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Eisenberg DTA, Ryan CP, Lee NR, Carba DB, MacIsaac JL, Dever K, Atashzay P, Kobor MS, Kuzawa C. DNA methylation-based estimators of telomere length show low correspondence with paternal age at conception and other measures of external validity of telomere length. GeroScience 2024; 46:3957-3969. [PMID: 38466455 PMCID: PMC11226585 DOI: 10.1007/s11357-024-01114-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
In humans, DNA methylation (DNAm) based estimators of telomere length (TL) have been shown to better predict TL-associated variables (e.g., age, sex, and mortality) than TL itself. The biological significance of DNAm-based estimators of TL (DNAmTL) is unclear. In vitro DNAmTL shortens with cell replications, even when telomerase is maintaining TL. Telomerase is typically suppressed in humans, except in testes. Accordingly, sperm TL increases with age, and offspring with greater paternal age at conception (PAC) have longer TL. Thus, we expect that PAC associations with DNAmTL can shed light on whether in vivo cell replications in the presence of high telomerase activity (production of sperm) shorten DNAmTL or if PAC-lengthened TL causes lengthened DNAmTL. In a pre-registered analysis, using data from 1733 blood samples from the Philippines, we examined the association between paternal age at conception (PAC) and offspring DNAmTL. We did not find an association between PAC and DNAmTL but found a positive association of paternal grandfather's age at father's conception predicting grandchild's DNAmTL. In post hoc analyses, we examined how DNAmTL versus qPCR-measured TL (qPCR-TL) correlated with measures typically associated with TL. Contrary to previous findings, on almost all measures of external validity (correlations with parental TLs, southern blot TL, and age), qPCR-TL outperformed DNAmTL. The "kilobase" units of DNAm-based estimators of TL showed considerable deviations from southern blot-derived kilobase measures. Our findings suggest that DNAmTL is not a reliable index of inherited aspects of TL and underscores uncertainty about the biological meaning of DNAmTL.
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Affiliation(s)
- Dan T A Eisenberg
- Department of Anthropology, University of Washington, Seattle, WA, USA.
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, USA.
| | - Calen P Ryan
- Columbia Aging Center GeroScience Computational Core, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | - Delia B Carba
- USC-Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | - Julie L MacIsaac
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kristy Dever
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Parmida Atashzay
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Christopher Kuzawa
- Department of Anthropology, Northwestern University; Institute for Policy Research, Northwestern University, Evanston, IL, USA
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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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Sawant S, Oluwayiose OA, Nowak K, Maxwell DL, Houle E, Paskavitz AL, Saddiki H, Bertolla RP, Pilsner JR. Associations between Sperm Epigenetic Age and Semen Parameters: An Evaluation of Clinical and Non-Clinical Cohorts. Curr Issues Mol Biol 2024; 46:1567-1578. [PMID: 38392219 PMCID: PMC10887546 DOI: 10.3390/cimb46020101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
The well-documented relationship between chronological age and the sperm methylome has allowed for the construction of epigenetic clocks that estimate the biological age of sperm based on DNA methylation, which we previously termed sperm epigenetic age (SEA). Our lab demonstrated that SEA is positively associated with the time taken to achieve pregnancy; however, its relationship with semen parameters is unknown. A total of 379 men from the Longitudinal Investigation of Fertility and Environment (LIFE) study, a non-clinical cohort, and 192 men seeking fertility treatment from the Sperm Environmental Epigenetics and Development Study (SEEDS) were included in the study. Semen analyses were conducted for both cohorts, and SEA was previously generated using a machine learning algorithm and DNA methylation array data. Association analyses were conducted via multivariable linear regression models adjusting for BMI and smoking status. We found that SEA was not associated with standard semen characteristics in SEEDS and LIFE cohorts. However, SEA was significantly associated with higher sperm head length and perimeter, the presence of pyriform and tapered sperm, and lower sperm elongation factor in the LIFE study (p < 0.05). Based on our results, SEA is mostly associated with defects in sperm head morphological factors that are less commonly evaluated during male infertility assessments. SEA shows promise to be an independent biomarker of sperm quality to assess male fecundity.
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Affiliation(s)
- Savni Sawant
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology, Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Oladele A Oluwayiose
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Karolina Nowak
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - DruAnne L Maxwell
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Emily Houle
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Amanda L Paskavitz
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Hachem Saddiki
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ricardo P Bertolla
- Department of Surgery, Division of Urology, Human Reproduction Section, São Paulo Federal University, São Paulo 04024-001, Brazil
| | - J Richard Pilsner
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA
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Sciorio R, Tramontano L, Adel M, Fleming S. Decrease in Sperm Parameters in the 21st Century: Obesity, Lifestyle, or Environmental Factors? An Updated Narrative Review. J Pers Med 2024; 14:198. [PMID: 38392631 PMCID: PMC10890002 DOI: 10.3390/jpm14020198] [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: 01/18/2024] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Semen quality represents a compelling factor for fertility, and delineating the normal values has proven difficult. In the last four decades, several authors have reported a noticeable decline in sperm parameters. Also, studies investigating 'time to pregnancy' have shown that fecundity begins to be reduced when sperm numbers decrease below 30 million, even though according to the 6th edition of the WHO manual, the normal value is currently 16 million/mL or 39 million per ejaculate. There exists sufficient data to suggest a decline in sperm counts over time, even though the clear reason for this adverse trend is not well established, but some associations have been hypothesised, such as maternal smoking during pregnancy. Additional potential factors have yet to be fully illustrated but involve poor diet, increased obesity, and exposure to environmental toxins. Moreover, the change in environmental conditions and more common exposure to endocrine-disrupting chemicals (EDCs), such as pesticides and herbicides, as well as bisphenol A, phthalates, polychlorinated biphenyls, and heavy metals, starting from prenatal life and continuing into adulthood, may exhibit probable features explaining the reduction in sperm parameters. Therefore, the main goal of this narrative review is to furnish an overview of the possible effects of exposure to EDCs on testicular function and spermatogenesis and, also, to summarise the evidence regarding a decrease in sperm quality and examine its potential consequences.
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Affiliation(s)
- Romualdo Sciorio
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman-Mother-Child, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Luca Tramontano
- Department of Women, Infants and Adolescents, Division of Obstetrics, Geneva University Hospitals, 1211 Geneve, Switzerland
| | - Mohammed Adel
- Zoology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11651, Egypt
| | - Steven Fleming
- Discipline of Anatomy & Histology, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia
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5
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Stirland I, Soares MR, Furtado CLM, Dos Reis RM, Aston KI, Smith RP, Jenkins TG. An assessment of alterations to human sperm methylation patterns in coronavirus disease 2019 infected and healthy control males. F&S SCIENCE 2024; 5:2-15. [PMID: 38070681 DOI: 10.1016/j.xfss.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024]
Abstract
OBJECTIVE To determine whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affects male reproductive health, considering the many potential factors that contribute to declines in male fertility on a semiglobal scale. DESIGN In total, 64 human semen samples-32 treatment and 32 control-were laboratory processed and bioinformatically analyzed to assess differences in DNA methylation patterns. Implementing multiple bioinformatic tools, the analyses conducted will elicit between-group differences with respect to epigenetic age, epigenetic instability, semiglobal, and regional methylation, in addition to methylation patterns as a function of time since infection. SETTING University hospital. PATIENTS The study cohort of 64 individuals was drawn from a larger population of 94 volunteer participants recruited at the Human Reproduction Center at the Clinical Hospital of the Ribeirao Preto Medical School-University of São Paulo between June 2021 and January 2022 as well as in accordance with the ethical guidelines established by the Declaration of Helsinki. INTERVENTION Exposure to SARS-CoV-2. MAIN OUTCOME MEASURE(S) Effects on male reproductive health were reported as differences in DNA methylation measured using an array. Mean β values at key regulatory loci for human spermatocytes were analyzed and compared between groups. Further analysis of β values using epigenetic age, instability, semiglobal, and regional methylation tools provided an analysis with substantial breadth and depth. RESULTS In all analyses, there were no differences between groups. Considering these results, it can be inferred that infection with SARS-CoV-2 does not alter the epigenome of human spermatocytes in significant and/or persistent ways. Tangentially, these data also suggest that human male reproductive health is minimally altered by the virus, or that it is altered in a way that is independent of epigenetic programming. CONCLUSION Infection with SARS-CoV-2 has been reportedly associated with alterations in male fertility. This study asserts that such alterations do not have an epigenetic basis but are likely a result of concomitant symptomatology, i.e., fever and inflammation. Across the multiple bioinformatic analyses conducted, the results of this test did not detect any differences in DNA methylation patterns between coronavirus disease 2019 and noncoronavirus disease semen donor groups.
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Affiliation(s)
- Isaac Stirland
- Department of Cell Biology and Physiology, Brigham Young University, Provo, Utah
| | - Murilo Racy Soares
- Department of Obstetrics and Gynecology, Ribeirao Preto Medical School University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Cristiana Libardi Miranda Furtado
- Department of Obstetrics and Gynecology, Ribeirao Preto Medical School University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil; University of Fortaleza, Experimental Biology Center, Fortaleza, Ceara, Brazil
| | - Rosana Maria Dos Reis
- Department of Obstetrics and Gynecology, Ribeirao Preto Medical School University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Kenneth I Aston
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah
| | - R Parker Smith
- Department of Cell Biology and Physiology, Brigham Young University, Provo, Utah
| | - Timothy G Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, Utah; Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah.
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Dutta S, Goodrich JM, Dolinoy DC, Ruden DM. Biological Aging Acceleration Due to Environmental Exposures: An Exciting New Direction in Toxicogenomics Research. Genes (Basel) 2023; 15:16. [PMID: 38275598 PMCID: PMC10815440 DOI: 10.3390/genes15010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Biological clock technologies are designed to assess the acceleration of biological age (B-age) in diverse cell types, offering a distinctive opportunity in toxicogenomic research to explore the impact of environmental stressors, social challenges, and unhealthy lifestyles on health impairment. These clocks also play a role in identifying factors that can hinder aging and promote a healthy lifestyle. Over the past decade, researchers in epigenetics have developed testing methods that predict the chronological and biological age of organisms. These methods rely on assessing DNA methylation (DNAm) levels at specific CpG sites, RNA levels, and various biomolecules across multiple cell types, tissues, and entire organisms. Commonly known as 'biological clocks' (B-clocks), these estimators hold promise for gaining deeper insights into the pathways contributing to the development of age-related disorders. They also provide a foundation for devising biomedical or social interventions to prevent, reverse, or mitigate these disorders. This review article provides a concise overview of various epigenetic clocks and explores their susceptibility to environmental stressors.
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Affiliation(s)
- Sudipta Dutta
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (J.M.G.); (D.C.D.)
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (J.M.G.); (D.C.D.)
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Douglas M. Ruden
- C. S. Mott Center for Human Health and Development, Department of Obstetrics and Gynecology, Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA
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7
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Klutstein M, Gonen N. Epigenetic aging of mammalian gametes. Mol Reprod Dev 2023; 90:785-803. [PMID: 37997675 DOI: 10.1002/mrd.23717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023]
Abstract
The process of aging refers to physiological changes that occur to an organism as time progresses and involves changes to DNA, proteins, metabolism, cells, and organs. Like the rest of the cells in the body, gametes age, and it is well established that there is a decline in reproductive capabilities in females and males with aging. One of the major pathways known to be involved in aging is epigenetic changes. The epigenome is the multitude of chemical modifications performed on DNA and chromatin that affect the ability of chromatin to be transcribed. In this review, we explore the effects of aging on female and male gametes with a focus on the epigenetic changes that occur in gametes throughout aging. Quality decline in oocytes occurs at a relatively early age. Epigenetic changes constitute an important part of oocyte aging. DNA methylation is reduced with age, along with reduced expression of DNA methyltransferases (DNMTs). Histone deacetylases (HDAC) expression is also reduced, and a loss of heterochromatin marks occurs with age. As a consequence of heterochromatin loss, retrotransposon expression is elevated, and aged oocytes suffer from DNA damage. In sperm, aging affects sperm number, motility and fecundity, and epigenetic changes may constitute a part of this process. 5 methyl-cytosine (5mC) methylation is elevated in sperm from aged men, but methylation on Long interspersed nuclear elements (LINE) elements is reduced. Di and trimethylation of histone 3 lysine 9 (H3K9me2/3) is reduced in sperm from aged men and trimethylation of histone 3 lysine 27 (H3K27me3) is elevated. The protamine makeup of sperm from aged men is also changed, with reduced protamine expression and a misbalanced ratio between protamine proteins protamine P1 and protamine P2. The study of epigenetic reproductive aging is recently gaining interest. The current status of the field suggests that many aspects of gamete epigenetic aging are still open for investigation. The clinical applications of these investigations have far-reaching consequences for fertility and sociological human behavior.
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Affiliation(s)
- Michael Klutstein
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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8
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Potabattula R, Prell A, Dittrich M, Nava C, Depienne C, Bejaoui Y, El Hajj N, Hahn T, Schorsch M, Haaf T. Effects of paternal and chronological age on BEGAIN methylation and its possible role in autism. Aging (Albany NY) 2023; 15:12763-12779. [PMID: 38019471 DOI: 10.18632/aging.205275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 11/30/2023]
Abstract
Children from old fathers carry an increased risk for autism spectrum (ASD) and other neurodevelopmental disorders, which may at least partially be mediated by paternal age effects on the sperm epigenome. The brain enriched guanylate kinase associated (BEGAIN) protein is involved in protein-protein interactions at and transmission across synapses. Since several epigenome-wide methylation screens reported a paternal age effect on sperm BEGAIN methylation, here we confirmed a significant negative correlation between BEGAIN promoter methylation and paternal age, using more sensitive bisulfite pyrosequencing and a larger number of sperm samples. Paternal age-associated BEGAIN hypomethylation was also observed in fetal cord blood (FCB) of male but not of female offspring. There was no comparable maternal age effect on FCB methylation. In addition, we found a significant negative correlation between BEGAIN methylation and chronological age (ranging from 1 to 70 years) in peripheral blood samples of male but not of female donors. BEGAIN hypomethylation was more pronounced in male children, adolescents and adults suffering from ASD compared to controls. Both genetic variation (CC genotype of SNP rs7141087) and epigenetic factors may contribute to BEGAIN promoter hypomethylation. The age- and sex-specific BEGAIN methylation trajectories in the male germ line and somatic tissues, in particular the brain, support a role of this gene in ASD development.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Caroline Nava
- U.F. de Neurogénétique Moléculaire et Cellulaire, Dpt. de Génétique et Cytogénétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Yosra Bejaoui
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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Kotková L, Drábek J. Age-related changes in sperm DNA methylation and their forensic and clinical implications. Epigenomics 2023; 15:1157-1173. [PMID: 38031735 DOI: 10.2217/epi-2023-0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
As a link between a stable genome and a dynamic environment, epigenetics is a promising tool for mapping age-related changes in human DNA. Methylated cytosine changes at specific loci are generally less studied in sperm DNA than in somatic cell DNA. Age-related methylation changes can be connected to various reproductive health problems and multiple disorders in offspring. In addition, they can be helpful in forensic fields, where testing of specific loci in semen samples found at sexual assault crime scenes can predict a perpetrator's age and narrow down the police investigation. This review focuses on age-related methylation changes in sperm. It covers the biological role of methylation, methylation testing techniques and the implications of methylation changes in forensics and clinical practice.
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Affiliation(s)
- Lucie Kotková
- Institute of Molecular & Translational Medicine, Faculty of Medicine & Dentistry, Palacky University Olomouc and University Hospital Olomouc, 77900, Czech Republic
| | - Jiří Drábek
- Institute of Molecular & Translational Medicine, Faculty of Medicine & Dentistry, Palacky University Olomouc and University Hospital Olomouc, 77900, Czech Republic
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10
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Xiao C, Li Y, Chen M, Yi S, Huang D. Improved age estimation from semen using sperm-specific age-related CpG markers. Forensic Sci Int Genet 2023; 67:102941. [PMID: 37820545 DOI: 10.1016/j.fsigen.2023.102941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/25/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
Accurate age estimation from semen has the potential to greatly narrow the pool of unidentified suspects in sexual assault investigations. However, previous efforts utilizing semen age-related CpG (AR-CpG) markers have shown lower accuracy compared to blood AR-CpG-based methods. This discrepancy may be attributed to DNA methylation (DNAm) interferences from "round cells" such as leukocytes and immature sperm cells in semen. This study aimed to develop age calculators based on sperm-specific AR-CpG markers and to achieve performance-improved age estimates from sperm DNA. Through an analysis of publicly available MethylationEPIC microarray data from 90 sperm samples of healthy males aged 22-51 years, we identified 31 sperm-specific AR-CpG markers with absolute Pearson's R values > 0.5 and Benjamini-Hochberg adjusted p values < 0.013. The top 19 AR-CpG markers with the largest absolute R values and beta ranges > 0.10, along with 3 reported semen AR-CpG markers (cg06304190, cg06979108, and cg12837463), were integrated into two methylation SNaPshot panels (Ⅰ and Ⅱ), each containing 11 markers. The 21 qualified AR-CpG markers showed absolute R values ≥ 0.427 in an independent validation cohort of 253 sperm DNA samples (22-67 years), with cg21843517 exhibiting the strongest age correlation (R = 0.853). The optimal models, constructed using sperm DNAm data of the training set (n = 214, 22-67 years) and markers from panel Ⅰ (n = 11), panel Ⅱ (n = 10), or both panels, achieved mean absolute errors (MAEs) of 2.526-4.746, 3.890-5.715, and > 9.800 years on the test sets of sperm (n = 39, 23-64 years), semen (same donors as the sperm test set), and whole blood (n = 40, 22-65 years), respectively. The simplified models incorporating 3, 5, 9, or 14 AR-CpG markers (MAE = 2.918-4.139 years for sperm) still outperformed the Lee et al. original model (MAE = 6.444 years for semen) and the reconstructed panel Lee model (MAE = 6.011 years for sperm). The final models, utilizing all sperm DNAm data (n = 253) and markers from panel Ⅰ, panel Ⅱ, or both panels, yielded mean MAEs of 2.587, 2.766, and 2.200 years, respectively, on the 50 test sets generated by 5 repeats of 10-fold cross-validations. Additionally, multiple markers in both panels demonstrated the ability to discern sperm or semen from blood with 100% accuracy. In summary, our study substantiates the potential of sperm-specific AR-CpG markers for precise age estimation from sperm DNA, providing an improved toolset for forensic investigations.
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Affiliation(s)
- Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China; Hubei Key Laboratory of the Forensic Science, Hubei University of Police, Wuhan, Hubei 430035, PR China.
| | - Ya Li
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Maomin Chen
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
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Avraham S, Schütz L, Käver L, Dankers A, Margalit S, Michaeli Y, Zirkin S, Torchinsky D, Gilat N, Bahr O, Nifker G, Koren-Michowitz M, Weinhold E, Ebenstein Y. Chemo-Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5-Methylcytosine And 5-Hydroxymethylcytosine. Chembiochem 2023; 24:e202300400. [PMID: 37518671 DOI: 10.1002/cbic.202300400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/05/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
5-Methylcytosine and 5-hydroxymethylcytosine are epigenetic modifications involved in gene regulation and cancer. We present a new, simple, and high-throughput platform for multi-color epigenetic analysis. The novelty of our approach is the ability to multiplex methylation and de-methylation signals in the same assay. We utilize an engineered methyltransferase enzyme that recognizes and labels all unmodified CpG sites with a fluorescent cofactor. In combination with the already established labeling of the de-methylation mark 5-hydroxymethylcytosine via enzymatic glycosylation, we obtained a robust platform for simultaneous epigenetic analysis of these marks. We assessed the global epigenetic levels in multiple samples of colorectal cancer and observed a 3.5-fold reduction in 5hmC levels but no change in DNA methylation levels between sick and healthy individuals. We also measured epigenetic modifications in chronic lymphocytic leukemia and observed a decrease in both modification levels (5-hydroxymethylcytosine: whole blood 30 %; peripheral blood mononuclear cells (PBMCs) 40 %. 5-methylcytosine: whole blood 53 %; PBMCs 48 %). Our findings propose using a simple blood test as a viable method for analysis, simplifying sample handling in diagnostics. Importantly, our results highlight the assay's potential for epigenetic evaluation of clinical samples, benefiting research and patient management.
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Affiliation(s)
- Sigal Avraham
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Larissa Käver
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Andreas Dankers
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Sapir Margalit
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shahar Zirkin
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Dmitry Torchinsky
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Noa Gilat
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Omer Bahr
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gil Nifker
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | | | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
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12
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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13
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de Sena Brandine G, Aston KI, Jenkins TG, Smith AD. Global effects of identity and aging on the human sperm methylome. Clin Epigenetics 2023; 15:127. [PMID: 37550724 PMCID: PMC10408082 DOI: 10.1186/s13148-023-01541-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND As the average age of fatherhood increases worldwide, so too does the need for understanding effects of aging in male germline cells. Molecular change, including epigenomic alterations, may impact offspring. Age-associated change to DNA cytosine methylation in the cytosine-guanine (CpG) context is a hallmark of aging tissues, including sperm. Prior studies have led to accurate models that predict a man's age based on specific methylation features in the DNA of sperm, but the relationship between aging and global DNA methylation in sperm remains opaque. Further clarification requires a more complete survey of the methylome with assessment of variability within and between individuals. RESULTS We collected sperm methylome data in a longitudinal study of ten healthy fertile men. We used whole-genome bisulfite sequencing of samples collected 10 to 18 years apart from each donor. We found that, overall, variability between donors far exceeds age-associated variation. After controlling for donor identity, we see significant age-dependent genome-wide change to the methylome. Notably, trends of change with age depend on genomic location or annotation, with contrasting signatures that correlate with gene density and proximity to centromeres and promoter regions. CONCLUSIONS We uncovered epigenetic signatures that reflect a stable process which begins in early adulthood, progressing steadily through most of the male lifespan, and warrants consideration in any future study of the aging sperm epigenome.
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Affiliation(s)
- Guilherme de Sena Brandine
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, USA
| | - Timothy G Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, USA
| | - Andrew D Smith
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA.
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Lahimer M, Montjean D, Cabry R, Capelle S, Lefranc E, Bach V, Ajina M, Ben Ali H, Khorsi-Cauet H, Benkhalifa M. Paternal Age Matters: Association with Sperm Criteria's- Spermatozoa DNA Integrity and Methylation Profile. J Clin Med 2023; 12:4928. [PMID: 37568329 PMCID: PMC10420110 DOI: 10.3390/jcm12154928] [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: 06/02/2023] [Revised: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Advanced age has been reported to negatively affect sperm parameters and spermatozoa DNA integrity. A decline in sperm criteria was also associated with altered epigenetic marks such as DNA methylation with a potential downstream impact on in vitro fertilization success and clinical outcomes. The aim of the present retrospective study was to clarify the association between advanced paternal age (APA) and sperm parameters, DNA integrity and DNA methylation profile. A total of 671 patients consulting for infertility underwent sperm analysis, sperm DNA integrity assessment and methylation level measurement. The principal finding was that individuals over 40 years of age exhibit a significant increase in DNA fragmentation levels compared to the younger group (15% versus 9%, respectively, p = 0.04). However, there was no significant difference in DNA decondensation and sperm parameters in association with APA. In addition, a drop in the global methylation level was also found in men over 40 years (6% in the young group versus 2% in the old group, p = 0.03). As a conclusion, men over 40 years are at higher risk of elevated sperm DNA fragmentation and lower methylation level. Based on these observations, it is recommended that the assessment of sperm DNA fragmentation should be taken into consideration particularly after the age of 40. Our findings support the idea that paternal age is a crucial factor that should not be neglected during fertility evaluation and treatment since it is associated with epigenetics changes in sperm. Although the underlying mechanism remains to be clarified, we believe that environmental and professional exposure factors are likely involved in the process.
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Affiliation(s)
- Marwa Lahimer
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
- Exercise Physiology and Physiopathology: From Integrated to Molecular “Biology, Medicine and Health” (Code: LR19ES09), Sousse 4002, Tunisia
| | - Debbie Montjean
- Fertilys, Centres de Fertilité, Laval and Brossard, Québec, QC H7S 1Z5, Canada;
| | - Rosalie Cabry
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
| | - Severine Capelle
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
| | - Elodie Lefranc
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
| | - Véronique Bach
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
| | - Mounir Ajina
- Unit of Reproductive Medicine, University Hospital Farhat Hached, Sousse 4000, Tunisia;
| | - Habib Ben Ali
- Faculty of Medicine of Sousse, University of Sousse, Sousse 4000, Tunisia;
| | - Hafida Khorsi-Cauet
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
| | - Moncef Benkhalifa
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
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15
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Kayser M, Branicki W, Parson W, Phillips C. Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age. Forensic Sci Int Genet 2023; 65:102870. [PMID: 37084623 DOI: 10.1016/j.fsigen.2023.102870] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland,; Institute of Forensic Research, Kraków, Poland
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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16
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Bernhardt L, Dittrich M, Prell A, Potabattula R, Drummer C, Behr R, Hahn T, Schorsch M, Müller T, Haaf T. Age-related methylation changes in the human sperm epigenome. Aging (Albany NY) 2023; 15:1257-1278. [PMID: 36849136 PMCID: PMC10042684 DOI: 10.18632/aging.204546] [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: 11/02/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
Advanced paternal age is associated with increased risks for reproductive and offspring medical problems. Accumulating evidence suggests age-related changes in the sperm epigenome as one underlying mechanism. Using reduced representation bisulfite sequencing on 73 sperm samples of males attending a fertility center, we identified 1,162 (74%) regions which were significantly (FDR-adjusted) hypomethylated and 403 regions (26%) being hypermethylated with age. There were no significant correlations with paternal BMI, semen quality, or ART outcome. The majority (1,152 of 1,565; 74%) of age-related differentially methylated regions (ageDMRs) were located within genic regions, including 1,002 genes with symbols. Hypomethylated ageDMRs were closer to transcription start sites than hypermethylated DMRs, half of which reside in gene-distal regions. In this and conceptually related genome-wide studies, so far 2,355 genes have been reported with significant sperm ageDMRs, however most (90%) of them in only one study. The 241 genes which have been replicated at least once showed significant functional enrichments in 41 biological processes associated with development and the nervous system and in 10 cellular components associated with synapses and neurons. This supports the hypothesis that paternal age effects on the sperm methylome affect offspring behaviour and neurodevelopment. It is interesting to note that sperm ageDMRs were not randomly distributed throughout the human genome; chromosome 19 showed a highly significant twofold enrichment with sperm ageDMRs. Although the high gene density and CpG content have been conserved, the orthologous marmoset chromosome 22 did not appear to exhibit an increased regulatory potential by age-related DNA methylation changes.
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Affiliation(s)
- Laura Bernhardt
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Charis Drummer
- Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Göttingen and German Center for Cardiovascular Research, Partner Site Göttingen, Göttingen, Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Göttingen and German Center for Cardiovascular Research, Partner Site Göttingen, Göttingen, Germany
| | | | | | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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Odroniec A, Olszewska M, Kurpisz M. Epigenetic markers in the embryonal germ cell development and spermatogenesis. Basic Clin Androl 2023; 33:6. [PMID: 36814207 PMCID: PMC9948345 DOI: 10.1186/s12610-022-00179-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/25/2022] [Indexed: 02/24/2023] Open
Abstract
Spermatogenesis is the process of generation of male reproductive cells from spermatogonial stem cells in the seminiferous epithelium of the testis. During spermatogenesis, key spermatogenic events such as stem cell self-renewal and commitment to meiosis, meiotic recombination, meiotic sex chromosome inactivation, followed by cellular and chromatin remodeling of elongating spermatids occur, leading to sperm cell production. All the mentioned events are at least partially controlled by the epigenetic modifications of DNA and histones. Additionally, during embryonal development in primordial germ cells, global epigenetic reprogramming of DNA occurs. In this review, we summarized the most important epigenetic modifications in the particular stages of germ cell development, in DNA and histone proteins, starting from primordial germ cells, during embryonal development, and ending with histone-to-protamine transition during spermiogenesis.
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Affiliation(s)
- Amadeusz Odroniec
- grid.413454.30000 0001 1958 0162Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60–479 Poznan, Poland
| | - Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.
| | - Maciej Kurpisz
- grid.413454.30000 0001 1958 0162Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60–479 Poznan, Poland
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Stalker K, Pollard C, Aston K, Jenkins T. Tissue specific age acceleration patterns in the sperm of oligozoospermic men. FRONTIERS IN REPRODUCTIVE HEALTH 2022; 4:1043904. [PMID: 36505395 PMCID: PMC9727134 DOI: 10.3389/frph.2022.1043904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
To determine if disease can modify aging patterns in an affected tissue without altering the aging patterns of other tissues, blood and semen of individuals with oligozoospermia (n = 10) were compared to the blood and semen of individuals with normozoospermia (n = 24). DNA methylation data was obtained via Illumina's 850 K array. The Horvath and Jenkins age calculators were then utilized to predict the epigenetic age of blood and sperm. Epigenetic age of sperm was approximated using germ-line age differential (GLAD) values. Using nonpaired t-tests, it was found that sperm of oligozoospermic men (mean GLAD score of 0.078) were predicted to be significantly older than the sperm of normozoospermic men (mean GLAD score of -0.017), returning a p-value of 0.03. However, there was not a significant epigenetic age difference between the blood of those with oligozoospermia (mean GLAD equivalent score of -0.027) and normozoospermia (mean GLAD equivalent score of 0.048), producing a p-value of 0.20. These results lead to the conclusion that tissue specific aging is occurring in sperm of oligozoospermic individuals but not in unaffected somatic tissues (in this case, blood).
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Affiliation(s)
- Kelaney Stalker
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, United States
| | - Chad Pollard
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, United States
| | - Kenneth Aston
- Department of Surgery, Division of Urology, University of Utah, Salt Lake City, UT, United States
| | - Tim Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, United States,Department of Surgery, Division of Urology, University of Utah, Salt Lake City, UT, United States,Correspondence: Tim Jenkins
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Ambroa-Conde A, Girón-Santamaría L, Mosquera-Miguel A, Phillips C, Casares de Cal M, Gómez-Tato A, Álvarez-Dios J, de la Puente M, Ruiz-Ramírez J, Lareu M, Freire-Aradas A. Epigenetic age estimation in saliva and in buccal cells. Forensic Sci Int Genet 2022; 61:102770. [DOI: 10.1016/j.fsigen.2022.102770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/04/2022]
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Epigenetic clock: A promising biomarker and practical tool in aging. Ageing Res Rev 2022; 81:101743. [PMID: 36206857 DOI: 10.1016/j.arr.2022.101743] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
As a complicated process, aging is characterized by various changes at the cellular, subcellular and nuclear levels, one of which is epigenetic aging. With increasing awareness of the critical role that epigenetic alternations play in aging, DNA methylation patterns have been employed as a measure of biological age, currently referred to as the epigenetic clock. This review provides a comprehensive overview of the epigenetic clock as a biomarker of aging and a useful tool to manage healthy aging. In this burgeoning scientific field, various kinds of epigenetic clocks continue to emerge, including Horvath's clock, Hannum's clock, DNA PhenoAge, and DNA GrimAge. We hereby present the most classic epigenetic clocks, as well as their differences. Correlations of epigenetic age with morbidity, mortality and other factors suggest the potential of epigenetic clocks for risk prediction and identification in the context of aging. In particular, we summarize studies on promising age-reversing interventions, with epigenetic clocks employed as a practical tool in the efficacy evaluation. We also discuss how the lack of higher-quality information poses a major challenge, and offer some suggestions to address existing obstacles. Hopefully, our review will help provide an appropriate understanding of the epigenetic clocks, thereby enabling novel insights into the aging process and how it can be manipulated to promote healthy aging.
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Oluwayiose OA, Houle E, Wu H, Whitcomb BW, Mumford SL, Schisterman EF, Suvorov A, Balzer LB, Pilsner JR. Urinary phthalate metabolites and their mixtures are associated with advanced sperm epigenetic aging in a general population. ENVIRONMENTAL RESEARCH 2022; 214:114115. [PMID: 35988832 DOI: 10.1016/j.envres.2022.114115] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/22/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION We have recently shown that sperm epigenetic age (SEA), a surrogate measure of biological aging in sperm, is associated with couples' time-to-pregnancy (TTP). Advanced SEA was also observed among smokers, suggesting its susceptibility to environmental exposures. Therefore, we assessed the association between urinary phthalate metabolites and SEA in male partners of couples planning to conceive among the general population. METHOD The Longitudinal Investigation of Fertility and the Environment (LIFE) Study was a prospective multi-site and general population cohort study of couples who were interested in becoming pregnant. Among male partners (n = 333), eleven urinary phthalate metabolites were measured and SEA was previously developed using Super Learner ensemble algorithm. Multivariable linear regression was used to evaluate associations of SEA with individual metabolites. Bayesian kernel machine regression (BKMR), quantile g-computation (qgcomp) and weighted quantile sum (WQS) models were used for mixture analyses. Covariates included were BMI, cotinine, race and urinary creatinine. RESULT In the single metabolite multivariate analyses, nine (82%) phthalate metabolites displayed positive trends with SEA (range: 0.05-0.47 years). Of these metabolites, advanced SEA was significantly associated with interquartile range increases in exposure of three phthalates [MEHHP (β = 0.23, 95% CI: 0.03, 0.43, p = 0.03), MMP (β = 0.24, 95% CI: 0.01, 0.47, p = 0.04), and MiBP (β = 0.47, 95% CI: 0.14, 0.81, p = 0.01)]. Additionally, in BKMR and qgcomp (p = 0.06), but not WQS models, phthalate mixtures showed an overall positive trend with SEA, with MiBP, MMP and MBzP as major drivers of the mixture effects. CONCLUSION This is the first study that combined single exposure and mixture models to associate male phthalate exposures with advanced epigenetic aging of sperm in men planning to conceive among the general population. Our findings suggest that phthalate exposure may contribute to the acceleration of biological aging of sperm.
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Affiliation(s)
- Oladele A Oluwayiose
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Emily Houle
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 W 168th St, New York, NY, 10032, USA
| | - Brian W Whitcomb
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, USA
| | - Sunni L Mumford
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Enrique F Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexander Suvorov
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, MA, USA
| | - Laura B Balzer
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, USA
| | - J Richard Pilsner
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA; Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
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22
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Oluwayiose OA, Wu H, Gao F, Baccarelli AA, Sofer T, Pilsner JR. Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses. Bioinformatics 2022; 38:4820-4822. [PMID: 36028931 PMCID: PMC9563687 DOI: 10.1093/bioinformatics/btac583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/27/2022] [Accepted: 08/25/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION A wide range of computational packages has been developed for regional DNA methylation analyses of Illumina's Infinium array data. Aclust, one of the first unsupervised algorithms, was originally designed to analyze regional methylation of Infinium's 27K and 450K arrays by clustering neighboring methylation sites prior to downstream analyses. However, Aclust relied on outdated packages that rendered it largely non-operational especially with the newer Infinium EPIC and mouse arrays. RESULTS We have created Aclust2.0, a streamlined pipeline that involves five steps for the analyses of human (450K and EPIC) and mouse array data. Aclust2.0 provides a user-friendly pipeline and versatile for regional DNA methylation analyses for molecular epidemiological and mouse studies. AVAILABILITY AND IMPLEMENTATION Aclust2.0 is freely available on Github (https://github.com/OluwayioseOA/Alcust2.0.git).
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Affiliation(s)
- Oladele A Oluwayiose
- Department of Obstetrics and Gynecology, School of Medicine, C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI 48201, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Feng Gao
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Tamar Sofer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - J Richard Pilsner
- Department of Obstetrics and Gynecology, School of Medicine, C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI 48201, USA
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA
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23
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Dong S, Chen C, Zhang J, Gao Y, Zeng X, Zhang X. Testicular aging, male fertility and beyond. Front Endocrinol (Lausanne) 2022; 13:1012119. [PMID: 36313743 PMCID: PMC9606211 DOI: 10.3389/fendo.2022.1012119] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/26/2022] [Indexed: 11/15/2022] Open
Abstract
Normal spermatogenesis and sperm function are crucial for male fertility. The effects of healthy testicular aging and testicular premature aging on spermatogenesis, sperm function, and the spermatogenesis microenvironment cannot be ignored. Compared with younger men, the testis of older men tends to have disturbed spermatogenic processes, sperm abnormalities, sperm dysfunction, and impaired Sertoli and Leydig cells, which ultimately results in male infertility. Various exogenous and endogenous factors also contribute to pathological testicular premature aging, such as adverse environmental stressors and gene mutations. Mechanistically, Y-chromosomal microdeletions, increase in telomere length and oxidative stress, accumulation of DNA damage with decreased repair ability, alterations in epigenetic modifications, miRNA and lncRNA expression abnormalities, have been associated with impaired male fertility due to aging. In recent years, the key molecules and signaling pathways that regulate testicular aging and premature aging have been identified, thereby providing new strategies for diagnosis and treatment. This review provides a comprehensive overview of the underlying mechanisms of aging on spermatogenesis. Furthermore, potential rescue measures for reproductive aging have been discussed. Finally, the inadequacy of testicular aging research and future directions for research have been envisaged to aid in the diagnosis and treatment of testicular aging and premature aging.
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Affiliation(s)
- Shijue Dong
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Chen Chen
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Jiali Zhang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Yuan Gao
- Laboratory Animal Center, Nantong University, Nantong, China
| | - Xuhui Zeng
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Xiaoning Zhang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
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24
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Ashapkin V, Suvorov A, Pilsner JR, Krawetz SA, Sergeyev O. Age-associated epigenetic changes in mammalian sperm: implications for offspring health and development. Hum Reprod Update 2022; 29:24-44. [PMID: 36066418 PMCID: PMC9825272 DOI: 10.1093/humupd/dmac033] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 08/05/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Modern reproductive behavior in most developed countries is characterized by delayed parenthood. Older gametes are generally less fertile, accumulating and compounding the effects of varied environmental exposures that are modified by lifestyle factors. Clinicians are primarily concerned with advanced maternal age, while the influence of paternal age on fertility, early development and offspring health remains underappreciated. There is a growing trend to use assisted reproductive technologies for couples of advanced reproductive age. Thus, the number of children born from older gametes is increasing. OBJECTIVE AND RATIONALE We review studies reporting age-associated epigenetic changes in mammals and humans in sperm, including DNA methylation, histone modifications and non-coding RNAs. The interplay between environment, fertility, ART and age-related epigenetic signatures is explored. We focus on the association of sperm epigenetics on epigenetic and phenotype events in embryos and offspring. SEARCH METHODS Peer-reviewed original and review articles over the last two decades were selected using PubMed and the Web of Science for this narrative review. Searches were performed by adopting the two groups of main terms. The first group included 'advanced paternal age', 'paternal age', 'postponed fatherhood', 'late fatherhood', 'old fatherhood' and the second group included 'sperm epigenetics', 'sperm', 'semen', 'epigenetic', 'inheritance', 'DNA methylation', 'chromatin', 'non-coding RNA', 'assisted reproduction', 'epigenetic clock'. OUTCOMES Age is a powerful factor in humans and rodent models associated with increased de novo mutations and a modified sperm epigenome. Age affects all known epigenetic mechanisms, including DNA methylation, histone modifications and profiles of small non-coding (snc)RNA. While DNA methylation is the most investigated, there is a controversy about the direction of age-dependent changes in differentially hypo- or hypermethylated regions with advanced age. Successful development of the human sperm epigenetic clock based on cross-sectional data and four different methods for DNA methylation analysis indicates that at least some CpG exhibit a linear relationship between methylation levels and age. Rodent studies show a significant overlap between genes regulated through age-dependent differentially methylated regions and genes targeted by age-dependent sncRNA. Both age-dependent epigenetic mechanisms target gene networks enriched for embryo developmental, neurodevelopmental, growth and metabolic pathways. Thus, age-dependent changes in the sperm epigenome cannot be described as a stochastic accumulation of random epimutations and may be linked with autism spectrum disorders. Chemical and lifestyle exposures and ART techniques may affect the epigenetic aging of sperm. Although most epigenetic modifications are erased in the early mammalian embryo, there is growing evidence that an altered offspring epigenome and phenotype is linked with advanced paternal age due to the father's sperm accumulating epigenetic changes with time. It has been hypothesized that age-induced changes in the sperm epigenome are profound, physiological and dynamic over years, yet stable over days and months, and likely irreversible. WIDER IMPLICATIONS This review raises a concern about delayed fatherhood and age-associated changes in the sperm epigenome that may compromise reproductive health of fathers and transfer altered epigenetic information to subsequent generations. Prospective studies using healthy males that consider confounders are recommended. We suggest a broader discussion focused on regulation of the father's age in natural and ART conceptions is needed. The professional community should be informed and should raise awareness in the population and when counseling older men.
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Affiliation(s)
| | | | - J Richard Pilsner
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Oleg Sergeyev
- Correspondence address. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory, House 1, Building 40, Room 322, Moscow 119992, Russia. E-mail: https://orcid.org/0000-0002-5745-3348
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25
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Borgstrøm MB, Grøndahl ML, W. Klausen T, K. Danielsen A, Thomsen T, Bentin-Ley U, B. Knudsen U, Laursen S, R. Petersen M, Haahr K, Petersen K, Lemmen JG, Hindkjær J, Kirk J, Fedder J, J. Almind G, Hnida C, Troest B, B. Povlsen B, Zedeler A, Gabrielsen A, Larsen T, S. Kesmodel U. Is paternal age associated with transfer day, developmental stage, morphology, and initial hCG-rise of the competent blastocyst leading to live birth? A multicenter cohort study. PLoS One 2022; 17:e0270664. [PMID: 35901038 PMCID: PMC9333207 DOI: 10.1371/journal.pone.0270664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/14/2022] [Indexed: 11/18/2022] Open
Abstract
In this study we investigated whether age of men undergoing assisted reproductive technology (ART) treatment was associated with day of transfer, stage, morphology, and initial hCG-rise of the competent blastocyst leading to a live birth? The design was a multicenter historical cohort study based on exposure (age) and outcome data (blastocyst stage and morphology and initial hCG-rise) from men whose partner underwent single blastocyst transfer resulting in singleton pregnancy/birth. The ART treatments were carried out at sixteen private and university-based public fertility clinics. We included 7246 men and women, who between 2014 and 2018 underwent controlled ovarian stimulation (COS) or Frozen-thawed Embryo Transfer (FET) with a single blastocyst transfer resulting in singleton pregnancy were identified. 4842 men with a partner giving birth were included, by linking data to the Danish Medical Birth Registry. We showed that the adjusted association between paternal age and transfer day in COS treatments was OR 1.06, 95% CI (1.00;1.13). Meaning that for every increase of one year, men had a 6% increased probability that the competent blastocyst was transferred on day 6 compared to day 5. Further we showed that the mean difference in hCG values when comparing paternal age group 30–34, 35–39 and 40–45 with the age group 25–29 in those receiving COS treatment, all showed significantly lower adjusted values for older men. In conclusion we hypothesize that the later transfer (day 6) in female partners of older men may be due to longer time spent by the oocyte to repair fragmented DNA of the sperm cells, which should be a focus of future research in men.
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Affiliation(s)
- Maria Buhl Borgstrøm
- Department of Obstetrics and Gynecology, The Fertility Clinic, Copenhagen University Hospital Herlev, Herlev, Denmark
- Aalborg University, Aalborg, Denmark
- * E-mail:
| | - Marie Louise Grøndahl
- Department of Obstetrics and Gynecology, The Fertility Clinic, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Tobias W. Klausen
- Department of Hematology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Anne K. Danielsen
- Department of Gastroenterology, Copenhagen University Hospital Herlev, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Thordis Thomsen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Anaesthesiology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Ursula Bentin-Ley
- Danish Fertility Clinic, The Fertility Partnership Denmark, Copenhagen, Denmark
| | - Ulla B. Knudsen
- The Fertility Clinic at Horsens regional hospital, Horsens, Deenmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Morten R. Petersen
- Department of Obstetrics and Gynecology, The Fertility Clinic, Copenhagen University hospital, Rigshospitalet, Denmark
| | | | | | | | | | - John Kirk
- Maigaard Fertility Clinic, Aarhus, Denmark
| | - Jens Fedder
- The Fertility Clinic, Odense University Hospital, Odense, Denmark
| | | | - Christina Hnida
- The Fertility Clinic, Zealand University Hospital Køge, Køge, Denmark
| | - Bettina Troest
- Aalborg University, Aalborg, Denmark
- The Fertility Unit, Aalborg University Hospital, Aalborg, Denmark
| | | | - Anne Zedeler
- Department of Obstetrics and Gynecology, The Fertility Clinic, Copenhagen University Hospital, Hvidovre, Denmark
| | - Anette Gabrielsen
- The Fertility Clinic at Horsens regional hospital, Horsens, Deenmark
| | | | - Ulrik S. Kesmodel
- Aalborg University, Aalborg, Denmark
- The Fertility Unit, Aalborg University Hospital, Aalborg, Denmark
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26
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Setti AS, Braga DPDAF, Guilherme P, Vingris L, Iaconelli A, Borges E. Paternal ageing impacts blastulation and the outcomes of pregnancy at different levels of maternal age: A clustering analysis of 21,960 oocytes and 3837 ICSI cycles. Andrologia 2022; 54:e14485. [PMID: 35698244 DOI: 10.1111/and.14485] [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: 02/14/2022] [Revised: 04/20/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
The objective of this cross-sectional study was to investigate the impact of paternal age on the outcomes of intracytoplasmic sperm injection (ICSI) cycles at different values of maternal age. A total of 21,960 injected oocytes deriving from 3837 ICSI cycles performed between January 2014 and October 2020, performed in a private university-affiliated in vitro fertilization centre was included. The main effects of maternal and paternal age, as well as the effect of their product (interaction term) on embryo development and pregnancy outcomes were investigated considering the clustering of data. The coefficients for the interaction term were statistically significant for blastocyst development, top-quality blastocyst, implantation, pregnancy, miscarriage, and live-birth rates. For every 1-year increase in paternal age, the odds ratio of live-birth reduces by 1% in females aged 37 years, 1.6% in those aged 38 years, 2.4% in 39-year-old females, 5% in 42-year-old females and so on. An increase in the interaction term by 1 year decreases the pregnancy rate by 0.4% and live-birth rate by 0.8 and increases the miscarriage rate by 1.2%. The slopes of maternal age on blastulation, blastocyst quality, and implantation, pregnancy, miscarriage, and live-birth rate significantly changed (worsened) for every year increase in paternal age.
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Affiliation(s)
- Amanda Souza Setti
- Fertility Medical Group, São Paulo, Brazil.,Sapientiae Institute - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, Brazil
| | | | | | | | - Assumpto Iaconelli
- Fertility Medical Group, São Paulo, Brazil.,Sapientiae Institute - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, Brazil
| | - Edson Borges
- Fertility Medical Group, São Paulo, Brazil.,Sapientiae Institute - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, Brazil
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27
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Pilsner JR, Saddiki H, Whitcomb BW, Suvorov A, Buck Louis GM, Mumford SL, Schisterman EF, Oluwayiose OA, Balzer LB. Sperm epigenetic clock associates with pregnancy outcomes in the general population. Hum Reprod 2022; 37:1581-1593. [PMID: 35552703 PMCID: PMC9247414 DOI: 10.1093/humrep/deac084] [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: 12/14/2021] [Revised: 03/28/2022] [Indexed: 12/25/2022] Open
Abstract
STUDY QUESTION Is sperm epigenetic aging (SEA) associated with probability of pregnancy among couples in the general population? SUMMARY ANSWER We observed a 17% lower cumulative probability at 12 months for couples with male partners in the older compared to the younger SEA categories. WHAT IS KNOWN ALREADY The strong relation between chronological age and DNA methylation profiles has enabled the estimation of biological age as epigenetic 'clock' metrics in most somatic tissue. Such clocks in male germ cells are less developed and lack clinical relevance in terms of their utility to predict reproductive outcomes. STUDY DESIGN, SIZE, DURATION This was a population-based prospective cohort study of couples discontinuing contraception to become pregnant recruited from 16 US counties from 2005 to 2009 and followed for up to 12 months. PARTICIPANTS/MATERIALS, SETTING, METHODS Sperm DNA methylation from 379 semen samples was assessed via a beadchip array. A state-of-the-art ensemble machine learning algorithm was employed to predict age from the sperm DNA methylation data. SEA was estimated from clocks derived from individual CpGs (SEACpG) and differentially methylated regions (SEADMR). Probability of pregnancy within 1 year was compared by SEA, and discrete-time proportional hazards models were used to evaluate the relations with time-to-pregnancy (TTP) with adjustment for covariates. MAIN RESULTS AND THE ROLE OF CHANCE Our SEACpG clock had the highest predictive performance with correlation between chronological and predicted age (r = 0.91). In adjusted discrete Cox models, SEACpG was negatively associated with TTP (fecundability odds ratios (FORs)=0.83; 95% CI: 0.76, 0.90; P = 1.2×10-5), indicating a longer TTP with advanced SEACpG. For subsequent birth outcomes, advanced SEACpG was associated with shorter gestational age (n = 192; -2.13 days; 95% CI: -3.67, -0.59; P = 0.007). Current smokers also displayed advanced SEACpG (P < 0.05). Finally, SEACpG showed a strong performance in an independent IVF cohort (n = 173; r = 0.83). SEADMR performance was comparable to SEACpG but with attenuated effect sizes. LIMITATIONS, REASONS FOR CAUTION This prospective cohort study consisted primarily of Caucasian men and women, and thus analysis of large diverse cohorts is necessary to confirm the associations between SEA and couple pregnancy success in other races/ethnicities. WIDER IMPLICATIONS OF THE FINDINGS These data suggest that our sperm epigenetic clocks may have utility as a novel biomarker to predict TTP among couples in the general population and underscore the importance of the male partner for reproductive success. STUDY FUNDING/COMPETING INTEREST(S) This work was funded in part by grants the National Institute of Environmental Health Sciences, National Institutes of Health (R01 ES028298; PI: J.R.P. and P30 ES020957); Robert J. Sokol, MD Endowed Chair of Molecular Obstetrics and Gynecology (J.R.P.); and the Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland (Contracts N01-HD-3-3355, N01-HD-3-3356 and N01-HD-3-3358). S.L.M. was supported by the Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health. The authors declare no competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- J Richard Pilsner
- Correspondence address. Department of Obstetrics and Gynecology, Wayne State University, 275 East Hancock, Detroit, MI 48201, USA. E-mail: (J.R.P.); Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 N. Pleasant Street, Amherst, MA 01003, USA. E-mail: (L.B.B.)
| | - Hachem Saddiki
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Brian W Whitcomb
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Alexander Suvorov
- Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Sunni L Mumford
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enrique F Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oladele A Oluwayiose
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Laura B Balzer
- Correspondence address. Department of Obstetrics and Gynecology, Wayne State University, 275 East Hancock, Detroit, MI 48201, USA. E-mail: (J.R.P.); Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 N. Pleasant Street, Amherst, MA 01003, USA. E-mail: (L.B.B.)
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28
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Olszewska M, Kordyl O, Kamieniczna M, Fraczek M, Jędrzejczak P, Kurpisz M. Global 5mC and 5hmC DNA Levels in Human Sperm Subpopulations with Differentially Protaminated Chromatin in Normo- and Oligoasthenozoospermic Males. Int J Mol Sci 2022; 23:ijms23094516. [PMID: 35562907 PMCID: PMC9099774 DOI: 10.3390/ijms23094516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/14/2022] [Accepted: 04/17/2022] [Indexed: 12/17/2022] Open
Abstract
Epigenetic modifications play a special role in the male infertility aetiology. Published data indicate the link between sperm quality and sperm chromatin protamination. This study aimed to determine the relationship between methylation (5mC) and hydroxymethylation (5hmC) in sperm DNA, with respect to sperm chromatin protamination in three subpopulations of fertile normozoospermic controls and infertile patients with oligo-/oligoasthenozoospermia. For the first time, a sequential staining protocol was applied, which allowed researchers to analyse 5mC/5hmC levels by immunofluorescence staining, with a previously determined chromatin protamination status (aniline blue staining), using the same spermatozoa. TUNEL assay determined the sperm DNA fragmentation level. The 5mC/5hmC levels were diversified with respect to chromatin protamination status in both studied groups of males, with the highest values observed in protaminated spermatozoa. The linkage between chromatin protamination and 5mC/5hmC levels in control males disappeared in patients with deteriorated semen parameters. A relationship between 5mC/5hmC and sperm motility/morphology was identified in the patient group. Measuring the 5mC/5hmC status of sperm DNA according to sperm chromatin integrity provides evidence of correct spermatogenesis, and its disruption may represent a prognostic marker for reproductive failure.
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Affiliation(s)
- Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland; (M.K.); (M.F.)
- Correspondence: (M.O.); (M.K.)
| | - Oliwia Kordyl
- Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland;
| | - Marzena Kamieniczna
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland; (M.K.); (M.F.)
| | - Monika Fraczek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland; (M.K.); (M.F.)
| | - Piotr Jędrzejczak
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, 60-535 Poznan, Poland;
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland; (M.K.); (M.F.)
- Correspondence: (M.O.); (M.K.)
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29
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Prell A, Sen MO, Potabattula R, Bernhardt L, Dittrich M, Hahn T, Schorsch M, Zacchini F, Ptak GE, Niemann H, Haaf T. Species-Specific Paternal Age Effects and Sperm Methylation Levels of Developmentally Important Genes. Cells 2022; 11:cells11040731. [PMID: 35203380 PMCID: PMC8870257 DOI: 10.3390/cells11040731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/11/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
A growing number of sperm methylome analyses have identified genomic loci that are susceptible to paternal age effects in a variety of mammalian species, including human, bovine, and mouse. However, there is little overlap between different data sets. Here, we studied whether or not paternal age effects on the sperm epigenome have been conserved in mammalian evolution and compared methylation patterns of orthologous regulatory regions (mainly gene promoters) containing both conserved and non-conserved CpG sites in 94 human, 36 bovine, and 94 mouse sperm samples, using bisulfite pyrosequencing. We discovered three (NFKB2, RASGEF1C, and RPL6) age-related differentially methylated regions (ageDMRs) in humans, four (CHD7, HDAC11, PAK1, and PTK2B) in bovines, and three (Def6, Nrxn2, and Tbx19) in mice. Remarkably, the identified sperm ageDMRs were all species-specific. Most ageDMRs were in genomic regions with medium methylation levels and large methylation variation. Orthologous regions in species not showing this age effect were either hypermethylated (>80%) or hypomethylated (<20%). In humans and mice, ageDMRs lost methylation, whereas bovine ageDMRs gained methylation with age. Our results are in line with the hypothesis that sperm ageDMRs are in regions under epigenomic evolution and may be part of an epigenetic mechanism(s) for lineage-specific environmental adaptations and provide a solid basis for studies on downstream effects in the genes analyzed here.
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Affiliation(s)
- Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Mustafa Orkun Sen
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Laura Bernhardt
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Thomas Hahn
- Fertility Center, 65189 Wiesbaden, Germany; (T.H.); (M.S.)
| | | | - Federica Zacchini
- PERCUROS BV, 2333 CL Leiden, The Netherlands;
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland;
- Wolfson Centre for Age-Related Diseases, King’s College London, London SE1 1UL, UK
| | - Grazyna Ewa Ptak
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland;
| | - Heiner Niemann
- Clinic for Gastroenterology, Hepatology and Endocrinology, Medical University Hannover, 30625 Hannover, Germany;
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
- Correspondence: ; Tel.: +49-931-3188738
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Heidegger A, Pisarek A, de la Puente M, Niederstätter H, Pośpiech E, Woźniak A, Schury N, Unterländer M, Sidstedt M, Junker K, Ventayol Garcia M, Laurent FX, Ulus A, Vannier J, Bastisch I, Hedman J, Sijen T, Branicki W, Xavier C, Parson W. Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis. Forensic Sci Int Genet 2021; 56:102596. [PMID: 34763164 DOI: 10.1016/j.fsigen.2021.102596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022]
Abstract
The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority from blood. Age prediction from semen requires different DNA methylation markers and the only assays currently developed for forensic analysis are based on SNaPshot or pyrosequencing. Here, we describe a new assay using massively parallel sequencing to analyse 13 candidate CpG sites targeted in two multiplex PCRs. The assay has been validated by five consortium laboratories of the VISible Attributes through GEnomics (VISAGE) project within a collaborative exercise and was tested for reproducible quantification of DNA methylation levels and sensitivity with DNA methylation controls. Furthermore, DNA extracts and stains on Whatman FTA cards from two semen samples were used to evaluate concordance and mimic casework samples. Overall, the assay yielded high read depths (> 1000 reads) at all 13 marker positions. The methylation values obtained indicated robust quantification with an average standard deviation of 2.8% at the expected methylation level of 50% across the 13 markers and a good performance with 50 ng DNA input into bisulfite conversion. The absolute difference of quantifications from one participating laboratory to the mean quantifications of concordance and semen stains of remaining laboratories was approximately 1%. These results demonstrated the assay to be robust and suitable for age estimation from semen in forensic investigations. In addition to the 13-marker assay, a more streamlined protocol combining only five age markers in one multiplex PCR was developed. Preliminary results showed no substantial differences in DNA methylation quantification between the two assays, indicating its applicability with the VISAGE age model for semen developed with data from the complete 13-marker tool.
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Affiliation(s)
- A Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - A Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - M de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - H Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - A Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - N Schury
- Federal Criminal Police Office, Wiesbaden, Germany
| | | | - M Sidstedt
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - K Junker
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - M Ventayol Garcia
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | - F X Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - A Ulus
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - J Vannier
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - I Bastisch
- Federal Criminal Police Office, Wiesbaden, Germany
| | - J Hedman
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - T Sijen
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands; University of Amsterdam, Swammerdam Institute of Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Central Forensic Laboratory of the Police, Warsaw, Poland
| | - C Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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The impact of zinc and folic acid supplementation on sperm DNA methylation: results from the folic acid and zinc supplementation randomized clinical trial (FAZST). Fertil Steril 2021; 117:75-85. [PMID: 34656303 DOI: 10.1016/j.fertnstert.2021.09.009] [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: 06/25/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To determine if 6-month folic acid (5 mg) and zinc (30 mg) supplementation impacts sperm DNA methylation patterns. DESIGN A multicenter, double-blind, block randomized, placebo-controlled trial titled "The Folic Acid and Zinc Supplementation Trial (FAZST)." SETTING Infertility care centers. PATIENT(S) Male partners (18 years and older) from heterosexual couples (female partners aged 18-45 years) seeking fertility treatment were recruited. INTERVENTION(S) Men were randomized 1:1 to receive folic acid (5 mg) and elemental zinc (30 mg) (n = 713) or a matching placebo (n = 757) daily for 6 months. MAIN OUTCOME MEASURE(S) Sperm DNA methylation was analyzed using the EPIC methylation array (Illumina) at 6 months. Differential sperm DNA methylation was assessed at multiple levels (regional, single cytosine phosphate guanine, etc.). We additionally assessed the impact of supplementation on epigenetic age. RESULT(S) No significant differences were identified between the treatment and placebo groups although some trends appeared to be present. To determine if these trends were noteworthy, we implemented various permutations and found that the patterns we identified were no more than would be expected by random chance. CONCLUSION(S) The data presented here strongly suggest that this supplementation regimen is not effective at altering sperm DNA methylation. These data comport well with previous findings from the FAZST study that found no impact of supplementation on basic semen analysis parameters or live birth. CLINICAL TRIAL REGISTRATION NUMBER ClinicalTrials.gov Identifier: NCT01857310.
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Epigenetic age prediction in semen - marker selection and model development. Aging (Albany NY) 2021; 13:19145-19164. [PMID: 34375949 PMCID: PMC8386575 DOI: 10.18632/aging.203399] [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: 03/16/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
Abstract
DNA methylation analysis is becoming increasingly useful in biomedical research and forensic practice. The discovery of differentially methylated sites (DMSs) that continuously change over an individual's lifetime has led to breakthroughs in molecular age estimation. Although semen samples are often used in forensic DNA analysis, previous epigenetic age prediction studies mainly focused on somatic cell types. Here, Infinium MethylationEPIC BeadChip arrays were applied to semen-derived DNA samples, which identified numerous novel DMSs moderately correlated with age. Validation of the ten most age-correlated novel DMSs and three previously known sites in an independent set of semen-derived DNA samples using targeted bisulfite massively parallel sequencing, confirmed age-correlation for nine new and three previously known markers. Prediction modelling revealed the best model for semen, based on 6 CpGs from newly identified genes SH2B2, EXOC3, IFITM2, and GALR2 as well as the previously known FOLH1B gene, which predict age with a mean absolute error of 5.1 years in an independent test set. Further increases in the accuracy of age prediction from semen DNA will require technological progress to allow sensitive, simultaneous analysis of a much larger number of age correlated DMSs from the compromised DNA typical of forensic semen stains.
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Noroozi R, Ghafouri-Fard S, Pisarek A, Rudnicka J, Spólnicka M, Branicki W, Taheri M, Pośpiech E. DNA methylation-based age clocks: From age prediction to age reversion. Ageing Res Rev 2021; 68:101314. [PMID: 33684551 DOI: 10.1016/j.arr.2021.101314] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
Aging as an irretrievable occurrence throughout the entire life is characterized by a progressive decline in physiological functionality and enhanced disease vulnerability. Numerous studies have demonstrated that epigenetic modifications, particularly DNA methylation (DNAm), correlate with aging and age-related diseases. Several investigations have attempted to predict chronological age using the age-related alterations in the DNAm of certain CpG sites. Here we categorize different studies that tracked the aging process in the DNAm landscape to show how epigenetic age clocks evolved from a chronological age estimator to an indicator of lifespan and healthspan. We also describe the health and disease predictive potential of estimated epigenetic age acceleration regarding different clinical conditions and lifestyle factors. Considering the revealed age-related epigenetic changes, the recent age-reprogramming strategies are discussed which are promising methods for resetting the aging clocks.
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Affiliation(s)
- Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Joanna Rudnicka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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Zhang J, Fu H, Xu Y. Age Prediction of Human Based on DNA Methylation by Blood Tissues. Genes (Basel) 2021; 12:genes12060870. [PMID: 34204075 PMCID: PMC8228382 DOI: 10.3390/genes12060870] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/27/2021] [Accepted: 06/05/2021] [Indexed: 12/14/2022] Open
Abstract
In recent years, scientists have found a close correlation between DNA methylation and aging in epigenetics. With the in-depth research in the field of DNA methylation, researchers have established a quantitative statistical relationship to predict the individual ages. This work used human blood tissue samples to study the association between age and DNA methylation. We built two predictors based on healthy and disease data, respectively. For the health data, we retrieved a total of 1191 samples from four previous reports. By calculating the Pearson correlation coefficient between age and DNA methylation values, 111 age-related CpG sites were selected. Gradient boosting regression was utilized to build the predictive model and obtained the R2 value of 0.86 and MAD of 3.90 years on testing dataset, which were better than other four regression methods as well as Horvath’s results. For the disease data, 354 rheumatoid arthritis samples were retrieved from a previous study. Then, 45 CpG sites were selected to build the predictor and the corresponded MAD and R2 were 3.11 years and 0.89 on the testing dataset respectively, which showed the robustness of our predictor. Our results were better than the ones from other four regression methods. Finally, we also analyzed the twenty-four common CpG sites in both healthy and disease datasets which illustrated the functional relevance of the selected CpG sites.
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Kerepesi C, Zhang B, Lee SG, Trapp A, Gladyshev VN. Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. SCIENCE ADVANCES 2021; 7:eabg6082. [PMID: 34172448 PMCID: PMC8232908 DOI: 10.1126/sciadv.abg6082] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
The notion that the germ line does not age goes back to the 19th-century ideas of August Weismann. However, being metabolically active, the germ line accumulates damage and other changes over time, i.e., it ages. For new life to begin in the same young state, the germ line must be rejuvenated in the offspring. Here, we developed a multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e., rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (ground zero) marks the beginning of organismal aging.
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Affiliation(s)
- Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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36
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Åsenius F, Danson AF, Marzi SJ. DNA methylation in human sperm: a systematic review. Hum Reprod Update 2021; 26:841-873. [PMID: 32790874 DOI: 10.1093/humupd/dmaa025] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Studies in non-human mammals suggest that environmental factors can influence spermatozoal DNA methylation, and some research suggests that spermatozoal DNA methylation is also implicated in conditions such as subfertility and imprinting disorders in the offspring. Together with an increased availability of cost-effective methods of interrogating DNA methylation, this premise has led to an increasing number of studies investigating the DNA methylation landscape of human spermatozoa. However, how the human spermatozoal DNA methylome is influenced by environmental factors is still unclear, as is the role of human spermatozoal DNA methylation in subfertility and in influencing offspring health. OBJECTIVE AND RATIONALE The aim of this systematic review was to critically appraise the quality of the current body of literature on DNA methylation in human spermatozoa, summarize current knowledge and generate recommendations for future research. SEARCH METHODS A comprehensive literature search of the PubMed, Web of Science and Cochrane Library databases was conducted using the search terms 'semen' OR 'sperm' AND 'DNA methylation'. Publications from 1 January 2003 to 2 March 2020 that studied human sperm and were written in English were included. Studies that used sperm DNA methylation to develop methodologies or forensically identify semen were excluded, as were reviews, commentaries, meta-analyses or editorial texts. The Grading of Recommendations, Assessment, Development and Evaluations (GRADE) criteria were used to objectively evaluate quality of evidence in each included publication. OUTCOMES The search identified 446 records, of which 135 were included in the systematic review. These 135 studies were divided into three groups according to area of research; 56 studies investigated the influence of spermatozoal DNA methylation on male fertility and abnormal semen parameters, 20 studies investigated spermatozoal DNA methylation in pregnancy outcomes including offspring health and 59 studies assessed the influence of environmental factors on spermatozoal DNA methylation. Findings from studies that scored as 'high' and 'moderate' quality of evidence according to GRADE criteria were summarized. We found that male subfertility and abnormal semen parameters, in particular oligozoospermia, appear to be associated with abnormal spermatozoal DNA methylation of imprinted regions. However, no specific DNA methylation signature of either subfertility or abnormal semen parameters has been convincingly replicated in genome-scale, unbiased analyses. Furthermore, although findings require independent replication, current evidence suggests that the spermatozoal DNA methylome is influenced by cigarette smoking, advanced age and environmental pollutants. Importantly however, from a clinical point of view, there is no convincing evidence that changes in spermatozoal DNA methylation influence pregnancy outcomes or offspring health. WIDER IMPLICATIONS Although it appears that the human sperm DNA methylome can be influenced by certain environmental and physiological traits, no findings have been robustly replicated between studies. We have generated a set of recommendations that would enhance the reliability and robustness of findings of future analyses of the human sperm methylome. Such studies will likely require multicentre collaborations to reach appropriate sample sizes, and should incorporate phenotype data in more complex statistical models.
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Affiliation(s)
| | - Amy F Danson
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London W12 0NN, UK.,Department of Brain Sciences, Imperial College London, London, UK
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McCarter K, Setton R, Chung A, An A, Rosenwaks Z, Spandorfer S. Is increasing paternal age negatively associated with donor oocyte recipient success? A paired analysis using sibling oocytes. Fertil Steril 2021; 116:373-379. [PMID: 33926719 DOI: 10.1016/j.fertnstert.2021.03.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVE To determine if increasing paternal age has an adverse effect on pregnancy outcomes in paired donor egg recipients who received oocytes from the same donor in the same stimulation cycle. DESIGN Retrospective cohort study. SETTING Reproductive Medicine Center. PATIENT(S) The study included 154 recipients who received oocytes from a split donor oocyte cycle and received sperm from men in discrepant age groups (group A: <45 years old; group B: ≥45 years old). INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Implantation rate, pregnancy loss rate, pregnancy rate, and live birth rate. RESULT(S) The median paternal age was 41 years old for group A and 48 years old for group B. The pregnancy rate was 81% in group A compared with 69% in group B. The live birth rate was 65% in group A compared with 53% in group B. The rate of pregnancy loss was 19% in group A and 23% in group B. The implantation rate was 69% in group A compared with 66% in group B. The adjusted odds of pregnancy were found to be 65% lower for patients in the older partner age group (95% confidence interval [CI], 0.13, 0.95). The adjusted odds of live birth rate (odds ratio [OR], 0.45; 95% CI, 0.20, 1.00), implantation rate (OR, 0.91; 95% CI, 0.43, 1.92), and rate of pregnancy loss (OR, 1.5; 95% CI, 0.5, 4.5) favored the younger partner age group; however, these results were not statistically significant. CONCLUSION(S) In this model that controlled for oocyte quality to the greatest degree possible by using paired recipients from the same donor from the same stimulation cycle, we found that increased paternal age had a negative effect on pregnancy rates.
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Affiliation(s)
- Kelly McCarter
- Department of Obstetrics and Gynecology, New York Presbyterian/Weill Cornell, New York.
| | - Robert Setton
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York
| | - Alice Chung
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York
| | - Anjile An
- Division of Biostatistics, Department of Population Health Science, Weill Cornell Medicine, New York
| | - Zev Rosenwaks
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York
| | - Steven Spandorfer
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York
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Vidaki A, Montiel González D, Planterose Jiménez B, Kayser M. Male-specific age estimation based on Y-chromosomal DNA methylation. Aging (Albany NY) 2021; 13:6442-6458. [PMID: 33744870 PMCID: PMC7993701 DOI: 10.18632/aging.202775] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022]
Abstract
Although DNA methylation variation of autosomal CpGs provides robust age predictive biomarkers, no male-specific age predictor exists based on Y-CpGs yet. Since sex chromosomes play an important role in aging, a Y-chromosome-based age predictor would allow studying male-specific aging effects and would also be useful in forensics. Here, we used blood-based DNA methylation microarray data of 1,057 males from six cohorts aged 15-87 and identified 75 Y-CpGs with an interquartile range of ≥0.1. Of these, 22 and six were significantly hyper- and hypomethylated with age (p(cor)<0.05, Bonferroni), respectively. Amongst several machine learning algorithms, a model based on support vector machines with radial kernel performed best in male-specific age prediction. We achieved a mean absolute deviation (MAD) between true and predicted age of 7.54 years (cor=0.81, validation) when using all 75 Y-CpGs, and a MAD of 8.46 years (cor=0.73, validation) based on the most predictive 19 Y-CpGs. The accuracies of both age predictors did not worsen with increased age, in contrast to autosomal CpG-based age predictors that are known to predict age with reduced accuracy in the elderly. Overall, we introduce the first-of-its-kind male-specific epigenetic age predictor for future applications in aging research and forensics.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
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Oluwayiose OA, Wu H, Saddiki H, Whitcomb BW, Balzer LB, Brandon N, Suvorov A, Tayyab R, Sites CK, Hill L, Marcho C, Pilsner JR. Sperm DNA methylation mediates the association of male age on reproductive outcomes among couples undergoing infertility treatment. Sci Rep 2021; 11:3216. [PMID: 33547328 PMCID: PMC7864951 DOI: 10.1038/s41598-020-80857-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
Parental age at time of offspring conception is increasing in developed countries. Advanced male age is associated with decreased reproductive success and increased risk of adverse neurodevelopmental outcomes in offspring. Mechanisms for these male age effects remain unclear, but changes in sperm DNA methylation over time is one potential explanation. We assessed genome-wide methylation of sperm DNA from 47 semen samples collected from male participants of couples seeking infertility treatment. We report that higher male age was associated with lower likelihood of fertilization and live birth, and poor embryo development (p < 0.05). Furthermore, our multivariable linear models showed male age was associated with alterations in sperm methylation at 1698 CpGs and 1146 regions (q < 0.05), which were associated with > 750 genes enriched in embryonic development, behavior and neurodevelopment among others. High dimensional mediation analyses identified four genes (DEFB126, TPI1P3, PLCH2 and DLGAP2) with age-related sperm differential methylation that accounted for 64% (95% CI 0.42-0.86%; p < 0.05) of the effect of male age on lower fertilization rate. Our findings from this modest IVF population provide evidence for sperm methylation as a mechanism of age-induced poor reproductive outcomes and identifies possible candidate genes for mediating these effects.
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Affiliation(s)
- Oladele A Oluwayiose
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA, 01003, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 W 168th St, New York, NY, 10032, USA
| | - Hachem Saddiki
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, USA
| | - Brian W Whitcomb
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, USA
| | - Laura B Balzer
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, USA
| | - Nicole Brandon
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA, 01003, USA
| | - Alexander Suvorov
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA, 01003, USA
| | - Rahil Tayyab
- Division of Reproductive Endocrinology and Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA, USA
| | - Cynthia K Sites
- Division of Reproductive Endocrinology and Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA, USA
| | - Lisa Hill
- Division of Reproductive Endocrinology and Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA, USA
| | - Chelsea Marcho
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA, 01003, USA
| | - J Richard Pilsner
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA, 01003, USA.
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40
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Oluwayiose OA, Josyula S, Houle E, Marcho C, Brian W Whitcomb, Rahil T, Sites CK, Pilsner JR. Association between sperm mitochondarial DNA copy number and nuclear DNA methylation. Epigenomics 2020; 12:2141-2153. [PMID: 33320694 DOI: 10.2217/epi-2020-0253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Accumulating evidence associates sperm mitochondria DNA copy number (mtDNAcn) with male infertility and reproductive success. However, the mechanism underlying mtDNAcn variation is largely unknown. Patients & methods: Sperm mtDNAcn and genome-wide DNA methylation were assessed using triplex probe-based quantitative PCR and Illumina's 450K array, respectively. Multivariable models assessed the association between sperm mtDNAcn and DNA methylation profiles of 47 men seeking infertility treatment. Results: A priori candidate-gene approach showed sperm mtDNAcn was associated with 16 CpGs located at/near POLG and TWNK genes. Unbiased genome-wide analysis revealed that sperm mtDNAcn was associated with 218 sperm differentially methylated regions (q < 0.05), which displayed predominantly (94%) increases in methylation. Conclusion: Findings suggest that DNA methylation may play a role in regulating sperm mtDNAcn.
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Affiliation(s)
- Oladele A Oluwayiose
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Srinihaari Josyula
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Emily Houle
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Chelsea Marcho
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Brian W Whitcomb
- Department of Biostatistics & Epidemiology, School of Public Health & Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA 01002, USA
| | - Tayyab Rahil
- Division of Reproductive Endocrinology & Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA 01199, USA
| | - Cynthia K Sites
- Division of Reproductive Endocrinology & Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA 01199, USA
| | - J Richard Pilsner
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, MA 01003, USA
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Cao M, Shao X, Chan P, Cheung W, Kwan T, Pastinen T, Robaire B. High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations. Clin Epigenetics 2020; 12:192. [PMID: 33317634 PMCID: PMC7735420 DOI: 10.1186/s13148-020-00988-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/25/2020] [Indexed: 12/23/2022] Open
Abstract
Background Children of aged fathers are at a higher risk of developing mental disorders. Alterations in sperm DNA methylation have been implicated as a potential cause. However, age-dependent modifications of the germ cells’ epigenome remain poorly understood. Our objective was to assess the DNA methylation profile of human spermatozoa during aging.
Results We used a high throughput, customized methylC-capture sequencing (MCC-seq) approach to characterize the dynamic DNA methylation in spermatozoa from 94 fertile and infertile men, who were categorized as young, 48 men between 18–38 years or old 46 men between 46–71 years. We identified more than 150,000 age-related CpG sites that are significantly differentially methylated among 2.65 million CpG sites covered. We conducted machine learning using our dataset to predict the methylation age of subjects; the age prediction accuracy based on our assay provided a more accurate prediction than that using the 450 K chip approach. In addition, we found that there are more hypermethylated (62%) than hypomethylated (38%) CpG sites in sperm of aged men, corresponding to 798 of total differential methylated regions (DMRs), of which 483 are hypermethylated regions (HyperDMR), and 315 hypomethylated regions (HypoDMR). Moreover, the distribution of age-related hyper- and hypomethylated CpGs in sperm is not random; the CpG sites that were hypermethylated with advanced age were frequently located in the distal region to genes, whereas hypomethylated sites were near to gene transcription start sites (TSS). We identified a high density of age-associated CpG changes in chromosomes 4 and 16, particularly HyperDMRs with localized clusters, the chr4 DMR cluster overlaps PGC1α locus, a protein involved in metabolic aging and the chr16 DMR cluster overlaps RBFOX1 locus, a gene implicated in neurodevelopmental disease. Gene ontology analysis revealed that the most affected genes by age were associated with development, neuron projection, differentiation and recognition, and behaviour, suggesting a potential link to the higher risk of neurodevelopmental disorders in children of aged fathers. Conclusion We identified thousands of age-related and sperm-specific epigenetic alterations. These findings provide novel insight in understanding human sperm DNA methylation dynamics during paternal aging, and the subsequently affected genes potentially related to diseases in offspring.
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Affiliation(s)
- Mingju Cao
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,McGill University Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,Digital Technologies Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Peter Chan
- Department of Urology, McGill University Health Centre, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
| | - Warren Cheung
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,McGill University Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,McGill University Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Bernard Robaire
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada. .,Department of Obstetric and Gynecology, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada.
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Salas-Huetos A, James ER, Salas-Salvadó J, Bulló M, Aston KI, Carrell DT, Jenkins TG. Sperm DNA methylation changes after short-term nut supplementation in healthy men consuming a Western-style diet. Andrology 2020; 9:260-268. [PMID: 32966683 DOI: 10.1111/andr.12911] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Many environmental and lifestyle factors have been implicated in the decline of sperm quality, with diet being one of the most plausible factors identified in recent years. Moreover, several studies have reported a close association between the alteration of specific sperm DNA methylation signatures and semen quality. OBJECTIVES To evaluate the effect of tree nut consumption on sperm DNA methylation patterns in healthy individuals reporting eating a Western-style diet. MATERIAL AND METHODS This is a post hoc analysis conducted in a subset of participants (healthy, non-smoking, and young) from the FERTINUTS 14-wk randomized-controlled, parallel trial, recruited between December 2015 and February 2017. The participants included in the current study (n = 72) were randomly selected in a proportion 2:1 from the original FERTINUTS trial between the 98 participants that completed the entire dietary intervention (nut group, n = 48; control group, n = 24). Sperm DNA methylation patterns were examined at baseline and after 14 weeks in 48 individuals consuming 60 g/d of mixed nuts (nut group) and in 24 individuals following the usual Western-style diet avoiding consumption of nuts (control group). RESULTS Over the course of the trial, no significant changes in global methylation were observed between groups. However, in the nut group, we identified 36 genomic regions that were significantly differentially methylated between the baseline and the end of the trial and 97.2% of the regions displayed hypermethylation. We identified no such change in the control group over the same period of time. We also utilized the recently developed germ line age calculator to determine if nut consumption resulted in alterations to the epigenetic age of cells and no significant differences were found. DISCUSSION AND CONCLUSION Adding nuts to a regular Western-style diet subtly impacts sperm DNA methylation in specific regions, demonstrating that there are some sperm epigenome regions that could respond to diet.
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Affiliation(s)
- Albert Salas-Huetos
- Human Nutrition Unit, Biochemistry and Biotechnology Department, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), Reus, Spain.,Institut d'Investigació Sanitària Pere i Virgili (IISPV), Reus, Spain.,Consorcio CIBER, M.P., Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Emma R James
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jordi Salas-Salvadó
- Human Nutrition Unit, Biochemistry and Biotechnology Department, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), Reus, Spain.,Institut d'Investigació Sanitària Pere i Virgili (IISPV), Reus, Spain.,Consorcio CIBER, M.P., Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Hospital Universitari Sant Joan de Reus (HUSJR), Reus, Spain
| | - Mònica Bulló
- Human Nutrition Unit, Biochemistry and Biotechnology Department, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), Reus, Spain.,Institut d'Investigació Sanitària Pere i Virgili (IISPV), Reus, Spain.,Consorcio CIBER, M.P., Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Douglas T Carrell
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Timothy G Jenkins
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, USA
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43
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Morgan CP, Shetty AC, Chan JC, Berger DS, Ament SA, Epperson CN, Bale TL. Repeated sampling facilitates within- and between-subject modeling of the human sperm transcriptome to identify dynamic and stress-responsive sncRNAs. Sci Rep 2020; 10:17498. [PMID: 33060642 PMCID: PMC7562703 DOI: 10.1038/s41598-020-73867-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Epidemiological studies from the last century have drawn strong associations between paternal life experiences and offspring health and disease outcomes. Recent studies have demonstrated sperm small non-coding RNA (sncRNA) populations vary in response to diverse paternal insults. However, for studies in retrospective or prospective human cohorts to identify changes in paternal germ cell epigenetics in association with offspring disease risk, a framework must first be built with insight into the expected biological variation inherent in human populations. In other words, how will we know what to look for if we don't first know what is stable and what is dynamic, and what is consistent within and between men over time? From sperm samples from a 'normative' cohort of healthy human subjects collected repeatedly from each subject over 6 months, 17 healthy male participants met inclusion criteria and completed donations and psychological evaluations of perceived stress monthly. sncRNAs (including miRNA, piRNA, and tRNA) isolated from mature sperm from these samples were subjected to Illumina small RNA sequencing, aligned to subtype-specific reference transcriptomes, and quantified. The repeated measures design allowed us to define both within- and between-subject variation in the expression of 254 miRNA, 194 tRNA, and 937 piRNA in sperm over time. We developed screening criteria to identify a subset of potential environmentally responsive 'dynamic' sperm sncRNA. Implementing complex modeling of the relationships between individual dynamic sncRNA and perceived stress states in these data, we identified 5 miRNA (including let-7f-5p and miR-181a-5p) and 4 tRNA that are responsive to the dynamics of prior stress experience and fit our established mouse model. In the current study, we aligned repeated sampling of human sperm sncRNA expression data with concurrent measures of perceived stress as a novel framework that can now be applied across a range of studies focused on diverse environmental factors able to influence germ cell programming and potentially impact offspring development.
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Affiliation(s)
- Christopher P Morgan
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jennifer C Chan
- Department of Biomedical Sciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dara S Berger
- Division of Reproductive Endocrinology and Infertility, Perelman School of Medicine, Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - C Neill Epperson
- Department of Psychiatry, University of Colorado School of Medicine, CU-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Tracy L Bale
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Departments of Pharmacology and Psychiatry, Center for Epigenetic Research in Child Health and Brain Development, HSF3, Room 9-171, University of Maryland School of Medicine, 670 W. Baltimore St., Baltimore, MD, 21201, USA.
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44
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Åsenius F, Gorrie-Stone TJ, Brew A, Panchbhaya Y, Williamson E, Schalkwyk LC, Rakyan VK, Holland ML, Marzi SJ, Williams DJ. The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations. PLoS Genet 2020; 16:e1009035. [PMID: 33048947 PMCID: PMC7584170 DOI: 10.1371/journal.pgen.1009035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/23/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022] Open
Abstract
Epidemiological research suggests that paternal obesity may increase the risk of fathering small for gestational age offspring. Studies in non-human mammals indicate that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in spermatozoa. We profiled genome-wide DNA methylation using the Illumina MethylationEPIC array in a cross-sectional study of matched human blood and sperm from lean (discovery n = 47; replication n = 21) and obese (n = 22) males to analyse tissue covariation of DNA methylation, and identify obesity-associated methylomic signatures. We found that DNA methylation signatures of human blood and spermatozoa are highly discordant, and methylation levels are correlated at only a minority of CpG sites (~1%). At the majority of these sites, DNA methylation appears to be influenced by genetic variation. Obesity-associated DNA methylation in blood was not generally reflected in spermatozoa, and obesity was not associated with altered covariation patterns or accelerated epigenetic ageing in the two tissues. However, one cross-tissue obesity-specific hypermethylated site (cg19357369; chr4:2429884; P = 8.95 × 10-8; 2% DNA methylation difference) was identified, warranting replication and further investigation. When compared to a wide range of human somatic tissue samples (n = 5,917), spermatozoa displayed differential DNA methylation across pathways enriched in transcriptional regulation. Overall, human sperm displays a unique DNA methylation profile that is highly discordant to, and practically uncorrelated with, that of matched peripheral blood. We observed that obesity was only nominally associated with differential DNA methylation in sperm, and therefore suggest that spermatozoal DNA methylation is an unlikely mediator of intergenerational effects of metabolic traits.
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Affiliation(s)
- Fredrika Åsenius
- UCL EGA Institute for Women’s Health, University College London, London, United Kingdom
| | | | - Ama Brew
- The Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Yasmin Panchbhaya
- UCL Genomics, Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Elizabeth Williamson
- Fertility & reproductive medicine laboratory, University College Hospital, London, United Kingdom
| | | | - Vardhman K. Rakyan
- The Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Michelle L. Holland
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Sarah J. Marzi
- UK Dementia Research Institute, Imperial College London, London, United Kingdom
- Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - David J. Williams
- UCL EGA Institute for Women’s Health, University College London, London, United Kingdom
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45
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Laurentino S, Cremers J, Horsthemke B, Tüttelmann F, Czeloth K, Zitzmann M, Pohl E, Rahmann S, Schröder C, Berres S, Redmann K, Krallmann C, Schlatt S, Kliesch S, Gromoll J. A germ cell-specific ageing pattern in otherwise healthy men. Aging Cell 2020; 19:e13242. [PMID: 32951333 PMCID: PMC7576283 DOI: 10.1111/acel.13242] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022] Open
Abstract
Life‐long sperm production leads to the assumption that male fecundity remains unchanged throughout life. However, recently it was shown that paternal age has profound consequences for male fertility and offspring health. Paternal age effects are caused by an accumulation of germ cell mutations over time, causing severe congenital diseases. Apart from these well‐described cases, molecular patterns of ageing in germ cells and their impact on DNA integrity have not been studied in detail. In this study, we aimed to assess the effects of ‘pure’ ageing on male reproductive health and germ cell quality. We assembled a cohort of 198 healthy men (18–84 years) for which end points such as semen and hormone profiles, sexual health and well‐being, and sperm DNA parameters were evaluated. Sperm production and hormonal profiles were maintained at physiological levels over a period of six decades. In contrast, we identified a germ cell‐specific ageing pattern characterized by a steady increase of telomere length in sperm and a sharp increase in sperm DNA instability, particularly after the sixth decade. Importantly, we found sperm DNA methylation changes in 236 regions, mostly nearby genes associated with neuronal development. By in silico analysis, we found that 10 of these regions are located in loci which can potentially escape the first wave of genome‐wide demethylation after fertilization. In conclusion, human male germ cells present a unique germline‐specific ageing process, which likely results in diminished fecundity in elderly men and poorer health prognosis for their offspring.
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Affiliation(s)
- Sandra Laurentino
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | | | - Bernhard Horsthemke
- Institute of Human Genetics University of Duisburg‐EssenUniversity Hospital Essen Essen Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics University of Münster Münster Germany
| | - Karen Czeloth
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | - Michael Zitzmann
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | - Eva Pohl
- Institute of Human Genetics University of Münster Münster Germany
| | - Sven Rahmann
- Genome Informatics University of Duisburg‐EssenUniversity Hospital Essen Essen Germany
| | - Christopher Schröder
- Genome Informatics University of Duisburg‐EssenUniversity Hospital Essen Essen Germany
| | - Sven Berres
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | - Klaus Redmann
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | - Claudia Krallmann
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | - Stefan Schlatt
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and Andrology University of Münster Münster Germany
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46
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Gladyshev VN. The Ground Zero of Organismal Life and Aging. Trends Mol Med 2020; 27:11-19. [PMID: 32980264 DOI: 10.1016/j.molmed.2020.08.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023]
Abstract
Cells may naturally proceed or be forced to transition to a state with a radically lower biological age, that is, be rejuvenated. Examples are the conversion of somatic cells to induced pluripotent stem cells and rejuvenation of the germline with each generation. We posit that these processes converge to the same 'ground zero', the mid-embryonic state characterized by the lowest biological age where both organismal life and aging begin. It may also be related to the phylotypic state. The ground zero model clarifies the relationship between aging, development, rejuvenation, and de-differentiation, which are distinct throughout life. By extending the rejuvenation phase during early embryogenesis and editing the genome, it may be possible to achieve the biological age at the ground zero lower than that achieved naturally.
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Affiliation(s)
- Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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47
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The combined effect of obesity and aging on human sperm DNA methylation signatures: inclusion of BMI in the paternal germ line age prediction model. Sci Rep 2020; 10:15409. [PMID: 32958862 PMCID: PMC7506015 DOI: 10.1038/s41598-020-71979-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/17/2020] [Indexed: 11/08/2022] Open
Abstract
Male aging and obesity have both been shown to contribute to declines in fertility in men. Recent work in aging has shown consistent epigenetic changes to sperm as a man ages. In fact, our lab has built a tool that utilizes DNA methylation signatures from sperm to effectively predict an individual’s age. Herein, we performed this preliminary cohort study to determine if increased BMI accelerates the epigenetic aging in sperm. A total of 96 participants were divided into four age groups (22–24, 30, 40–41, and > 48 years of age) and additionally parsed into two BMI sub-categories (normal and high/obese). We found no statistically significant epigenetic age acceleration. However, it is important to note that within each age category, high BMI individuals were predicted to be older on average than their actual age (~ 1.4 years), which was not observed in the normal BMI group. To further investigate this, we re-trained a model using only the present data with and without BMI as a feature. We found a modest but non-significant improvement in prediction with BMI [r2 = 0.8814, mean absolute error (MAE) = 3.2913] compared to prediction without BMI (r2 = 0.8739, MAE = 3.3567). Future studies with higher numbers of age-matched individuals are needed to definitively understand the impact of BMI on epigenetic aging in sperm.
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48
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Potabattula R, Zacchini F, Ptak GE, Dittrich M, Müller T, El Hajj N, Hahn T, Drummer C, Behr R, Lucas‐Hahn A, Niemann H, Schorsch M, Haaf T. Increasing methylation of sperm rDNA and other repetitive elements in the aging male mammalian germline. Aging Cell 2020; 19:e13181. [PMID: 32608562 PMCID: PMC7431825 DOI: 10.1111/acel.13181] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/06/2020] [Accepted: 06/01/2020] [Indexed: 01/08/2023] Open
Abstract
In somatic cells/tissues, methylation of ribosomal DNA (rDNA) increases with age and age‐related pathologies, which has a direct impact on the regulation of nucleolar activity and cellular metabolism. Here, we used bisulfite pyrosequencing and show that methylation of the rDNA transcription unit including upstream control element (UCE), core promoter, 18S rDNA, and 28S rDNA in human sperm also significantly increases with donor's age. This positive correlation between sperm rDNA methylation and biological age is evolutionarily conserved among mammals with widely different life spans such as humans, marmoset, bovine, and mouse. Similar to the tandemly repeated rDNA, methylation of human α‐satellite and interspersed LINE1 repeats, marmoset α‐satellite, bovine alpha‐ and testis satellite I, mouse minor and major satellite, and LINE1‐T repeats increases in the aging male germline, probably related to their sperm histone packaging. Deep bisulfite sequencing of single rDNA molecules in human sperm revealed that methylation does not only depend on donor's age, but also depend on the region and sequence context (A vs. G alleles). Both average rDNA methylation of all analyzed DNA molecules and the number of fully (>50%) methylated alleles, which are thought to be epigenetically silenced, increase with donor's age. All analyzed CpGs in the sperm rDNA transcription unit show comparable age‐related methylation changes. Unlike other epigenetic aging markers, the rDNA clock appears to operate in similar ways in germline and soma in different mammalian species. We propose that sperm rDNA methylation, directly or indirectly, influences nucleolar formation and developmental potential in the early embryo.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Federica Zacchini
- Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
- Percuros B.V. Leiden The Netherlands
| | - Grazyna Ewa Ptak
- Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
| | - Marcus Dittrich
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Tobias Müller
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Nady El Hajj
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
- College of Health and Life Sciences Hamad Bin Khalifa University Doha Qatar
| | | | - Charis Drummer
- Platform Degenerative Diseases Leibniz Institute for Primate Research Göttingen Germany
- German Center for Cardiovascular Research, Partner Site Göttingen Göttingen Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases Leibniz Institute for Primate Research Göttingen Germany
- German Center for Cardiovascular Research, Partner Site Göttingen Göttingen Germany
| | - Andrea Lucas‐Hahn
- Institute of Farm Animal Genetics Friedrich‐Loeffler‐Institute Mariensee/Neustadt Germany
| | - Heiner Niemann
- Clinic for Gastroenterology, Hepatology and Endocrinology Medical University Hannover Hannover Germany
| | | | - Thomas Haaf
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
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Nwanaji-Enwerem JC, Jenkins TG, Colicino E, Cardenas A, Baccarelli AA, Boyer EW. Serum dioxin levels and sperm DNA methylation age: Findings in Vietnam war veterans exposed to Agent Orange. Reprod Toxicol 2020; 96:27-35. [PMID: 32522586 DOI: 10.1016/j.reprotox.2020.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Exposure to dioxin, a known endocrine disruptor and carcinogen, is associated with poor reproductive outcomes. Yet, few studies have explored the role of DNA methylation in these relationships. Utilizing a publicly available dataset from 37 male Air Force Health Study participants exposed to dioxin-contaminated Agent Orange during the Vietnam war, we cross-sectionally examined the relationship of serum dioxin levels with a novel DNA methylation-based measure of sperm age (DNAm-agesperm). DNAm-agesperm was calculated using CpG sites on the Illumina HumanMethylation450 BeadChip. We estimated associations of dioxin levels with DNAm-agesperm using linear regression models adjusted for chronological age, body mass index, and smoking status. Chronological age was highly correlated with DNAmagesperm (r = 0.80). In fully-adjusted linear models, a one percent increase in serum dioxin levels was significantly associated with a 0.0126-year (i.e. 4.6-day) increase in DNAm-agesperm (95%CI: 0.003, 0.022, p = 0.01). Further analyses demonstrated significant negative associations of dioxin levels (β = -0.0005, 95%CI: -0.0010, 0.00004, P = 0.03) and DNAm-agesperm (β = -0.02, 95%CI: -0.04, -0.001, P = 0.03) with methylation levels of FOXK2 - a gene previously reported to be hypomethylated in infertile men. In sum, we demonstrate associations of dioxin with increased methylation aging of sperm. DNAm-agesperm may provide utility for understanding how dioxin levels impact sperm health and potentially male reproductive capacity in human population studies. Moreover, our pilot study contributes further evidence that some environmental toxicants are associated with methylation aging. Additional studies are necessary to confirm these findings, and better characterize dioxin and sperm methylation relationships with male reproductive health.
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Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Belfer Center for Science and International Affairs, Harvard Kennedy School of Government, Department of Environmental Health, Harvard T.H. Chan School of Public Health, and MD/PhD Program, Harvard Medical School, Boston, MA, USA.
| | - Timothy G Jenkins
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, USA
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Edward W Boyer
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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50
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Abstract
A male factor is a contributor in 50% of cases of infertility. Although assisted reproductive techniques can often bypass the need to improve semen parameters, the evaluation of the infertile man remains critical. Current methods for evaluating the infertile man are discussed, beginning with the basic workup that all suspected infertile men should undergo, followed by subsequent evaluation steps. Although the fundamental components of the evaluation have remained consistent, several new tools are available to assist in identifying the underlying etiology. As our understanding of male fertility expands, the technologies available to diagnose and ultimately treat it continue to evolve.
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Affiliation(s)
- Ujval Ishu Pathak
- Scott Department of Urology, Baylor College of Medicine, 6624 Fannin Street, Suite 1700, Houston, TX 77030, USA
| | - Joseph Scott Gabrielsen
- Department of Urology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 656, Rochester, NY 14642, USA
| | - Larry I Lipshultz
- Scott Department of Urology, Baylor College of Medicine, 6624 Fannin Street, Suite 1700, Houston, TX 77030, USA.
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