diseases impacting on female fertility. Sequencing in patients with primary ovarian insufficiency (POI) have identified mutations in a large number of genes while GWAS have revealed shared genetic risk factors for POI and ovarian ageing. Studies on age at menopause implicate DNA damage/repair genes with implications for follicle health and ageing. In addition to the discovery of individual genes and pathways, the increasingly powerful studies on common genetic risk factors help interpret the underlying relationships and direction of causation in the regulation of reproductive lifespan, fertility and related traits.
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Affiliation(s)
| | | | - Grant W. Montgomery
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072, Australia; (I.M.M.); (S.M.)
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125
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Fang J, Gong C, Su P, Wan Y, Zhang Z, Tao F, Sun Y. Polygenic interactions with adiposity rebound in the prediction of thelarche. Pediatr Res 2021; 89:1026-1031. [PMID: 32512580 DOI: 10.1038/s41390-020-1001-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 04/18/2020] [Accepted: 05/14/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND The earliest onset of puberty had shifted downward, which may be due to the role of early growth and development factors in childhood. METHODS All of 1575 Kindergarten Two (K2) children from Anhui province, China were followed up to elementary school. Girls (n = 342) with available data on AR and breast development were included for this analysis. Polygenic risk score (PRS) was computed based on 17 single nucleotide polymorphisms for early puberty. Accelerate failure time (AFT) model was used to describe thelarche timing by early AR among girls with different polygenic susceptibility. RESULTS After adjustment for perinatal anthropometric, household income, parental education and prepuberty BMI-Z score, puberty started 4.12-month earlier in early AR girls compared with normal AR girls (TR: 0.96; 95% CI: 0.95, 0.98, p < 0.001). Furthermore, this puberty-accelerating effect was observed among girls with high (6.06-month earlier, TR: 0.94; 95% CI: 0.90, 0.99) and moderate PRS (4.20-month earlier, TR: 0.96; 95% CI: 0.93, 0.98). No similar results were observed in the low PRS groups (TR: 1.00; 95% CI: 0.96, 1.04). CONCLUSIONS Girls with early AR displayed younger age at thelarche; however, this accelerating effect was only observed among those with genetic susceptibility to early puberty. IMPACT Early AR plays a more important role in predicting earlier thelarche among girls with high and moderate PRS. This study combined with the hot topics of pubertal-related polygenic risk score (PRS) for pubertal timing to examine the longitudinal association between early AR with accelerated pubertal onset. Our results mean that accelerating growth in the early childhood years after birth might forecast early puberty only among girls with genetic predisposition to early puberty. Prevention strategies and management options should be emphasized to target early childhood to address secular trend for early puberty observed in the past decades in China.
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Affiliation(s)
- Jiao Fang
- Department of Maternal, Child & Adolescent Health, School of Public Health, Hefei, Anhui Province, China
| | - Chun Gong
- Department of Maternal, Child & Adolescent Health, School of Public Health, Hefei, Anhui Province, China
| | - Puyu Su
- Department of Maternal, Child & Adolescent Health, School of Public Health, Hefei, Anhui Province, China.,Anhui Provincial Key Laboratory of Population Health & Aristogenics, Hefei, Anhui Province, China
| | - Yuhui Wan
- Anhui Provincial Key Laboratory of Population Health & Aristogenics, Hefei, Anhui Province, China
| | - Zhihua Zhang
- Department of Epidemiology and Biostatistics, Anhui Medical University, Hefei, Anhui Province, China
| | - Fangbiao Tao
- Department of Maternal, Child & Adolescent Health, School of Public Health, Hefei, Anhui Province, China.,Anhui Provincial Key Laboratory of Population Health & Aristogenics, Hefei, Anhui Province, China
| | - Ying Sun
- Department of Maternal, Child & Adolescent Health, School of Public Health, Hefei, Anhui Province, China. .,Anhui Provincial Key Laboratory of Population Health & Aristogenics, Hefei, Anhui Province, China.
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126
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Bacon ER, Brinton RD. Epigenetics of the developing and aging brain: Mechanisms that regulate onset and outcomes of brain reorganization. Neurosci Biobehav Rev 2021; 125:503-516. [PMID: 33657435 DOI: 10.1016/j.neubiorev.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
Brain development is a life-long process that encompasses several critical periods of transition, during which significant cognitive changes occur. Embryonic development, puberty, and reproductive senescence are all periods of transition that are hypersensitive to environmental factors. Rather than isolated episodes, each transition builds upon the last and is influenced by consequential changes that occur in the transition before it. Epigenetic marks, such as DNA methylation and histone modifications, provide mechanisms by which early events can influence development, cognition, and health outcomes. For example, parental environment influences imprinting patterns in gamete cells, which ultimately impacts gene expression in the embryo which may result in hypersensitivity to poor maternal nutrition during pregnancy, raising the risks for cognitive impairment later in life. This review explores how epigenetics induce and regulate critical periods, and also discusses how early environmental interactions prime a system towards a particular health outcome and influence susceptibility to disease or cognitive impairment throughout life.
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Affiliation(s)
- Eliza R Bacon
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; The Center for Precision Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Roberta Diaz Brinton
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Center for Innovation in Brain Science, School of Medicine, University of Arizona, Tucson, AZ, 85721, USA.
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127
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Quilter CR, Harvey KM, Bauer J, Skinner BM, Gomez M, Shrivastava M, Doel AM, Drammeh S, Dunger DB, Moore SE, Ong KK, Prentice AM, Bernstein RM, Sargent CA, Affara NA. Identification of methylation changes associated with positive and negative growth deviance in Gambian infants using a targeted methyl sequencing approach of genomic DNA. FASEB Bioadv 2021; 3:205-230. [PMID: 33842847 PMCID: PMC8019263 DOI: 10.1096/fba.2020-00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/25/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Low birthweight and reduced height gain during infancy (stunting) may arise at least in part from adverse early life environments that trigger epigenetic reprogramming that may favor survival. We examined differential DNA methylation patterns using targeted methyl sequencing of regions regulating gene activity in groups of rural Gambian infants: (a) low and high birthweight (DNA from cord blood (n = 16 and n = 20, respectively), from placental trophoblast tissue (n = 21 and n = 20, respectively), and DNA from peripheral blood collected from infants at 12 months of age (n = 23 and n = 17, respectively)), and, (b) the top 10% showing rapid postnatal length gain (high, n = 20) and the bottom 10% showing slow postnatal length gain (low, n = 20) based on z score change between birth and 12 months of age (LAZ) (DNA from peripheral blood collected from infants at 12 months of age). Using BiSeq analysis to identify significant methylation marks, for birthweight, four differentially methylated regions (DMRs) were identified in trophoblast DNA, compared to 68 DMRs in cord blood DNA, and 54 DMRs in 12‐month peripheral blood DNA. Twenty‐five DMRs were observed to be associated with high and low length for age (LAZ) at 12 months. With the exception of five loci (associated with two different genes), there was no overlap between these groups of methylation marks. Of the 194 CpG methylation marks contained within DMRs, 106 were located to defined gene regulatory elements (promoters, CTCF‐binding sites, transcription factor‐binding sites, and enhancers), 58 to gene bodies (introns or exons), and 30 to intergenic DNA. Distinct methylation patterns associated with birthweight between comparison groups were observed in DNA collected at birth (at the end of intrauterine growth window) compared to those established by 12 months (near the infancy/childhood growth transition). The longitudinal differences in methylation patterns may arise from methylation adjustments, changes in cellular composition of blood or both that continue during the critical postnatal growth period, and in response to early nutritional and infectious environmental exposures with impacts on growth and longer‐term health outcomes.
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Affiliation(s)
- Claire R Quilter
- Department of Pathology University of Cambridge Cambridge UK.,Present address: East Midlands & East of England NHS Genomic Laboratory Hub, Genomics Laboratories Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Kerry M Harvey
- Department of Pathology University of Cambridge Cambridge UK
| | - Julien Bauer
- Department of Pathology University of Cambridge Cambridge UK
| | - Benjamin M Skinner
- Department of Pathology University of Cambridge Cambridge UK.,School of Life Sciences University of Essex Colchester UK
| | - Maria Gomez
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Kennedy Institute of Rheumatology University of Oxford Oxford UK
| | - Manu Shrivastava
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Oxford University Hospitals Oxford UK
| | - Andrew M Doel
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Saikou Drammeh
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - David B Dunger
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK
| | - Sophie E Moore
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Ken K Ong
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK.,Department of Paediatrics University of Cambridge School of Clinical Medicine Cambridge UK.,Institute of Metabolic Science Cambridge Biomedical Campus Cambridge Cambridge UK
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Robin M Bernstein
- Growth and Development Lab Department of Anthropology University of Colorado Boulder CO USA.,Institute of Behavioural Science University of Colorado Boulder CO USA
| | | | - Nabeel A Affara
- Department of Pathology University of Cambridge Cambridge UK
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128
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Marla S, Mortlock S, Houshdaran S, Fung J, McKinnon B, Holdsworth-Carson SJ, Girling JE, Rogers PAW, Giudice LC, Montgomery GW. Genetic risk factors for endometriosis near estrogen receptor 1 and coexpression of genes in this region in endometrium. Mol Hum Reprod 2021; 27:gaaa082. [PMID: 33394050 PMCID: PMC8453628 DOI: 10.1093/molehr/gaaa082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Indexed: 01/14/2023] Open
Abstract
The etiology and pathogenesis of endometriosis are complex with both genetic and environmental factors contributing to disease risk. Genome-wide association studies (GWAS) have identified multiple signals in the estrogen receptor 1 (ESR1) region associated with endometriosis and other reproductive traits and diseases. In addition, candidate gene association studies identified signals in the ESR1 region associated with endometriosis risk suggesting genetic regulation of genes in this region may be important for reproductive health. This study aimed to investigate hormonal and genetic regulation of genes in the ESR1 region in human endometrium. Changes in serum oestradiol and progesterone concentrations and expression of hormone receptors ESR1 and progesterone receptor (PGR) were assessed in endometrial samples from 135 women collected at various stages of the menstrual cycle. Correlation between hormone concentrations, receptor expression and expression of genes in the ESR1 locus was investigated. The effect of endometriosis risk variants on expression of genes in the region was analyzed to identify gene targets. Hormone concentrations and receptor expression varied significantly across the menstrual cycle. Expression of genes in the ESR1 region correlated with progesterone concentration; however, they were more strongly correlated with expression of ESR1 and PGR suggesting coregulation of genes. There was no evidence that endometriosis risk variants directly regulated expression of genes in the region. Limited sample size and cellular heterogeneity in endometrial tissue may impact the ability to detect significant genetic effects on gene expression. Effects of these variants should be validated in a larger dataset and in relevant individual cell types.
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Affiliation(s)
- S Marla
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - S Mortlock
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - S Houshdaran
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - J Fung
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - B McKinnon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Department of Gynaecology, Inselspital, Bern, Switzerland
| | - S J Holdsworth-Carson
- Department of Obstetrics and Gynaecology, Gynaecology Research Centre, Royal Women’s Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | - J E Girling
- Department of Obstetrics and Gynaecology, Gynaecology Research Centre, Royal Women’s Hospital, University of Melbourne, Parkville, VIC 3052, Australia
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - P A W Rogers
- Department of Obstetrics and Gynaecology, Gynaecology Research Centre, Royal Women’s Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | - L C Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - G W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
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129
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Ponomarenko I, Reshetnikov E, Polonikov A, Verzilina I, Sorokina I, Yermachenko A, Dvornyk V, Churnosov M. Candidate Genes for Age at Menarche Are Associated With Uterine Leiomyoma. Front Genet 2021; 11:512940. [PMID: 33552117 PMCID: PMC7863975 DOI: 10.3389/fgene.2020.512940] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 10/14/2020] [Indexed: 12/23/2022] Open
Abstract
Age at menarche (AAM) is an important marker of the pubertal development and function of the hypothalamic-pituitary-ovarian system. It was reported as a possible factor for a risk of uterine leiomyoma (UL). However, while more than 350 loci for AAM have been determined by genome-wide association studies (GWASs) to date, no studies of these loci for their association with UL have been conducted so far. In this study, we analyzed 52 candidate loci for AAM for possible association with UL in a sample of 569 patients and 981 controls. The results of the study suggested that 23 out of the 52 studied polymorphisms had association with UL. Locus rs7759938 LIN28B was individually associated with the disease according to the dominant model. Twenty loci were associated with UL within 11 most significant models of intergenic interactions. Nine loci involved in 16 most significant models of interactions between single-nucleotide polymorphism (SNP), induced abortions, and chronic endometritis were associated with UL. Among the 23 loci associated with UL, 16 manifested association also with either AAM (7 SNPs) or height and/or body mass index (BMI) (13 SNPs). The above 23 SNPs and 514 SNPs linked to them have non-synonymous, regulatory, and expression quantitative trait locus (eQTL) significance for 35 genes, which play roles in the pathways related to development of the female reproductive organs and hormone-mediated signaling [false discovery rate (FDR) ≤ 0.05]. This is the first study reporting associations of candidate genes for AAM with UL.
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Affiliation(s)
- Irina Ponomarenko
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Evgeny Reshetnikov
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russia
| | - Irina Verzilina
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Inna Sorokina
- Department of Social Epidemiology, Pierre Louis Institute of Epidemiology and Public Health, Sorbonne Universités, Paris, France
| | - Anna Yermachenko
- Department of Social Epidemiology, Pierre Louis Institute of Epidemiology and Public Health, Sorbonne Universités, Paris, France
| | - Volodymyr Dvornyk
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
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130
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Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. Cancers (Basel) 2021; 13:cancers13020350. [PMID: 33477877 PMCID: PMC7832865 DOI: 10.3390/cancers13020350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that such dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. Abstract Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. We highlight the relevance of HIF and 2-OGDs in the control of gene expression in response to hypoxia and their relevance to human biology and health.
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131
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Ellingjord-Dale M, Papadimitriou N, Katsoulis M, Yee C, Dimou N, Gill D, Aune D, Ong JS, MacGregor S, Elsworth B, Lewis SJ, Martin RM, Riboli E, Tsilidis KK. Coffee consumption and risk of breast cancer: A Mendelian randomization study. PLoS One 2021; 16:e0236904. [PMID: 33465101 PMCID: PMC7815134 DOI: 10.1371/journal.pone.0236904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Observational studies have reported either null or weak protective associations for coffee consumption and risk of breast cancer. METHODS We conducted a two-sample Mendelian randomization (MR) analysis to evaluate the relationship between coffee consumption and breast cancer risk using 33 single-nucleotide polymorphisms (SNPs) associated with coffee consumption from a genome-wide association (GWA) study on 212,119 female UK Biobank participants of White British ancestry. Risk estimates for breast cancer were retrieved from publicly available GWA summary statistics from the Breast Cancer Association Consortium (BCAC) on 122,977 cases (of which 69,501 were estrogen receptor (ER)-positive, 21,468 ER-negative) and 105,974 controls of European ancestry. Random-effects inverse variance weighted (IVW) MR analyses were performed along with several sensitivity analyses to assess the impact of potential MR assumption violations. RESULTS One cup per day increase in genetically predicted coffee consumption in women was not associated with risk of total (IVW random-effects; odds ratio (OR): 0.91, 95% confidence intervals (CI): 0.80-1.02, P: 0.12, P for instrument heterogeneity: 7.17e-13), ER-positive (OR = 0.90, 95% CI: 0.79-1.02, P: 0.09) and ER-negative breast cancer (OR: 0.88, 95% CI: 0.75-1.03, P: 0.12). Null associations were also found in the sensitivity analyses using MR-Egger (total breast cancer; OR: 1.00, 95% CI: 0.80-1.25), weighted median (OR: 0.97, 95% CI: 0.89-1.05) and weighted mode (OR: 1.00, CI: 0.93-1.07). CONCLUSIONS The results of this large MR study do not support an association of genetically predicted coffee consumption on breast cancer risk, but we cannot rule out existence of a weak association.
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Affiliation(s)
- Merete Ellingjord-Dale
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Nikos Papadimitriou
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Michail Katsoulis
- Institute of Health Informatics Research, Faculty of Population Health Sciences, University College London, London, United Kingdom
| | - Chew Yee
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Niki Dimou
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Dagfinn Aune
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Nutrition, Bjørknes University College, Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Jue-Sheng Ong
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Stuart MacGregor
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Benjamin Elsworth
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Sarah J. Lewis
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Richard M. Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, United Kingdom
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Konstantinos K. Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, Ioannina, Greece
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132
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Stamou MI, Balasubramanian R. Hypothalamic Ceramides and the Ovarian Sympathetic System: At the Crossroads of Obesity and Puberty. Cell Metab 2021; 33:6-8. [PMID: 33264644 PMCID: PMC8939237 DOI: 10.1016/j.cmet.2020.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Childhood obesity has been linked to early puberty in girls but the mechanism(s) by which overnutrition triggers pubertal onset remain unclear. In a recent issue of Cell Metabolism, Heras et al., 2020 implicate a non-canonical central ceramide to ovarian sympathetic innervation pathway as a novel mediator of obesity-induced pubertal acceleration in female rats.
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Affiliation(s)
- Maria I Stamou
- Harvard MGH Center for Reproductive Medicine and Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ravikumar Balasubramanian
- Harvard MGH Center for Reproductive Medicine and Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA.
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133
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Abstract
Puberty, which in humans is considered to include both gonadarche and adrenarche, is the period of becoming capable of reproducing sexually and is recognized by maturation of the gonads and development of secondary sex characteristics. Gonadarche referring to growth and maturation of the gonads is fundamental to puberty since it encompasses increased gonadal steroid secretion and initiation of gametogenesis resulting from enhanced pituitary gonadotropin secretion, triggered in turn by robust pulsatile GnRH release from the hypothalamus. This chapter reviews the development of GnRH pulsatility from before birth until the onset of puberty. In humans, GnRH pulse generation is restrained during childhood and juvenile development. This prepubertal hiatus in hypothalamic activity is considered to result from a neurobiological brake imposed upon the GnRH pulse generator resident in the infundibular nucleus. Reactivation of the GnRH pulse generator initiates pubertal development. Current understanding of the genetics and physiology of the brake will be discussed, as will hypotheses proposed to account for timing the resurgence in pulsatile GnRH and initiation of puberty. The chapter ends with a discussion of disorders associated with precocious or delayed puberty with a focus on those with etiologies attributed to aberrant GnRH neuron anatomy or function. A pediatric approach to patients with pubertal disorders is provided and contemporary treatments for both precocious and delayed puberty outlined.
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Affiliation(s)
- Selma Feldman Witchel
- Pediatric Endocrinology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States.
| | - Tony M Plant
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, United States
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134
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Marcos-Pasero H, Aguilar-Aguilar E, Ikonomopoulou MP, Loria-Kohen V. BDNF Gene as a Precision Skill of Obesity Management. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1331:233-248. [PMID: 34453302 DOI: 10.1007/978-3-030-74046-7_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The scarcity of the results obtained for the treatment of obesity leads us to consider new strategies, contemplating all the factors involved in the development of the disease. One of the key molecules for controlling body weight and energy homeostasis is the brain-derived neurotrophic factor (BDNF). This work summarizes the mechanisms in which BDNF gene regulates this multifactorial disease. In addition, we discuss the role of other BDNF polymorphisms as genetic determinants of obesity. In this context, a total of 14 SNPs near or inside BDNF/BDNF-AS related to BMI were identified in various GWASs. Finally, we assess gene-diet interaction as a novel tool to prevent obesity and formulate solid and personalized nutritional management. Our research group has performed the first study on the association of BDNF-AS rs925946 polymorphism and calcium intake as potential modulators of the nutritional status. Although these results should be confirmed in future studies, they open the path for new prevention opportunities.
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Affiliation(s)
- Helena Marcos-Pasero
- Nutrition and Clinical Trials Unit, GENYAL Platform, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Elena Aguilar-Aguilar
- Nutrition and Clinical Trials Unit, GENYAL Platform, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Maria P Ikonomopoulou
- Translational Venomics Group, IMDEA-Food, CEI UAM+CSIC, Madrid, Spain.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Viviana Loria-Kohen
- Nutrition and Clinical Trials Unit, GENYAL Platform, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain. .,Department of Nutrition and Food Science, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain.
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135
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Kim JH, Lim JS. Early menarche and its consequence in Korean female: reducing fructose intake could be one solution. Clin Exp Pediatr 2021; 64:12-20. [PMID: 32403898 PMCID: PMC7806406 DOI: 10.3345/cep.2019.00353] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 12/27/2019] [Accepted: 02/28/2020] [Indexed: 12/31/2022] Open
Abstract
The mean age at menarche (AAM) of Korean females has been rapidly decreasing over the last 50 years; currently, the prevalence of early menarche (<12 years) is 22.3%. Female adolescents who experience early menarche are known to be at greater risk of psychosocial and behavioral problems along with several physical health problems such as menstrual problems. They also tend to achieve a shorter final height and develop obesity. Population-based Korean studies have shown a strong association between early menarche and the risk of obesity, insulin resistance, metabolic syndrome, nonalcoholic fatty liver disease, diabetes, breast cancer, and cardiovascular disease in adulthood. Although the exact mechanism of how early menarche causes cardiometabolic derangement in later adulthood is unknown, childhood obesity and insulin resistance might be major contributors. Recent studies demonstrated that an excessive consumption of fructose might underlie the development of obesity and insulin resistance along with an earlier AAM. A positive association was observed between sugar-sweetened beverages (a major source of fructose) intake and obesity, metabolic syndrome, insulin resistance, and cardiometabolic risk in Korean females. In pediatrics, establishing risk factors is important in preventing disease in later life. In this regard, early menarche is a simple and good marker for the management of cardiometabolic diseases in adulthood. Decreasing one's fructose intake might prevent early menarche as well as the development of obesity, insulin resistance, and cardiometabolic diseases.
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Affiliation(s)
- Ji Hyun Kim
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, Korea
| | - Jung Sub Lim
- Department of Pediatrics, Korea Cancer Center Hospital, Seoul, Korea
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Canton APM, Krepischi ACV, Montenegro LR, Costa S, Rosenberg C, Steunou V, Sobrier ML, Santana L, Honjo RS, Kim CA, de Zegher F, Idkowiak J, Gilligan LC, Arlt W, Funari MFDA, Jorge AADL, Mendonca BB, Netchine I, Brito VN, Latronico AC. Insights from the genetic characterization of central precocious puberty associated with multiple anomalies. Hum Reprod 2020; 36:506-518. [DOI: 10.1093/humrep/deaa306] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Abstract
STUDY QUESTION
Is there an (epi)genetic basis in patients with central precocious puberty (CPP) associated with multiple anomalies that unmasks underlying mechanisms or reveals novel genetic findings related to human pubertal control?
SUMMARY ANSWER
In a group of 36 patients with CPP associated with multiple phenotypes, pathogenic or likely pathogenic (epi)genetic defects were identified in 12 (33%) patients, providing insights into the genetics of human pubertal control.
WHAT IS KNOWN ALREADY
A few studies have described patients with CPP associated with multiple anomalies, but without making inferences on causalities of CPP. Genetic-molecular studies of syndromic cases may reveal disease genes or mechanisms, as the presentation of such patients likely indicates a genetic disorder.
STUDY DESIGN, SIZE, DURATION
This translational study was based on a genetic-molecular analysis, including genome-wide high throughput methodologies, for searching structural or sequence variants implicated in CPP and DNA methylation analysis of candidate regions.
PARTICIPANTS/MATERIALS, SETTING, METHODS
A cohort of 197 patients (188 girls) with CPP without structural brain lesions was submitted to a detailed clinical evaluation, allowing the selection of 36 unrelated patients (32 girls) with CPP associated with multiple anomalies. Pathogenic allelic variants of genes known to cause monogenic CPP (KISS1R, KISS1, MKRN3 and DLK1) had been excluded in the entire cohort (197 patients). All selected patients with CPP associated with multiple anomalies (n = 36) underwent methylation analysis of candidate regions and chromosomal microarray analysis. A subset (n = 9) underwent whole-exome sequencing, due to presenting familial CPP and/or severe congenital malformations and neurocognitive abnormalities.
MAIN RESULTS AND THE ROLE OF CHANCE
Among the 36 selected patients with CPP, the more prevalent associated anomalies were metabolic, growth and neurocognitive conditions. In 12 (33%) of them, rare genetic abnormalities were identified: six patients presented genetic defects in loci known to be involved with CPP (14q32.2 and 7q11.23), whereas the other six presented defects in candidate genes or regions. In detail, three patients presented hypomethylation of DLK1/MEG3:IG-DMR (14q32.2 disruption or Temple syndrome), resulting from epimutation (n = 1) or maternal uniparental disomy of chromosome 14 (n = 2). Seven patients presented pathogenic copy number variants: three with de novo 7q11.23 deletions (Williams–Beuren syndrome), three with inherited Xp22.33 deletions, and one with de novo 1p31.3 duplication. Exome sequencing revealed potential pathogenic variants in two patients: a sporadic female case with frameshift variants in TNRC6B and AREL1 and a familial male case with a missense substitution in UGT2B4 and a frameshift deletion in MKKS.
LIMITATIONS, REASONS FOR CAUTION
The selection of patients was based on a retrospective clinical characterization, lacking a longitudinal inclusion of consecutive patients. In addition, future studies are needed, showing the long-term (mainly reproductive) outcomes in the included patients, as most of them are not in adult life yet.
WIDER IMPLICATIONS OF THE FINDINGS
The results highlighted the relevance of an integrative clinical-genetic approach in the elucidation of mechanisms and factors involved in pubertal control. Chromosome 14q32.2 disruption indicated the loss of imprinting of DLK1 as a probable mechanism of CPP. Two other chromosomal regions (7q11.23 and Xp22.33) represented new candidate loci potentially involved in this disorder of pubertal timing.
STUDY FUNDING/COMPETING INTEREST(S)
This work was supported by grant number 2018/03198-0 (to A.P.M.C.) and grant number 2013/08028-1 (to A.C.V.K) from the São Paulo Research Foundation (FAPESP), and grant number 403525/2016-0 (to A.C.L.) and grant number 302849/2015-7 (to A.C.L.) and grant number 141625/2016-3 (to A.C.V.K) from the National Council for Scientific and Technological Development (CNPq). The authors have nothing to disclose.
TRIAL REGISTRATION NUMBER
N/A.
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Affiliation(s)
- Ana Pinheiro Machado Canton
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Luciana Ribeiro Montenegro
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Silvia Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Virginie Steunou
- University Sorbonne, INSERM, UMR_S 938, Saint-Antoine Research Center, Paris, France
| | - Marie-Laure Sobrier
- University Sorbonne, INSERM, UMR_S 938, Saint-Antoine Research Center, Paris, France
| | - Lucas Santana
- Genetic Endocrinology Unit, LIM25, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Rachel Sayuri Honjo
- Clinical Genetics Unit, Children’s Institute, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Chong Ae Kim
- Clinical Genetics Unit, Children’s Institute, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Francis de Zegher
- Department of Development and Regeneration, University of Leuven, Leuven, Belgium
| | - Jan Idkowiak
- Institute of Metabolism and Systems Research (IMSR), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Endocrinology and Diabetes, Birmingham Women’s and Children’s Hospital NHS Foundation Trust, Birmingham, UK
| | - Lorna C Gilligan
- Institute of Metabolism and Systems Research (IMSR), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Wiebke Arlt
- Institute of Metabolism and Systems Research (IMSR), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Mariana Ferreira de Assis Funari
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Alexander Augusto de Lima Jorge
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Genetic Endocrinology Unit, LIM25, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Berenice Bilharinho Mendonca
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Irène Netchine
- University Sorbonne, INSERM, UMR_S 938, Saint-Antoine Research Center, Paris, France
- AP-HP, Armand Trousseau Hospital, Endocrine Functional Exploration Service, Paris, France
| | - Vinicius Nahime Brito
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Latronico
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
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137
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Willis SC, Hess JE, Fryer JK, Whiteaker JM, Brun C, Gerstenberger R, Narum SR. Steelhead ( Oncorhynchus mykiss) lineages and sexes show variable patterns of association of adult migration timing and age-at-maturity traits with two genomic regions. Evol Appl 2020; 13:2836-2856. [PMID: 33294026 PMCID: PMC7691471 DOI: 10.1111/eva.13088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age-at-maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139-0.170; females R 2 = 0.096-0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock-specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.
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Affiliation(s)
- Stuart C. Willis
- Hagerman Genetics LaboratoryColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Jon E. Hess
- Hagerman Genetics LaboratoryColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Jeff K. Fryer
- Fishery Science DepartmentColumbia River Inter‐Tribal Fish CommissionPortlandORUSA
| | - John M. Whiteaker
- Fishery Science DepartmentColumbia River Inter‐Tribal Fish CommissionPortlandORUSA
| | - Chris Brun
- Branch of Natural Resources – Fisheries, Confederated Tribes of Warm SpringsPortlandORUSA
| | - Ryan Gerstenberger
- Branch of Natural Resources – Fisheries, Confederated Tribes of Warm SpringsPortlandORUSA
| | - Shawn R. Narum
- Hagerman Genetics LaboratoryColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
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138
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Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
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Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA
- Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
- Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
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139
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Gohil A, Eugster EA. Delayed and Precocious Puberty: Genetic Underpinnings and Treatments. Endocrinol Metab Clin North Am 2020; 49:741-757. [PMID: 33153677 PMCID: PMC7705597 DOI: 10.1016/j.ecl.2020.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Delayed puberty may signify a common variation of normal development, or indicate the presence of a pathologic process. Constitutional delay of growth and puberty is a strongly familial type of developmental pattern and accounts for the vast majority of children who are "late bloomers." Individuals with sex chromosomal abnormalities frequently have hypergonadotropic hypogonadism. There are currently 4 known monogenic causes of central precocious puberty. The primary treatment goal in children with hypogonadism is to mimic normal pubertal progression, while the primary aims for the management of precocious puberty are preservation of height potential and prevention of further pubertal development.
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Affiliation(s)
- Anisha Gohil
- Division of Pediatric Endocrinology, Department of Pediatrics, Riley Hospital for Children at IU Health, Indiana University School of Medicine, 705 Riley Hospital Drive, Room 5960, Indianapolis, IN 46202, USA.
| | - Erica A Eugster
- Division of Pediatric Endocrinology, Department of Pediatrics, Riley Hospital for Children at IU Health, Indiana University School of Medicine, 705 Riley Hospital Drive, Room 5960, Indianapolis, IN 46202, USA
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140
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Escala-Garcia M, Morra A, Canisius S, Chang-Claude J, Kar S, Zheng W, Bojesen SE, Easton D, Pharoah PDP, Schmidt MK. Breast cancer risk factors and their effects on survival: a Mendelian randomisation study. BMC Med 2020; 18:327. [PMID: 33198768 PMCID: PMC7670589 DOI: 10.1186/s12916-020-01797-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/25/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Observational studies have investigated the association of risk factors with breast cancer prognosis. However, the results have been conflicting and it has been challenging to establish causality due to potential residual confounding. Using a Mendelian randomisation (MR) approach, we aimed to examine the potential causal association between breast cancer-specific survival and nine established risk factors for breast cancer: alcohol consumption, body mass index, height, physical activity, mammographic density, age at menarche or menopause, smoking, and type 2 diabetes mellitus (T2DM). METHODS We conducted a two-sample MR analysis on data from the Breast Cancer Association Consortium (BCAC) and risk factor summary estimates from the GWAS Catalog. The BCAC data included 86,627 female patients of European ancestry with 7054 breast cancer-specific deaths during 15 years of follow-up. Of these, 59,378 were estrogen receptor (ER)-positive and 13,692 were ER-negative breast cancer patients. For the significant association, we used sensitivity analyses and a multivariable MR model. All risk factor associations were also examined in a model adjusted by other prognostic factors. RESULTS Increased genetic liability to T2DM was significantly associated with worse breast cancer-specific survival (hazard ratio [HR] = 1.10, 95% confidence interval [CI] = 1.03-1.17, P value [P] = 0.003). There were no significant associations after multiple testing correction for any of the risk factors in the ER-status subtypes. For the reported significant association with T2DM, the sensitivity analyses did not show evidence for violation of the MR assumptions nor that the association was due to increased BMI. The association remained significant when adjusting by other prognostic factors. CONCLUSIONS This extensive MR analysis suggests that T2DM may be causally associated with worse breast cancer-specific survival and therefore that treating T2DM may improve prognosis.
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Affiliation(s)
- Maria Escala-Garcia
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Anna Morra
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg (UCCH), Cancer Epidemiology Group, Hamburg, Germany
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Stig E Bojesen
- Copenhagen University Hospital, Copenhagen General Population Study, Herlev and Gentofte Hospital, Herlev, Denmark
- Copenhagen University Hospital, Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Doug Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
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141
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Ceballos FC, Hazelhurst S, Clark DW, Agongo G, Asiki G, Boua PR, Xavier Gómez-Olivé F, Mashinya F, Norris S, Wilson JF, Ramsay M. Autozygosity influences cardiometabolic disease-associated traits in the AWI-Gen sub-Saharan African study. Nat Commun 2020; 11:5754. [PMID: 33188201 PMCID: PMC7666169 DOI: 10.1038/s41467-020-19595-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 10/12/2020] [Indexed: 11/10/2022] Open
Abstract
The analysis of the effects of autozygosity, measured as the change of the mean value of a trait among offspring of genetic relatives, reveals the existence of directional dominance or overdominance. In this study we detect evidence of the effect of autozygosity in 4 out of 13 cardiometabolic disease-associated traits using data from more than 10,000 sub-Saharan African individuals recruited from Ghana, Burkina Faso, Kenya and South Africa. The effect of autozygosity on these phenotypes is found to be sex-related, with inbreeding having a significant decreasing effect in men but a significant increasing effect in women for several traits (body mass index, subcutaneous adipose tissue, low-density lipoproteins and total cholesterol levels). Overall, the effect of inbreeding depression is more intense in men. Differential effects of inbreeding depression are also observed between study sites with different night-light intensity used as proxy for urban development. These results suggest a directional dominant genetic component mediated by environmental interactions and sex-specific differences in genetic architecture for these traits in the Africa Wits-INDEPTH partnership for Genomic Studies (AWI-Gen) cohort.
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Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - David W Clark
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Godfred Agongo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Navrongo Health Research Centre, Navrongo, Ghana
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
| | - Palwende R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Faculty of Health Sciences University of the Witwatersrand, Division of Human Genetics, National Health Laboratory Service and School of Pathology, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Felistas Mashinya
- Department of Pathology and Medical Science, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Shane Norris
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Faculty of Health Sciences University of the Witwatersrand, Division of Human Genetics, National Health Laboratory Service and School of Pathology, Johannesburg, South Africa
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Faculty of Health Sciences University of the Witwatersrand, Division of Human Genetics, National Health Laboratory Service and School of Pathology, Johannesburg, South Africa.
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142
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Quach BC, Bray MJ, Gaddis NC, Liu M, Palviainen T, Minica CC, Zellers S, Sherva R, Aliev F, Nothnagel M, Young KA, Marks JA, Young H, Carnes MU, Guo Y, Waldrop A, Sey NYA, Landi MT, McNeil DW, Drichel D, Farrer LA, Markunas CA, Vink JM, Hottenga JJ, Iacono WG, Kranzler HR, Saccone NL, Neale MC, Madden P, Rietschel M, Marazita ML, McGue M, Won H, Winterer G, Grucza R, Dick DM, Gelernter J, Caporaso NE, Baker TB, Boomsma DI, Kaprio J, Hokanson JE, Vrieze S, Bierut LJ, Johnson EO, Hancock DB. Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits. Nat Commun 2020; 11:5562. [PMID: 33144568 PMCID: PMC7642344 DOI: 10.1038/s41467-020-19265-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Cigarette smoking is the leading cause of preventable morbidity and mortality. Genetic variation contributes to initiation, regular smoking, nicotine dependence, and cessation. We present a Fagerström Test for Nicotine Dependence (FTND)-based genome-wide association study in 58,000 European or African ancestry smokers. We observe five genome-wide significant loci, including previously unreported loci MAGI2/GNAI1 (rs2714700) and TENM2 (rs1862416), and extend loci reported for other smoking traits to nicotine dependence. Using the heaviness of smoking index from UK Biobank (N = 33,791), rs2714700 is consistently associated; rs1862416 is not associated, likely reflecting nicotine dependence features not captured by the heaviness of smoking index. Both variants influence nearby gene expression (rs2714700/MAGI2-AS3 in hippocampus; rs1862416/TENM2 in lung), and expression of genes spanning nicotine dependence-associated variants is enriched in cerebellum. Nicotine dependence (SNP-based heritability = 8.6%) is genetically correlated with 18 other smoking traits (rg = 0.40-1.09) and co-morbidities. Our results highlight nicotine dependence-specific loci, emphasizing the FTND as a composite phenotype that expands genetic knowledge of smoking.
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Affiliation(s)
- Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Michael J Bray
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Nathan C Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
| | - Camelia C Minica
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Stephanie Zellers
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
| | - Fazil Aliev
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Faculty of Business, Karabuk University, 78050, Kılavuzlar/Karabük Merkez/Karabük, Turkey
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Hannah Young
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Megan U Carnes
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Yuelong Guo
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- GeneCentric Therapeutics, Research Triangle Park, NC, 27709, USA
| | - Alex Waldrop
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Nancy Y A Sey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Maria T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Daniel W McNeil
- Department of Psychology, West Virginia University, Morgantown, WV, 26505, USA
- Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, 26505, USA
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Christina A Markunas
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Jacqueline M Vink
- Behavioural Science Institute, Radboud University, 6500 HE, Nijmegen, The Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - William G Iacono
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- VISN 4 MIRECC, Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Nancy L Saccone
- Department of Genetics, Washington University, St. Louis, MO, 63130, USA
- Division of Biostatistics, Washington University, St. Louis, MO, 63130, USA
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Pamela Madden
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, 68159, Mannheim, Germany
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Matthew McGue
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Georg Winterer
- Experimental & Clinical Research Center, Department of Anesthesiology and Operative Intensive Care Medicine, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Richard Grucza
- Departments of Family and Community Medicine and Health and Clinical Outcomes Research, Saint Louis University, St. Louis, MO, 63130, USA
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Psychiatry, VA CT Healthcare Center, West Haven, CT, 06511, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA.
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143
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Moustakas-Verho JE, Kurko J, House AH, Erkinaro J, Debes P, Primmer CR. Developmental expression patterns of six6: A gene linked with spawning ecotypes in Atlantic salmon. Gene Expr Patterns 2020; 38:119149. [PMID: 33007443 DOI: 10.1016/j.gep.2020.119149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/11/2020] [Accepted: 09/22/2020] [Indexed: 11/30/2022]
Abstract
The Atlantic salmon has been studied extensively, particularly as a model for understanding the genetic and environmental contributions to the evolution and development of life history traits. Expression pattern analysis in situ, however, is mostly lacking in salmon. We examine the embryonic developmental expression of six6, a candidate gene previously identified to be associated with spawning ecotypes and age at sexual maturity, in Atlantic salmon. Six6 is a member of the sine oculis homeobox family of transcription factors and is known to regulate eye and brain development in other vertebrates. We assay the expression of this gene in embryonic Atlantic salmon Salmo salar by whole-mount in situ hybridization. In line with earlier studies in other vertebrate species, we find conserved expression in the developing brain and sensory organs, including optic and olfactory primordia. However, we also find previously unreported domains of expression that suggest additional roles in axial and appendicular development, cardiovascular, intestinal, and sensory organogenesis. Each of these systems are important in the sensory ecology of Atlantic salmon, suggesting it is plausible that six6 may have pleiotropic roles in this complex phenotype.
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Affiliation(s)
- Jacqueline Emmanuel Moustakas-Verho
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland.
| | - Johanna Kurko
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland
| | - Andrew H House
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland
| | | | - Paul Debes
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland
| | - Craig Robert Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland.
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144
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145
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Maione L, Naulé L, Kaiser UB. Makorin RING finger protein 3 and central precocious puberty. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2020; 14:152-159. [PMID: 32984644 PMCID: PMC7518508 DOI: 10.1016/j.coemr.2020.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Makorin RING finger protein 3 (MKRN3) is a key inhibitor of the hypothalamic-pituitary-gonadal axis. Loss-of-function mutations in MKRN3 cause familial and sporadic central precocious puberty (CPP), while polymorphisms are associated with age at menarche. To date, 115 patients with CPP carrying MKRN3 mutations have been described, harboring 48 different genetic variants. The prevalence of MKRN3 mutations in genetically screened populations with CPP is estimated at 9.0%. Girls are more commonly and more seriously affected than boys. MKRN3 is expressed in humans and rodents in the central nervous system. Circulating levels in humans and hypothalamic expression in rodents decrease during pubertal progression. Although some MKRN3 regulators have been identified, the precise mechanism by which MKRN3 inhibits the hypothalamic-pituitary-gonadal axis remains elusive. The role of makorins in developmental physiology and organ differentiation and the role of maternal imprinting are discussed herein.
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Affiliation(s)
- Luigi Maione
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lydie Naulé
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ursula B Kaiser
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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146
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Roberts SA, Kaiser UB. GENETICS IN ENDOCRINOLOGY: Genetic etiologies of central precocious puberty and the role of imprinted genes. Eur J Endocrinol 2020; 183:R107-R117. [PMID: 32698138 PMCID: PMC7682746 DOI: 10.1530/eje-20-0103] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Pubertal timing is regulated by the complex interplay of genetic, environmental, nutritional and epigenetic factors. Criteria for determining normal pubertal timing, and thus the definition of precocious puberty, have evolved based on published population studies. The significance of the genetic influence on pubertal timing is supported by familial pubertal timing and twin studies. In contrast to the many monogenic causes associated with hypogonadotropic hypogonadism, only four monogenic causes of central precocious puberty (CPP) have been described. Loss-of-function mutations in Makorin Ring Finger Protein 3(MKRN3), a maternally imprinted gene on chromosome 15 within the Prader-Willi syndrome locus, are the most common identified genetic cause of CPP. More recently, several mutations in a second maternally imprinted gene, Delta-like noncanonical Notch ligand 1 (DLK1), have also been associated with CPP. Polymorphisms in both genes have also been associated with the age of menarche in genome-wide association studies. Mutations in the genes encoding kisspeptin (KISS1) and its receptor (KISS1R), potent activators of GnRH secretion, have also been described in association with CPP, but remain rare monogenic causes. CPP has both short- and long-term health implications for children, highlighting the importance of understanding the mechanisms contributing to early puberty. Additionally, given the role of mutations in the imprinted genes MKRN3 and DLK1 in pubertal timing, other imprinted candidate genes should be considered for a role in puberty initiation.
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Affiliation(s)
- Stephanie A. Roberts
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Ursula B. Kaiser
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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147
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Candidate genes for age at menarche are associated with endometrial hyperplasia. Gene 2020; 757:144933. [PMID: 32640302 DOI: 10.1016/j.gene.2020.144933] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/12/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022]
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148
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Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon. PLoS Genet 2020; 16:e1009055. [PMID: 32997662 PMCID: PMC7549781 DOI: 10.1371/journal.pgen.1009055] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 10/12/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the early and late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits. Alternative life history strategies are an important source of diversity within populations and promote the maintenance of adaptive capacity and population resilience. However, in many cases the molecular basis of different life history strategies remains elusive. Age at maturity is a key adaptive life history trait in Atlantic salmon and has a relatively simple genetic basis. Using salmon age at maturity as a model, we report a mechanism whereby different transcript isoforms of the key age at maturity gene, vestigial-like 3 (vgll3), associate with variation in the timing of male puberty. Our results show how gene regulatory differences in conjunction with variation in gene transcript structure can encode for complex alternative life histories.
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149
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Abstract
During menopausal transition, decreased level of estrogen brings a number of physiological problems and hormonal changes. In this study, promoter methylation of RANKL and FSHR genes were identified in 30 premenopausal and 35 postmenopausal women using methylation-specific high resolution melting (MS-HRM) analysis. The statistical analyses and their association with patient characteristics were performed by Pearson χ2 and Fisher's exact test (p <0.05). The methylated RANKL gene was detected in 16 postmenopausal cases, and 12 (75.0%) of the RANKL methylated cases had hot flashes (p = 0.024). The methylated FSHR gene was detected in 18 postmenopausal cases, and 13 (75.0%) of the methylated cases had hot flashes (p = 0.028). In vitro studies demonstrated the association between RANKL expression, FSH level and hot flashes in the mouse. Although lack of epigenetic studies in this field proves our results crucial and therefore, our results showed magnitude of epigenetic profiles of Turkish Cypriot post-menopausal women. This was the first study which has investigated the RANKL and FSHR methylation and their relationship with hot flashes in postmenopausal women.
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150
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Wu X, Niculite CM, Preda MB, Rossi A, Tebaldi T, Butoi E, White MK, Tudoran OM, Petrusca DN, Jannasch AS, Bone WP, Zong X, Fang F, Burlacu A, Paulsen MT, Hancock BA, Sandusky GE, Mitra S, Fishel ML, Buechlein A, Ivan C, Oikonomopoulos S, Gorospe M, Mosley A, Radovich M, Davé UP, Ragoussis J, Nephew KP, Mari B, McIntyre A, Konig H, Ljungman M, Cousminer DL, Macchi P, Ivan M. Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS. Nat Commun 2020; 11:4755. [PMID: 32958772 PMCID: PMC7505984 DOI: 10.1038/s41467-020-18411-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/16/2020] [Indexed: 01/09/2023] Open
Abstract
We hereby provide the initial portrait of lincNORS, a spliced lincRNA generated by the MIR193BHG locus, entirely distinct from the previously described miR-193b-365a tandem. While inducible by low O2 in a variety of cells and associated with hypoxia in vivo, our studies show that lincNORS is subject to multiple regulatory inputs, including estrogen signals. Biochemically, this lincRNA fine-tunes cellular sterol/steroid biosynthesis by repressing the expression of multiple pathway components. Mechanistically, the function of lincNORS requires the presence of RALY, an RNA-binding protein recently found to be implicated in cholesterol homeostasis. We also noticed the proximity between this locus and naturally occurring genetic variations highly significant for sterol/steroid-related phenotypes, in particular the age of sexual maturation. An integrative analysis of these variants provided a more formal link between these phenotypes and lincNORS, further strengthening the case for its biological relevance.
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Affiliation(s)
- Xue Wu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Cristina M Niculite
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,"Victor Babes" National Institute of Pathology, Bucharest, Romania
| | - Mihai Bogdan Preda
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Annalisa Rossi
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Toma Tebaldi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Elena Butoi
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Mattie K White
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Oana M Tudoran
- The Oncology Institute "Prof Dr. Ion Chiricuta", Cluj-Napoca, Romania
| | - Daniela N Petrusca
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Amber S Jannasch
- Metabolite Profiling Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - William P Bone
- Department of Genetics, Department of Systems Pharmacology and Translational Therapeutics, Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xingyue Zong
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fang Fang
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alexandrina Burlacu
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brad A Hancock
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - George E Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sumegha Mitra
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA.,Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Melissa L Fishel
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA.,Department of Pharmacology and Toxicology, Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Aaron Buechlein
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, 47405, USA
| | - Cristina Ivan
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Spyros Oikonomopoulos
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, Canada
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Amber Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Milan Radovich
- Departments of Radiation Oncology and Environmental Health Sciences, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Utpal P Davé
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, Canada
| | - Kenneth P Nephew
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.,Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA.,Medical Sciences, Indiana University School of Medicine, Bloomington, IN, USA
| | - Bernard Mari
- CNRS, IPMC, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Alan McIntyre
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Heiko Konig
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Centre for Cancer Sciences, Biodiscovery Institute, Nottingham University, Nottingham, UK
| | - Diana L Cousminer
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Mircea Ivan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA.
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