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Friedman S, Thorarinsson CT, Wod M, Fedder J, Nørgård BM. Paternal Inflammatory Bowel Disease and the Risk of Pregnancy Loss. Inflamm Bowel Dis 2024:izae132. [PMID: 38944809 DOI: 10.1093/ibd/izae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Indexed: 07/01/2024]
Abstract
BACKGROUND Only about 30% of conceptions end in live births, yet there are little data on paternal causes of pregnancy loss. Men with inflammatory bowel disease may have multiple disease-related issues that may affect fertility. We aimed to examine pregnancy outcomes in women undergoing assisted reproduction whose male partners had Crohn's disease or ulcerative colitis. METHODS This nationwide study included all embryo transfers registered in the Danish Assisted Reproduction Registry from January 2, 2006, to September 3, 2019. The exposed cohort included embryo transfers from couples in which the male partners had Crohn's disease or ulcerative colitis. The unexposed cohort included embryo transfers in which male partners did not have inflammatory bowel disease. RESULTS For fathers with ulcerative colitis, the adjusted odds ratio for a positive biochemical pregnancy (positive human chorionic gonadotropin) was 1.14 (95% confidence interval [CI], 0.92-1.42), for a clinical pregnancy (positive vaginal ultrasonography at 7-8 weeks) was 0.91 (95% CI, 0.59-1.40), and for a live birth was 0.99 (95% CI, 0.71-1.60). For fathers with Crohn's disease, the adjusted odds ratio for a biochemical pregnancy was 0.83 (95% CI, 0.63-1.09), for a clinical pregnancy was 0.58 (95% CI, 0.34-0.97), and for a live birth was 0.88 (95% CI, 0.51-1.55). CONCLUSIONS These findings may indicate that partners of men with Crohn's disease may have an increased risk of early pregnancy loss. Future studies should confirm these results and examine the impact of paternal medications, paternal disease activity, and other factors associated with chronic inflammatory bowel disease.
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Affiliation(s)
- Sonia Friedman
- Gastroenterology Division, Tufts Medical Center, Tufts University School of Medicine, Boston Massachusetts, USA
- Center for Clinical Epidemiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Epidemiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Caroline Thingholm Thorarinsson
- Center for Clinical Epidemiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Epidemiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mette Wod
- Center for Clinical Epidemiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Epidemiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Fedder
- Center of Andrology and Fertility, Odense University Hospital, Odense, Denmark
| | - Bente Mertz Nørgård
- Gastroenterology Division, Tufts Medical Center, Tufts University School of Medicine, Boston Massachusetts, USA
- Center for Clinical Epidemiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Epidemiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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2
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Crafa A, Cannarella R, Calogero AE, Gunes S, Agarwal A. Behind the Genetics: The Role of Epigenetics in Infertility-Related Testicular Dysfunction. Life (Basel) 2024; 14:803. [PMID: 39063558 PMCID: PMC11277947 DOI: 10.3390/life14070803] [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: 05/27/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
In recent decades, we have witnessed a progressive decline in male fertility. This is partly related to the increased prevalence of chronic diseases (e.g., obesity and diabetes mellitus) and risky lifestyle behaviors. These conditions alter male fertility through various non-genetic mechanisms. However, there is increasing evidence that they are also capable of causing sperm epigenetic alterations, which, in turn, can cause infertility. Furthermore, these modifications could be transmitted to offspring, altering their general and reproductive health. Therefore, these epigenetic modifications could represent one of the causes of the progressive decline in sperm count recorded in recent decades. This review focuses on highlighting epigenetic modifications at the sperm level induced by non-genetic causes of infertility. In detail, the effects on DNA methylation, histone modifications, and the expression profiles of non-coding RNAs are evaluated. Finally, a focus on the risk of transgenerational inheritance is presented. Our narrative review aims to demonstrate how certain conditions can alter gene expression, potentially leading to the transmission of anomalies to future generations. It emphasizes the importance of the early detection and treatment of reversible conditions (such as obesity and varicocele) and the modification of risky lifestyle behaviors. Addressing these issues is crucial for individual health, in preserving fertility, and in ensuring the well-being of future generations.
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Affiliation(s)
- Andrea Crafa
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (A.C.); (R.C.); (A.E.C.)
- Global Andrology Forum, Moreland Hills, OH 44022, USA
| | - Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (A.C.); (R.C.); (A.E.C.)
- Global Andrology Forum, Moreland Hills, OH 44022, USA
- Glickman Urological & Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Aldo E. Calogero
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (A.C.); (R.C.); (A.E.C.)
- Global Andrology Forum, Moreland Hills, OH 44022, USA
| | - Sezgin Gunes
- Global Andrology Forum, Moreland Hills, OH 44022, USA
- Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, 55280 Samsun, Türkiye
| | - Ashok Agarwal
- Global Andrology Forum, Moreland Hills, OH 44022, USA
- Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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3
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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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4
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Trapphoff T, Ontrup C, Krug S, Dieterle S. Consumption of hookahs, e-cigarettes, and classic cigarettes and the impact on medically assisted reproduction treatment. Sci Rep 2024; 14:9597. [PMID: 38671174 PMCID: PMC11053167 DOI: 10.1038/s41598-024-60251-y] [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: 02/15/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
Smoking of classic cigarettes has been well-established as a health risk factor, including cardiovascular, neurological, and pulmonary diseases. Adverse effects on human reproduction have also been shown. Smokers are assumed to have a significantly lower chance of pregnancy, however, the impact of smoking on medically assisted reproduction (MAR) treatment outcomes is controversial. Moreover, smoking habits have changed during the last decades since e-cigarettes and hookahs, or water pipes, have become very popular, yet little is known regarding vaping or hookah-smoking patients undergoing MAR treatments. This prospective study aimed to examine the presence of benzo[a]pyrene, nicotine, and its main metabolite, cotinine, in human follicular fluid (FF) in non-smoking, smoking, and vaping/hookah-smoking patients and to evaluate the impact on female fertility. Human FF samples were collected from 320 women subjected to intracytoplasmic sperm injection (ICSI) cycles due to male subfertility. Gas chromatography combined with mass spectrometry was used to analyse the presence of benzo[a]pyrene, nicotine, and cotinine. A questionnaire was provided to assess patient consumption behaviour and to identify (1) non-smoking patients, (2) patients who consumed cigarettes, and (3) patients with exclusive consumption of e-cigarettes or hookahs. Data were analysed using linear and logistic regression, Fisher's exact test, and the Mann-Whitney U Test. Nicotine was present in 22 (6.8%) and cotinine in 65 (20.3%) of the 320 samples. The nicotine and cotinine concentrations per sample ranged from 0 to 26.3 ng/ml and 0-363.0 ng/ml, respectively. Benzo[a]pyrene was not detectable in any of the samples analysed. Nicotine and cotinine were also present in the FF of patients with exclusive consumption of e-cigarettes or hookahs. The clinical pregnancy rate, fertilization and maturation rates, and number of oocytes per oocyte pick-up were not statistically significantly different between non-smoking, smoking, or vaping/hookah-smoking patients. Smoking and the accumulation of smoking toxins in the FF have no impact on the outcome of MAR treatments-neither the clinical pregnancy rate, maturation and fertilization rates, nor the number of retrieved oocytes were affected. For the first time, nicotine and cotinine were quantified in the FF of patients exclusively vaping e-cigarettes or smoking hookahs. Since vaping liquids and hookah tobaccos contain potentially harmful substances, other adverse effects cannot be excluded.Trial registration ClinicalTrials.gov Identifier: NCT03414567.
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Affiliation(s)
- Tom Trapphoff
- Fertility Center Dortmund, Olpe 19, 44135, Dortmund, Germany.
| | - Carolin Ontrup
- Fertility Center Dortmund, Olpe 19, 44135, Dortmund, Germany
| | - Sonja Krug
- Fertility Center Dortmund, Olpe 19, 44135, Dortmund, Germany
| | - Stefan Dieterle
- Fertility Center Dortmund, Olpe 19, 44135, Dortmund, Germany
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University Witten/Herdecke, 44135, Dortmund, Germany
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5
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Birch G, Meniri M, Cant MA, Blount JD. Defence against the intergenerational cost of reproduction in males: oxidative shielding of the germline. Biol Rev Camb Philos Soc 2024; 99:70-84. [PMID: 37698166 DOI: 10.1111/brv.13012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 09/13/2023]
Abstract
Reproduction is expected to carry an oxidative cost, yet in many species breeders appear to sustain lower levels of oxidative damage compared to non-breeders. This paradox may be explained by considering the intergenerational costs of reproduction. Specifically, a reduction in oxidative damage upon transitioning to a reproductive state may represent a pre-emptive shielding strategy to protect the next generation from intergenerational oxidative damage (IOD) - known as the oxidative shielding hypothesis. Males may be particularly likely to transmit IOD, because sperm are highly susceptible to oxidative damage. Yet, the possibility of male-mediated IOD remains largely uninvestigated. Here, we present a conceptual and methodological framework to assess intergenerational costs of reproduction and oxidative shielding of the germline in males. We discuss variance in reproductive costs and expected payoffs of oxidative shielding according to species' life histories, and the expected impact on offspring fitness. Oxidative shielding presents an opportunity to incorporate intergenerational effects into the advancing field of life-history evolution.
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Affiliation(s)
- Graham Birch
- Centre for Ecology & Conservation, Faculty of Environment, Science & Economy, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Magali Meniri
- Centre for Ecology & Conservation, Faculty of Environment, Science & Economy, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Michael A Cant
- Centre for Ecology & Conservation, Faculty of Environment, Science & Economy, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Jonathan D Blount
- Centre for Ecology & Conservation, Faculty of Environment, Science & Economy, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
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6
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Metayer C, Morimoto LM, Kang AY, Alvarez JS, Winestone LE. Pre- and Postnatal Exposures to Tobacco Smoking and Survival of Childhood Acute Lymphoblastic and Myeloid Leukemias in California, United States. Cancer Epidemiol Biomarkers Prev 2024; 33:117-125. [PMID: 37921440 PMCID: PMC11008006 DOI: 10.1158/1055-9965.epi-23-0801] [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: 07/11/2023] [Revised: 10/16/2023] [Accepted: 11/01/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Tobacco smoke adversely affects the prognosis of adult cancers including myeloid leukemia, but less is known in children. METHODS We evaluated whether pre- and postnatal exposures to tobacco smoke decrease 5-year survival of 1,235 childhood acute lymphoblastic leukemia (ALL) and 188 childhood acute myeloid leukemia (AML) cases derived from a population-based case-control study in California. Cases were diagnosed between 1995 and 2015 (median follow-up time of 13.2 years overall). We obtained data on tobacco smoking (before conception, during pregnancy, after birth), parental education and income, clinical features, and vital status through 2020. Cox proportional hazards regression was used to calculate hazard ratios (HR) and 95% confidence intervals (CI) for mortality associated with smoking, adjusting for sociodemographic characteristics and risk group (ALL only). RESULTS About 23% of mothers and 39% of fathers reported smoking and 130 children with ALL and 52 with AML died within 5 years. For AML, increased risks of death were observed among children whose fathers smoked before conception compared with nonsmoking fathers [HR = 1.41; 95% confidence interval (CI), 0.95-3.44 and 3.47; 95% CI, 1.37-8.81, respectively for <20 vs. ≥20 cigarettes per day; Ptrend = 0.01]. HR for child's passive smoking was 1.74, 95% CI, 0.81-3.73. Paternal preconception smoking may also reduce 5-year survival among ALL with favorable prognostic molecular subtypes (high hyperdiploidy and absence of IKZF1 gene deletion), although the associations did not reach statistical significance (Pheterogeneity = 0.07). CONCLUSIONS Paternal preconception smoking decreased 5-year survival of childhood AML. IMPACT Knowledge of exposure to tobacco smoking should be integrated in the treatment plan of childhood leukemias.
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Affiliation(s)
- Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Libby M. Morimoto
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Alice Y. Kang
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Jacklyn Sanchez Alvarez
- Division of Allergy, Immunology, and BMT, Department of Pediatrics, University of California San Francisco Benioff Children’s Hospitals, San Francisco, California, USA
| | - Lena E. Winestone
- Division of Allergy, Immunology, and BMT, Department of Pediatrics, University of California San Francisco Benioff Children’s Hospitals, San Francisco, California, USA
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7
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Feinberg JI, Schrott R, Ladd-Acosta C, Newschaffer CJ, Hertz-Picciotto I, Croen LA, Daniele Fallin M, Feinberg AP, Volk HE. Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort. Mol Psychiatry 2024; 29:43-53. [PMID: 37100868 DOI: 10.1038/s41380-023-02046-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/28/2023]
Abstract
There is a need to consider paternal contributions to autism spectrum disorder (ASD) more strongly. Autism etiology is complex, and heritability is not explained by genetics alone. Understanding paternal gametic epigenetic contributions to autism could help fill this knowledge gap. In the present study, we explored whether paternal autistic traits, and the sperm epigenome, were associated with autistic traits in children at 36 months enrolled in the Early Autism Risk Longitudinal Investigation (EARLI) cohort. EARLI is a pregnancy cohort that recruited and enrolled pregnant women in the first half of pregnancy who already had a child with ASD. After maternal enrollment, EARLI fathers were approached and asked to provide a semen specimen. Participants were included in the present study if they had genotyping, sperm methylation data, and Social Responsiveness Scale (SRS) score data available. Using the CHARM array, we performed genome-scale methylation analyses on DNA from semen samples contributed by EARLI fathers. The SRS-a 65-item questionnaire measuring social communication deficits on a quantitative scale-was used to evaluate autistic traits in EARLI fathers (n = 45) and children (n = 31). We identified 94 significant child SRS-associated differentially methylated regions (DMRs), and 14 significant paternal SRS-associated DMRs (fwer p < 0.05). Many child SRS-associated DMRs were annotated to genes implicated in ASD and neurodevelopment. Six DMRs overlapped across the two outcomes (fwer p < 0.1), and, 16 DMRs overlapped with previous child autistic trait findings at 12 months of age (fwer p < 0.05). Child SRS-associated DMRs contained CpG sites independently found to be differentially methylated in postmortem brains of individuals with and without autism. These findings suggest paternal germline methylation is associated with autistic traits in 3-year-old offspring. These prospective results for autism-associated traits, in a cohort with a family history of ASD, highlight the potential importance of sperm epigenetic mechanisms in autism.
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Affiliation(s)
- Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rose Schrott
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Craig J Newschaffer
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, State College, PA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, University of California, Davis, CA, USA
| | - Lisa A Croen
- Autism Research Program, Division of Research, Kaiser Permanente, Oakland, CA, USA
| | - M Daniele Fallin
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Andrew P Feinberg
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Center for Epigenetics, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Heather E Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Chen T, Zhang CA, Li S, Schroeder AR, Shaw GM, Eisenberg ML. The association of preconception paternal metabolic syndrome on early childhood emergency department visits and hospitalizations. Andrology 2023; 11:1057-1066. [PMID: 36542456 DOI: 10.1111/andr.13370] [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: 07/22/2022] [Revised: 11/10/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Increasing preconception paternal comorbidity has been associated with adverse pregnancy outcomes. However, whether the father's health impacts the child after birth is uncertain. OBJECTIVES In the present study, we examined the association of preconception paternal metabolic syndrome status with childhood emergency department visits and hospitalizations. MATERIALS AND METHODS This is a longitudinal cohort study of children (295,355 boys and 278,735 girls) born to linked pairs of fathers and mothers in the United States between 2009 and 2016 within the IBM MarketScan Research database. Associations between paternal and maternal metabolic syndrome component diagnoses and subsequent hospitalizations and emergency department visits for offspring within the first 2 years of life were determined. RESULTS Note that, 35.5% (203,617/574,090) of children had at least one emergency room visit and 6.1% (35,141/574,090) of children had an inpatient admission. After adjustment, the odds of inpatient admission and emergency department visits increased in a dose-dependent fashion among fathers with higher comorbidities. Similar trends were seen for emergency department visit utilization. DISCUSSION AND CONCLUSION Increasing paternal preconception comorbidity is associated with a higher risk that a child requires the emergency department and inpatient care in the first years of life. An opportunity exists to engage men in preconception counseling to optimize their and their offspring's health.
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Affiliation(s)
- Tony Chen
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - Chiyuan A Zhang
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - Shufeng Li
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - Alan R Schroeder
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Michael L Eisenberg
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
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9
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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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10
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Laqqan MM, Al-Ghora SS, Yassin MM. Impact of waterpipe and tobacco cigarette smoking on global DNA methylation and nuclear proteins genes transcription in spermatozoa: a comparative investigation. Inhal Toxicol 2023:1-10. [PMID: 37145555 DOI: 10.1080/08958378.2023.2208608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Waterpipe smoking is harmful and dangerous, and it is a growing threat to public health. OBJECTIVES This study was performed to evaluate the influence of waterpipe smoking on global DNA methylation, DNA fragmentation, and protamine deficiency in spermatozoa compared to cigarette heavy smokers and nonsmokers, and to determine whether the transcription levels of spermatozoa nuclear proteins genes 'PRM1, PRM2, and H2BFWT' in waterpipe smokers are different compared to cigarette heavy smokers and nonsmokers. METHODS A total of 900 semen samples were collected from males with a mean age of 32.5 ± 6.3 years (300 waterpipe smokers, 300 cigarette heavy smokers, and 300 nonsmokers). The nucleic acids were isolated from purified spermatozoa, and then the global DNA methylation and transcription levels of the PRM1, PRM2, and H2BFWT genes were assessed using ELISA and qPCR, respectively. RESULTS A significant increase was found in the level of global DNA methylation (8.6 ± 0.6 ng/μl vs. 7.1 ± 0.6 ng/μl and 4.7 ± 0.6 ng/μl, p < 0.001), protamine deficiency (72.8 ± 15.3 vs. 51.7 ± 19.2 and 15.3 ± 5.9%, p < 0.001), and DNA fragmentation (73.4 ± 13.4 vs. 50.5 ± 18.9 and 9.3 ± 4.3%, p < 0.001) in waterpipe smokers compared to cigarette heavy smokers and nonsmokers. A significant increase was shown in the transcription levels of PRM1, PRM2, and H2BFWT genes in waterpipe smokers compared to cigarette heavy smokers and nonsmokers (p < 0.001). A down-regulation was found in the transcription level of these genes in different smoker groups compared to nonsmokers (<0.001). CONCLUSION This study suggests that waterpipe smoking is more harmful than cigarette smoking on semen parameters, global DNA methylation, and transcription of nuclear protein genes.
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Affiliation(s)
- Mohammed M Laqqan
- Faculty of Health Sciences, Department of Medical Laboratory Sciences, Islamic University of Gaza, Gaza, Palestine
| | - Said S Al-Ghora
- Faculty of Medicine, Islamic University of Gaza, Gaza, Palestine
| | - Maged M Yassin
- Faculty of Medicine, Department of Human Physiology, Islamic University of Gaza, Gaza, Palestine
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11
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Vidaki A, Planterose Jiménez B, Poggiali B, Kalamara V, van der Gaag KJ, Maas SCE, Ghanbari M, Sijen T, Kayser M. Targeted DNA methylation analysis and prediction of smoking habits in blood based on massively parallel sequencing. Forensic Sci Int Genet 2023; 65:102878. [PMID: 37116245 DOI: 10.1016/j.fsigen.2023.102878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/28/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023]
Abstract
Tobacco smoking is a frequent habit sustained by > 1.3 billion people in 2020 and the leading preventable factor for health risk and premature mortality worldwide. In the forensic context, predicting smoking habits from biological samples may allow broadening DNA phenotyping. In this study, we aimed to implement previously published smoking habit classification models based on blood DNA methylation at 13 CpGs. First, we developed a matching lab tool based on bisulfite conversion and multiplex PCR followed by amplification-free library preparation and targeted paired-end massively parallel sequencing (MPS). Analysis of six technical duplicates revealed high reproducibility of methylation measurements (Pearson correlation of 0.983). Artificially methylated standards uncovered marker-specific amplification bias, which we corrected via bi-exponential models. We then applied our MPS tool to 232 blood samples from Europeans of a wide age range, of which 90 were current, 71 former and 71 never smokers. On average, we obtained 189,000 reads/sample and 15,000 reads/CpG, without marker drop-out. Methylation distributions per smoking category roughly corresponded to previous microarray analysis, showcasing large inter-individual variation but with technology-driven bias. Methylation at 11 out of 13 smoking-CpGs correlated with daily cigarettes in current smokers, while solely one was weakly correlated with time since cessation in former smokers. Interestingly, eight smoking-CpGs correlated with age, and one displayed weak but significant sex-associated methylation differences. Using bias-uncorrected MPS data, smoking habits were relatively accurately predicted using both two- (current/non-current) and three- (never/former/current) category model, but bias correction resulted in worse prediction performance for both models. Finally, to account for technology-driven variation, we built new, joint models with inter-technology corrections, which resulted in improved prediction results for both models, with or without PCR bias correction (e.g. MPS cross-validation F1-score > 0.8; 2-categories). Overall, our novel assay takes us one step closer towards the forensic application of viable smoking habit prediction from blood traces. However, future research is needed towards forensically validating the assay, especially in terms of sensitivity. We also need to further shed light on the employed biomarkers, particularly on the mechanistics, tissue specificity and putative confounders of smoking epigenetic signatures.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Brando Poggiali
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vivian Kalamara
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Silvana C E Maas
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Titia Sijen
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands; Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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12
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Lo JO, D’Mello RJ, Watch L, Schust DJ, Murphy SK. An epigenetic synopsis of parental substance use. Epigenomics 2023; 15:453-473. [PMID: 37282544 PMCID: PMC10308258 DOI: 10.2217/epi-2023-0064] [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: 02/21/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023] Open
Abstract
The rate of substance use is rising, especially among reproductive-age individuals. Emerging evidence suggests that paternal pre-conception and maternal prenatal substance use may alter offspring epigenetic regulation (changes to gene expression without modifying DNA) and outcomes later in life, including neurodevelopment and mental health. However, relatively little is known due to the complexities and limitations of existing studies, making causal interpretations challenging. This review examines the contributions and influence of parental substance use on the gametes and potential transmissibility to the offspring's epigenome as possible areas to target public health warnings and healthcare provider counseling of individuals or couples in the pre-conception and prenatal periods to ultimately mitigate short- and long-term offspring morbidity and mortality.
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Affiliation(s)
- Jamie O Lo
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; Department of Obstetrics & Gynecology, Maternal Fetal Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rahul J D’Mello
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; Department of Obstetrics & Gynecology, Maternal Fetal Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lester Watch
- Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Danny J Schust
- Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
- Division of Reproductive Endocrinology & Infertility, Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Susan K Murphy
- Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
- Division of Reproductive Sciences, Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27701, USA; Division of Environmental Sciences & Policy, Duke Nicholas School of the Environment, Duke University, Durham, NC 27708, USA; Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
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13
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Greeson KW, Crow KMS, Edenfield RC, Easley CA. Inheritance of paternal lifestyles and exposures through sperm DNA methylation. Nat Rev Urol 2023:10.1038/s41585-022-00708-9. [PMID: 36653672 DOI: 10.1038/s41585-022-00708-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2022] [Indexed: 01/19/2023]
Abstract
Many different lifestyle factors and chemicals present in the environment are a threat to the reproductive tracts of humans. The potential for parental preconception exposure to alter gametes and for these alterations to be passed on to offspring and negatively affect embryo growth and development is of concern. The connection between maternal exposures and offspring health is a frequent focus in epidemiological studies, but paternal preconception exposures are much less frequently considered and are also very important determinants of offspring health. Several environmental and lifestyle factors in men have been found to alter sperm epigenetics, which can regulate gene expression during early embryonic development. Epigenetic information is thought to be a mechanism that evolved for organisms to pass on information about their lived experiences to offspring. DNA methylation is a well-studied epigenetic regulator that is sensitive to environmental exposures in somatic cells and sperm. The continuous production of sperm from spermatogonial stem cells throughout a man's adult life and the presence of spermatogonial stem cells outside of the blood-testis barrier makes them susceptible to environmental insults. Furthermore, altered sperm DNA methylation patterns can be maintained throughout development and ultimately result in impairments, which could predispose offspring to disease. Innovations in human stem cell-based spermatogenic models can be used to elucidate the paternal origins of health and disease.
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Affiliation(s)
- Katherine W Greeson
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Krista M S Crow
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - R Clayton Edenfield
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Charles A Easley
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA. .,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA.
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14
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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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15
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Kidera N, Ishikawa T, Kawamura T, Miyasaka N. Impact of paternal age on IVF and pregnancy outcomes with only normal sperm parameters. Taiwan J Obstet Gynecol 2022; 61:1015-1020. [DOI: 10.1016/j.tjog.2022.02.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2022] [Indexed: 11/23/2022] Open
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16
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Liu D, Ren Y, Wu T, Shen H, Yan P, Meng Y, Zhang Q, Zhang J, Bai P, Zhao J. Parental smoking exposure before and during pregnancy and offspring attention-deficit/hyperactivity disorder risk: A Chinese child and adolescent cohort study. Front Public Health 2022; 10:1017046. [PMID: 36299741 PMCID: PMC9589153 DOI: 10.3389/fpubh.2022.1017046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 01/28/2023] Open
Abstract
Background Previous studies revealed that maternal smoking exposure during pregnancy was an essential risk factor for offspring developing attention-deficit/hyperactivity disorder (ADHD). The impact of paternal smoking exposure 1 year before pregnancy on offspring ADHD risk is still unclear. Methods The present study included 2,477 school-age children and their parents from the Shanghai Child and Adolescent Health Cohort who had complete data for offspring ADHD diagnosis and parents' smoking exposure before and during pregnancy information. A multivariate logistic regression model and Firth's logistic regression model were used to determine the associations of paternal smoking and parental smoke exposure patterns before and during pregnancy with offspring ADHD risk. Results Children whose fathers smoked before pregnancy had a higher risk of developing ADHD [odds ratio (OR) = 2.59, 95% confidence interval (CI): 1.35-4.98] compared to those whose fathers had never been exposed to smoking. Similarly, parents who were exposed to smoking or second-hand smoke before pregnancy had 1.96 times (OR = 1.96, 95% CI: 1.19-3.22) more likely to have offspring with ADHD. Moreover, children whose parents were exposed to smoking both before and during pregnancy were 2.01 times (OR = 2.01, 95% CI: 1.29-3.12) more likely to develop ADHD. Conclusion Paternal smoking before pregnancy and parental smoking exposure 1 year ahead of and throughout pregnancy were all risk factors for offspring developing ADHD.
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Affiliation(s)
- Dong Liu
- The Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaping Ren
- Department of School Health, Food Nutrition and Safety, Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Tianfeng Wu
- Department of School Health, Food Nutrition and Safety, Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Huiping Shen
- Department of School Health, Food Nutrition and Safety, Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Peijing Yan
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Yu Meng
- The Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianlong Zhang
- The Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- The Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pinqing Bai
- Department of School Health, Food Nutrition and Safety, Pudong New Area Center for Disease Control and Prevention, Shanghai, China,Pinqing Bai
| | - Jian Zhao
- The Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Jian Zhao
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17
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Marttila S, Tamminen H, Rajić S, Mishra PP, Lehtimäki T, Raitakari O, Kähönen M, Kananen L, Jylhävä J, Hägg S, Delerue T, Peters A, Waldenberger M, Kleber ME, März W, Luoto R, Raitanen J, Sillanpää E, Laakkonen EK, Heikkinen A, Ollikainen M, Raitoharju E. Methylation status of VTRNA2-1/ nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Epigenomics 2022; 14:1105-1124. [PMID: 36200237 DOI: 10.2217/epi-2022-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims & methods: The aim of this study was to characterize the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues.48 datasets, consisting of more than 30 tissues and >30,000 individuals, were used. Results: nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, whereas ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle. Conclusion: The nc886 imprint may be established in the oocyte, and, after implantation, the methylation status is stable, excluding a few specific tissues.
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Affiliation(s)
- Saara Marttila
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Gerontology Research Center, Tampere University, Tampere, 33014, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku & Turku University Hospital, Turku, 20014, Finland.,Research Centre of Applied & Preventive Cardiovascular Medicine, University of Turku, Turku, 20014, Finland.,Department of Clinical Physiology & Nuclear Medicine, Turku University Hospital, Turku, 20014, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
| | - Laura Kananen
- Faculty of Medicine & Health Technology, & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520,Finland.,Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Juulia Jylhävä
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Delerue
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,Competence Cluster for Nutrition & Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, 07743, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg, 86156, Germany.,Clinical Institute of Medical & Chemical Laboratory Diagnostics, Medical University of Graz, Graz, 8010, Austria
| | - Riitta Luoto
- The Social Insurance Institute of Finland (Kela), Helsinki, 00250, Finland.,The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland
| | - Jani Raitanen
- The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland.,Faculty of Social Sciences (Health Sciences), Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Elina Sillanpää
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland.,Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Eija K Laakkonen
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
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18
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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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19
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Li J, Xu J, Yang T, Chen J, Li F, Shen B, Fan C. Genome-wide methylation analyses of human sperm unravel novel differentially methylated regions in asthenozoospermia. Epigenomics 2022; 14:951-964. [PMID: 36004499 DOI: 10.2217/epi-2022-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims & objectives: To investigate DNA methylation patterns in asthenozoospermic and normozoospermic sperm and to explore the potential roles of differential methylations in the etiology of the disease. Materials & methods: The authors performed whole-genome bisulfite sequencing analysis between normozoospermic controls and asthenozoospermic individuals. Results: The authors identified 238 significant differentially methylated regions. These differentially methylated regions were annotated to 114 protein-coding genes, with many genes showing associations with spermatogenesis, sperm motility etc. Conclusion: There are plenty of genomic regions exhibiting altered DNA methylation in asthenozoospermia, a number of which are located within or adjacent to sperm-related genes, suggesting novel methylation markers of asthenozoospermia and potential epigenetic regulation mechanisms through DNA methylation in the disease.
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Affiliation(s)
- Jingjing Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Jinyan Xu
- Human Sperm Bank, Key Laboratory of Birth Defects & Related Diseases of Women & Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
| | - Tingting Yang
- Human Sperm Bank, Key Laboratory of Birth Defects & Related Diseases of Women & Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
| | - Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuping Li
- Human Sperm Bank, Key Laboratory of Birth Defects & Related Diseases of Women & Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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20
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Sperm concentration and semen volume increase after smoking cessation in infertile men. Int J Impot Res 2022; 34:614-619. [PMID: 35963898 PMCID: PMC9375087 DOI: 10.1038/s41443-022-00605-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Smoking has negative reproductive consequences. This study investigated the effect of smoking cessation on the main semen parameters. We included 90 participants who applied to our infertility clinic and smoked at least 20 cigarettes a day for at least 1 year. Of the 90 participants, 48 were in the study group and 42 were in the control group. Semen analysis was performed before and at least 3 months after quitting smoking in the study group. Semen analysis was repeated at baseline and at least 3 months later in the control group. Semen parameters such as volume, sperm concentration, total sperm count, morphology, and motility were evaluated according to the World Health Organization criteria. Patient characteristics as well as the duration of the smoking period, the number of cigarettes smoked per day and the time elapsed since smoking cessation were recorded. The mean age of the participants was 34.69 ± 5.3 years, and the duration of infertility was 34.12 ± 12.1 months (n = 90). The number of cigarettes smoked per day was 30.14 ± 6.69, and the smoking time was 8.31 ± 3.53 years. The average time to quit smoking was 104.2 ± 11.51 days (n = 48). A significant increase in semen volume, sperm concentration and total sperm count was observed 3 months after smoking cessation (2.48 ± 0.79 ml vs. 2.90 ± 0.77 ml, p = 0.002; 18.45 × 106/ml ± 8.56 vs. 22.64 × 106/ml ± 11.69, p = 0.001; 45.04 ± 24.38 × 106 vs. 65.1 ± 34.9 × 106, p < 0.001, respectively). This study showed that smoking cessation had a positive effect on sperm concentration, semen volume, and total sperm count. Although smoking cessation contributed positively to sperm motility and morphology, the difference was not statistically significant.
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Vieujean S, Caron B, Haghnejad V, Jouzeau JY, Netter P, Heba AC, Ndiaye NC, Moulin D, Barreto G, Danese S, Peyrin-Biroulet L. Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models. Int J Mol Sci 2022; 23:7611. [PMID: 35886959 PMCID: PMC9321337 DOI: 10.3390/ijms23147611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that encompass two main phenotypes, namely Crohn's disease and ulcerative colitis. These conditions occur in genetically predisposed individuals in response to environmental factors. Epigenetics, acting by DNA methylation, post-translational histones modifications or by non-coding RNAs, could explain how the exposome (or all environmental influences over the life course, from conception to death) could influence the gene expression to contribute to intestinal inflammation. We performed a scoping search using Medline to identify all the elements of the exposome that may play a role in intestinal inflammation through epigenetic modifications, as well as the underlying mechanisms. The environmental factors epigenetically influencing the occurrence of intestinal inflammation are the maternal lifestyle (mainly diet, the occurrence of infection during pregnancy and smoking); breastfeeding; microbiota; diet (including a low-fiber diet, high-fat diet and deficiency in micronutrients); smoking habits, vitamin D and drugs (e.g., IBD treatments, antibiotics and probiotics). Influenced by both microbiota and diet, short-chain fatty acids are gut microbiota-derived metabolites resulting from the anaerobic fermentation of non-digestible dietary fibers, playing an epigenetically mediated role in the integrity of the epithelial barrier and in the defense against invading microorganisms. Although the impact of some environmental factors has been identified, the exposome-induced epimutations in IBD remain a largely underexplored field. How these environmental exposures induce epigenetic modifications (in terms of duration, frequency and the timing at which they occur) and how other environmental factors associated with IBD modulate epigenetics deserve to be further investigated.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, 4000 Liege, Belgium;
| | - Bénédicte Caron
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Vincent Haghnejad
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Jean-Yves Jouzeau
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Patrick Netter
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Anne-Charlotte Heba
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - Ndeye Coumba Ndiaye
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - David Moulin
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Guillermo Barreto
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Universidad de la Salud del Estado de Puebla, Puebla 72000, Mexico
| | - Silvio Danese
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and University Vita-Salute San Raffaele, 20132 Milan, Italy;
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
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Wang T, Xia P, Su P. High-Dimensional DNA Methylation Mediates the Effect of Smoking on Crohn's Disease. Front Genet 2022; 13:831885. [PMID: 35450213 PMCID: PMC9016182 DOI: 10.3389/fgene.2022.831885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenome-wide mediation analysis aims to identify high-dimensional DNA methylation at cytosine–phosphate–guanine (CpG) sites that mediate the causal effect of linking smoking with Crohn’s disease (CD) outcome. Studies have shown that smoking has significant detrimental effects on the course of CD. So we assessed whether DNA methylation mediates the association between smoking and CD. Among 103 CD cases and 174 controls, we estimated whether the effects of smoking on CD are mediated through DNA methylation CpG sites, which we referred to as causal mediation effect. Based on the causal diagram, we first implemented sure independence screening (SIS) to reduce the pool of potential mediator CpGs from a very large to a moderate number; then, we implemented variable selection with de-sparsifying the LASSO regression. Finally, we carried out a comprehensive mediation analysis and conducted sensitivity analysis, which was adjusted for potential confounders of age, sex, and blood cell type proportions to estimate the mediation effects. Smoking was significantly associated with CD under odds ratio (OR) of 2.319 (95% CI: 1.603, 3.485, p < 0.001) after adjustment for confounders. Ninety-nine mediator CpGs were selected from SIS, and then, seven candidate CpGs were obtained by de-sparsifying the LASSO regression. Four of these CpGs showed statistical significance, and the average causal mediation effects (ACME) were attenuated from 0.066 to 0.126. Notably, three significant mediator CpGs had absolute sensitivity parameters of 0.40, indicating that these mediation effects were robust even when the assumptions were slightly violated. Genes (BCL3 and FKBP5) harboring these four CpGs were related to CD. These findings suggest that changes in methylation are involved in the mechanism by which smoking increases risk of CD.
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Affiliation(s)
- Tingting Wang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pingtian Xia
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ping Su
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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Laqqan MM, Yassin MM. Cigarette heavy smoking alters DNA methylation patterns and gene transcription levels in humans spermatozoa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:26835-26849. [PMID: 34855177 DOI: 10.1007/s11356-021-17786-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/27/2023]
Abstract
Tobacco smoking is considered the most common reason of death and infertility around the world. This study was designed to assess the impact of tobacco heavy smoking on sperm DNA methylation patterns and to determine whether the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes is different in heavy smokers compared to non-smokers. As a screening study, the 450 K array was used to assess the alteration in DNA methylation patterns between heavy smokers (n = 15) and non-smokers (n = 15). Then, four CpGs that have the highest difference in methylation level (cg16338278, cg08408433, cg05799088, and cg07227024) were selected for validation using deep bisulfite sequencing in an independent cohort of heavy smokers (n = 200) and non-smokers (n = 100). A significant variation was found between heavy smokers and non-smokers in the methylation level at all CpGs within the PRICKLE2 and ALS2CR12 gene amplicon (P < 0.001). Similarly, a significant variation was found in the methylation level at nine out of thirteen CpGs within the ALDH3B2 gene amplicon (P < 0.01). Additionally, eighteen CpGs out of the twenty-six within the PTGIR gene amplicon have a significant difference in the methylation level between heavy smokers and non-smokers (P < 0.01). The study showed a significant difference in sperm global DNA methylation, chromatin non-condensation, and DNA fragmentation (P < 0.001) between heavy smokers and non-smokers. A significant decline was shown in the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes (P < 0.001) in heavy smokers. In conclusion, heavy smoking influences DNA methylation at several CpGs, sperm global DNA methylation, and transcription level of the PRICKLE2, ALS2CR12, ALDH3B2, and PTGIR genes, which affects negatively the semen parameters of heavy smokers.
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Affiliation(s)
- Mohammed M Laqqan
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Islamic University, Gaza, Palestinian Territories, Palestine.
| | - Maged M Yassin
- Department of Human Physiology, Faculty of Medicine, Islamic University, Gaza, Palestinian Territories, Palestine
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Tommasi S, Kitapci TH, Blumenfeld H, Besaratinia A. Secondhand smoke affects reproductive functions by altering the mouse testis transcriptome, and leads to select intron retention in Pde1a. ENVIRONMENT INTERNATIONAL 2022; 161:107086. [PMID: 35063792 PMCID: PMC8891074 DOI: 10.1016/j.envint.2022.107086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Human exposure to secondhand smoke (SHS) is known to result in adverse effects in multiple organ systems. However, the impact of SHS on the male reproductive system, particularly on the regulation of genes and molecular pathways that govern sperm production, maturation, and functions remains largely understudied. OBJECTIVE We investigated the effects of SHS on the testis transcriptome in a validated mouse model. METHODS Adult male mice were exposed to SHS (5 h/day, 5 days/week for 4 months) as compared to controls (clean air-exposed). RNA-seq analysis was performed on the testis of SHS-exposed mice and controls. Variant discovery and plink association analyses were also conducted to detect exposure-related transcript variants in SHS-treated mice. RESULTS Exposure of mice to SHS resulted in the aberrant expression of 131 testicular genes. Whilst approximately two thirds of the differentially expressed genes were protein-coding, the remaining (30.5%) comprised noncoding elements, mostly lncRNAs (19.1%). Variant discovery analysis identified a homozygous frameshift variant that is statistically significantly associated with SHS exposure (P = 7.744e-06) and is generated by retention of a short intron within Pde1a, a key regulator of spermatogenesis. Notably, this SHS-associated intron variant harbors an evolutionarily conserved, premature termination codon (PTC) that disrupts the open reading frame of Pde1a, presumably leading to its degradation via nonsense-mediated decay. DISCUSSION SHS alters the expression of genes involved in molecular pathways that are crucial for normal testis development and function. Preferential targeting of lncRNAs in the testis of SHS-exposed mice is especially significant considering their crucial role in the spatial and temporal modulation of spermatogenesis. Equally important is our discovery of a novel homozygous frameshift variant that is exclusively and significantly associated with SHS-exposure and is likely to represent a safeguard mechanism to regulate transcription of Pde1a and preserve normal testis function during harmful exposure to environmental agents.
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Affiliation(s)
- Stella Tommasi
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA.
| | - Tevfik H Kitapci
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
| | - Hannah Blumenfeld
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
| | - Ahmad Besaratinia
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
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McCarthy DM, Zhang L, Wilkes BJ, Vaillancourt DE, Biederman J, Bhide PG. Nicotine and the developing brain: Insights from preclinical models. Pharmacol Biochem Behav 2022; 214:173355. [DOI: 10.1016/j.pbb.2022.173355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 11/26/2022]
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Vozdova M, Kubickova S, Kopecka V, Sipek J, Rubes J. Effects of the air pollution dynamics on semen quality and sperm DNA methylation in men living in urban industrial agglomeration. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:76-83. [PMID: 35246879 DOI: 10.1002/em.22474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Human populations living in urban industrial regions of developed countries are exposed to high levels of environmental pollutants. The reproductive consequences of the exposure to air pollution can be monitored through semen analysis and molecular methods. In this study, we tested the possible impact of seasonal changes in the level of air pollution on the semen quality and sperm DNA methylation of 24 men living and working in the industrial agglomeration of Ostrava (Czech Republic). The study participants were healthy non-smokers. The study group was homogeneous regarding their profession, moderate alcohol consumption, no drug abuse and no additional exposure to chemical toxicants. We performed targeted methylation next generation sequencing (NGS) using Agilent SureSelect Human Methyl-Seq and Illumina NextSeq 500 platform to analyze semen samples collected repeatedly from the same men following the season of high (winter) and low (summer) air pollution exposure. We did not detect any adverse effects of the increased exposure on the semen quality; neither we found any difference in average sperm DNA methylation between the two sampling periods. Our search for differentially methylated CpG sites did not reveal any specific CpG methylation change. Our data indicate that the seasonal changes in the level of the air pollution probably do not have any substantial effect on sperm DNA methylation of men living in the highly polluted industrial agglomeration for a long period of time.
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Affiliation(s)
- Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology, Veterinary Research Institute, Brno, Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology, Veterinary Research Institute, Brno, Czech Republic
| | - Vera Kopecka
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology, Veterinary Research Institute, Brno, Czech Republic
| | - Jaroslav Sipek
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology, Veterinary Research Institute, Brno, Czech Republic
| | - Jiri Rubes
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology, Veterinary Research Institute, Brno, Czech Republic
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Liu Y, Chen S, Pang D, Zhou J, Xu X, Yang S, Huang Z, Yu B. Effects of paternal exposure to cigarette smoke on sperm DNA methylation and long-term metabolic syndrome in offspring. Epigenetics Chromatin 2022; 15:3. [PMID: 35063005 PMCID: PMC8780762 DOI: 10.1186/s13072-022-00437-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although paternal exposure to cigarette smoke may contribute to obesity and metabolic syndrome in offspring, the underlying mechanisms remain uncertain. METHODS In the present study, we analyzed the sperm DNA-methylation profiles in tobacco-smoking normozoospermic (SN) men, non-tobacco-smoking normozoospermic (N) men, and non-smoking oligoasthenozoospermic (OA) men. Using a mouse model, we also analyzed global methylation and differentially methylated regions (DMRs) of the DLK1 gene in paternal spermatozoa and the livers of progeny. In addition, we quantified DLK1 expression, executed an intra-peritoneal glucose tolerance test (IPGTT), measured serum metabolites, and analyzed liver lipid accumulation in the F1 offspring. RESULTS Global sperm DNA-methylation levels were significantly elevated (p < 0.05) in the SN group, and the methylation patterns were different among N, SN, and OA groups. Importantly, the methylation level of the DLK1 locus (cg11193865) was significantly elevated in the SN group compared to both N and OA groups (p < 0.001). In the mouse model, the group exposed to cigarette smoke extract (CSE) exhibited a significantly higher global methylation DNA level in spermatozoa (p < 0.001) and on the DMR sites of Dlk1 in 10-week-old male offspring (p < 0.05), with a significant increase in Dlk1 expression in their livers (p < 0.001). In addition, IPGTT and LDL levels were significantly altered (p < 0.001), with elevated liver fat accumulation (p < 0.05) in F1 offspring. CONCLUSION Paternal exposure to cigarette smoke led to increased global methylation of sperm DNA and alterations to the DMR of the DLK1 gene in the F1 generation, which may be inherited parentally and may perturb long-term metabolic function.
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Affiliation(s)
- Yunyun Liu
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Shengzhu Chen
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Dejian Pang
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Jiayi Zhou
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Xiuting Xu
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Si Yang
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Zhaofeng Huang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bolan Yu
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China.
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You Y, Liu R, Zhou H, Wu R, Lin R, Li B, Liu H, Qiao Y, Guo P, Ding Z, Zhang Q. Effect of Exposure to Paternal Smoking on Overweight and Obesity in Children: Findings from the Children Lifeway Cohort in Shenzhen, Southern China. Obes Facts 2022; 15:609-620. [PMID: 35738239 PMCID: PMC9421693 DOI: 10.1159/000525544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 05/13/2022] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Paternal smoking associated with childhood overweight and obesity has been a concern, but studies have not investigated smoking exposure and smoking details. We investigated the association of exposures from paternal smoking as well as smoking details on offspring overweight/obesity. METHODS A total of 4,513 children (aged 7-8 years) in Shenzhen were enrolled. Four different exposures from paternal smoking as well as smoking quantity, duration of smoking, and age of starting smoking details were the exposure variables and demographic characteristics, and circumstances of birth, dietary intake, lifestyle, and nonpaternal-smoking exposure were covariates in the logistic regression analysis to determine the effect of paternal smoking on childhood overweight/obesity, estimating odds ratios (ORs), and 95% confidence intervals (CIs). RESULTS Paternal smoking was positively associated with childhood overweight/obesity (p < 0.05). Moreover, only preconception exposure, and both pre- and postconception exposure were significantly associated with childhood overweight/obesity (OR 1.54 [95% CI: 1.14-2.08] and OR 1.73 [95% CI: 1.14-2.61], respectively), restricted to boys but not girls. Furthermore, for children with only preconception paternal-smoking exposure, the dose-response relation was positive between smoking quantity, duration of smoking, age at starting, and overweight/obesity for boy offspring (p trend <0.001). We did not find any significant association between only postnatal exposure to paternal smoking and childhood overweight/obesity (p > 0.05). CONCLUSIONS Our findings suggest that paternal smoking is associated with boys' overweight/obesity, and this association may be due to the paternal-smoking exposure before conception rather than the postnatal exposure to paternal smoking. Reducing paternal-smoking exposure before conception might help reduce overweight/obesity in boys.
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Affiliation(s)
- Yingbin You
- Baoan Central Hospital of Shenzhen, Shenzhen, China
| | - Ruiguo Liu
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
| | - Hua Zhou
- Baoan Central Hospital of Shenzhen, Shenzhen, China
| | - Rong Wu
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
| | - Rongqing Lin
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
| | - Boya Li
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
| | - Hui Liu
- Baoan Central Hospital of Shenzhen, Shenzhen, China
| | | | - Pi Guo
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
| | - Zan Ding
- Baoan Central Hospital of Shenzhen, Shenzhen, China
| | - Qingying Zhang
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, China
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Patel DP, Hsieh TC. Can fever alone alter sperm parameters after severe acute respiratory syndrome coronavirus 2 infection? Fertil Steril 2021; 117:297. [PMID: 34980424 PMCID: PMC8719122 DOI: 10.1016/j.fertnstert.2021.11.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 11/20/2022]
Affiliation(s)
| | - Tung-Chin Hsieh
- Department of Urology, University of California-San Diego, La Jolla, California
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Lemesh VA, Kipen VN, Bahdanava MV, Burakova AA, Bulgak AG, Bayda AV, Bruskin SA, Zotova OV, Dobysh OI. Determination of Human Chronological Age from Biological Samples Based on the Analysis of Methylation of CpG Dinucleotides. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Aliferi A, Sundaram S, Ballard D, Freire-Aradas A, Phillips C, Lareu MV, Court DS. Combining current knowledge on DNA methylation-based age estimation towards the development of a superior forensic DNA intelligence tool. Forensic Sci Int Genet 2021; 57:102637. [PMID: 34852982 DOI: 10.1016/j.fsigen.2021.102637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 01/09/2023]
Abstract
The estimation of chronological age from biological fluids has been an important quest for forensic scientists worldwide, with recent approaches exploiting the variability of DNA methylation patterns with age in order to develop the next generation of forensic 'DNA intelligence' tools for this application. Drawing from the conclusions of previous work utilising massively parallel sequencing (MPS) for this analysis, this work introduces a DNA methylation-based age estimation method for blood that exhibits the best combination of prediction accuracy and sensitivity reported to date. Statistical evaluation of markers from 51 studies using microarray data from over 4000 individuals, followed by validation using in-house generated MPS data, revealed a final set of 11 markers with the greatest potential for accurate age estimation from minimal DNA material. Utilising an algorithm based on support vector machines, the proposed model achieved an average error (MAE) of 3.3 years, with this level of accuracy retained down to 5 ng of starting DNA input (~ 1 ng PCR input). The accuracy of the model was retained (MAE = 3.8 years) in a separate test set of 88 samples of Spanish origin, while predictions for donors of greater forensic interest (< 55 years of age) displayed even higher accuracy (MAE = 2.6 years). Finally, no sex-related bias was observed for this model, while there were also no signs of variation observed between control and disease-associated populations for schizophrenia, rheumatoid arthritis, frontal temporal dementia and progressive supranuclear palsy in microarray data relating to the 11 markers.
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Affiliation(s)
- Anastasia Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Sudha Sundaram
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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Laqqan MM, Yassin MM. Influence of tobacco cigarette heavy smoking on DNA methylation patterns and transcription levels of MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A genes in human spermatozoa. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2021. [DOI: 10.1186/s43043-021-00084-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Tobacco smoking is considered as one of the lifestyles factors that influence the sperm DNA methylation and global sperm DNA methylation and that may affect the sperm phenotype. This study was performed to investigate whether tobacco cigarette heavy smoking influences sperm DNA methylation patterns and semen parameters and to determine whether there is an alteration in the transcription level of MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A genes in heavy smokers compared to non-smokers. Thirty samples were subjected to 450K arrays as a screening study to assess the variation in sperm DNA methylation levels between heavy smokers and non-smokers. Five CpG sites have the highest difference in methylation levels (cg07869343, cg05813498, cg09785377, cg06833981, and cg02745784), which are located in the MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A genes, respectively, and were selected for further analysis using deep bisulfite sequencing in 280 independent samples (120 proven non-smokers and 160 heavy smokers) with a mean age of 33.8 ± 8.4 years. The global sperm DNA methylation, sperm DNA fragmentation, and chromatin non-condensation were evaluated also.
Results
A significant increase was found in the methylation level at seven, three, and seventeen CpGs within the GAA, ANXA2, and MAPK8IP3 genes amplicon, respectively (P< 0.01) in heavy smokers compared to non-smokers. Additionally, a significant increase was found in the methylation levels at all CpGs within PRRC2A and PDE11A gene amplicon (P< 0.01). A significant increase was found in the level of sperm chromatin non-condensation, DNA fragmentation, and global DNA methylation (P < 0.001) in heavy smokers compared to non-smokers.
Conclusion
These results indicate that tobacco cigarette smoking can alter the DNA methylation level at several CpGs, the status of global DNA methylation, and transcription level of the following genes “MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A” in human spermatozoa. These findings may affect negatively semen parameters and men’s fertility.
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Hu Y, Zhang X, Zhang A, Hou Y, Liu Y, Li Q, Wang Y, Yu Y, Hou M, Peng J, Yang X, Xu S. Global burden and attributable risk factors of acute lymphoblastic leukemia in 204 countries and territories in 1990-2019: Estimation based on Global Burden of Disease Study 2019. Hematol Oncol 2021; 40:92-104. [PMID: 34664286 DOI: 10.1002/hon.2936] [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: 08/03/2021] [Revised: 09/17/2021] [Accepted: 10/15/2021] [Indexed: 01/13/2023]
Abstract
To provide a foundational guideline for policy-makers to efficiently allocate medical resources in the context of population aging and growth, the latest spatial distribution and temporal trend of acute lymphoblastic leukemia (ALL) along with attributable risk factors by sex and age were mapped. Based on the Global Burden of Disease Study 2019, estimated annual percentage change (EAPC) was calculated according to the relativity between age-standardized rate and calendar year, to quantify temporal trends in morbidity and mortality of ALL. We used applied Spearman rank correlation to estimate the relationship between the EAPC and potential influence factors. The population attributable fraction of potential risk factors for ALL-related disability-adjusted life years were estimated by the comparative risk assessment framework. As a result, we found that new ALL cases increased significantly by 1.29% worldwide, and the age-standardized incidence rate increased by 1.61% annually. The proportion of elder patients sharply increased, especially within the higher socio-demographic index (SDI) region. Smoking and high body mass index remained the predominant risk factors for ALL-related mortality. Notably, the contribution of high body mass index presented an increasing trend. In conclusion, the global burden of ALL has steadily increased, especially in Middle SDI region. Health measures and new drugs should be taken into consideration to improve the management and treatment of elders with ALL due to an increasing proportion in the higher SDI region. For Low SDI areas, attention should be paid to the environmental problems caused by industrial development.
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Affiliation(s)
- Yuefen Hu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiuping Zhang
- Medical Experimental Diagnosis Center, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Aijun Zhang
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yu Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yang Liu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Qizhao Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yawen Wang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yafei Yu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ming Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jun Peng
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaorong Yang
- Clinical Epidemiology Unit, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Shuqian Xu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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Schuller A, Bellini C, Jenkins TG, Eden M, Matz J, Oakes J, Montrose L. Simulated Wildfire Smoke Significantly Alters Sperm DNA Methylation Patterns in a Murine Model. TOXICS 2021; 9:199. [PMID: 34564350 PMCID: PMC8473101 DOI: 10.3390/toxics9090199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/20/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022]
Abstract
Wildfires are now a common feature of the western US, increasing in both intensity and number of acres burned over the last three decades. The effects of this changing wildfire and smoke landscape are a critical public and occupational health issue. While respiratory morbidity due to smoke exposure is a priority, evaluating the molecular underpinnings that explain recent extrapulmonary observations is necessary. Here, we use an Apoe-/- mouse model to investigate the epigenetic impact of paternal exposure to simulated wildfire smoke. We demonstrate that 40 days of exposure to smoke from Douglas fir needles induces sperm DNA methylation changes in adult mice. DNA methylation was measured by reduced representation bisulfite sequencing and varied significantly in 3353 differentially methylated regions, which were subsequently annotated to 2117 genes. The differentially methylated regions were broadly distributed across the mouse genome, but the vast majority (nearly 80%) were hypermethylated. Pathway analyses, using gene-derived and differentially methylated region-derived gene ontology terms, point to a number of developmental processes that may warrant future investigation. Overall, this study of simulated wildfire smoke exposure suggests paternal reproductive risks are possible with prolonged exposure.
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Affiliation(s)
- Adam Schuller
- Department of Public Health and Population Science, Boise State University, Boise, ID 83725, USA;
| | - Chiara Bellini
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA; (C.B.); (M.E.); (J.M.); (J.O.)
| | - Timothy G. Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA;
| | - Matthew Eden
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA; (C.B.); (M.E.); (J.M.); (J.O.)
| | - Jacqueline Matz
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA; (C.B.); (M.E.); (J.M.); (J.O.)
| | - Jessica Oakes
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA; (C.B.); (M.E.); (J.M.); (J.O.)
| | - Luke Montrose
- Department of Public Health and Population Science, Boise State University, Boise, ID 83725, USA;
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Hines LA, Spry EA, Moreno-Betancur M, Mohamad Husin H, Becker D, Middleton M, Craig JM, Doyle LW, Olsson CA, Patton G. Cannabis and tobacco use prior to pregnancy and subsequent offspring birth outcomes: a 20-year intergenerational prospective cohort study. Sci Rep 2021; 11:16826. [PMID: 34413325 PMCID: PMC8376878 DOI: 10.1038/s41598-021-95460-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/20/2021] [Indexed: 11/15/2022] Open
Abstract
There is increasing evidence that the life-course origins of health and development begin before conception. We examined associations between timing and frequency of preconception cannabis and tobacco use and next generation preterm birth (PTB), low birth weight (LBW) and small for gestational age. 665 participants in a general population cohort were repeatedly assessed on tobacco and cannabis use between ages 14-29 years, before pregnancy. Associations were estimated using logistic regression. Preconception parent (either maternal or paternal) daily cannabis use age 15-17 was associated with sixfold increases in the odds of offspring PTB (aOR 6.65, 95% CI 1.92, 23.09), and offspring LBW (aOR 5.84, 95% CI 1.70-20.08), after adjusting for baseline sociodemographic factors, parent sex, offspring sex, family socioeconomic status, parent mental health at baseline, and concurrent tobacco use. There was little evidence of associations with preconception parental cannabis use at other ages or preconception parental tobacco use. Findings support the hypothesis that the early life origins of growth begin before conception and provide a compelling rationale for prevention of frequent use during adolescence. This is pertinent given liberalisation of cannabis policy.
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Affiliation(s)
- Lindsey A Hines
- Centre for Academic Mental Health, Population Health Sciences Institute, University of Bristol, Bristol, UK.
- MRC Integrative Epidemiology Unit, Population Health Sciences Institute, University of Bristol, Bristol, UK.
| | - Elizabeth A Spry
- Centre for Social and Early Emotional Development, Faculty of Health, Deakin University, Melbourne, Australia
- Centre for Adolescent Health, Murdoch Children's Research Institute, Melbourne, Australia
| | - Margarita Moreno-Betancur
- University of Melbourne, Melbourne, Australia
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Melbourne, Australia
| | - Hanafi Mohamad Husin
- Centre for Adolescent Health, Murdoch Children's Research Institute, Melbourne, Australia
| | - Denise Becker
- Biostatistics Unit, Faculty of Health, Deakin University, Melbourne, Australia
| | - Melissa Middleton
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Melbourne, Australia
| | - Jeffrey M Craig
- Centre for Molecular and Medical Research, Deakin University School of Medicine, Geelong, Australia
| | - Lex W Doyle
- Department of Obstetrics and Gynaecology, The Royal Women's Hospital, University of Melbourne, Melbourne, Australia
- Clinical Sciences, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paedatrics, University of Melbourne, Melbourne, Australia
| | - Craig A Olsson
- Centre for Social and Early Emotional Development, Faculty of Health, Deakin University, Melbourne, Australia
- Centre for Adolescent Health, Murdoch Children's Research Institute, Melbourne, Australia
| | - George Patton
- Centre for Adolescent Health, Murdoch Children's Research Institute, Melbourne, Australia
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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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Zhu W, Jiang L, Pan C, Sun J, Huang X, Ni W. Deoxyribonucleic acid methylation signatures in sperm deoxyribonucleic acid fragmentation. Fertil Steril 2021; 116:1297-1307. [PMID: 34253331 DOI: 10.1016/j.fertnstert.2021.06.025] [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: 01/22/2021] [Revised: 05/05/2021] [Accepted: 06/10/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To evaluate Deoxyribonucleic acid (DNA) methylation patterns in sperm from men with differential levels of sperm DNA fragmentation index (DFI). DESIGN Prospective study. SETTING University-affiliated reproductive medicine center. PATIENT(S) A total of 278 male patients consulting for couple infertility were recruited from the First Affiliated Hospital of Wenzhou Medical University. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Genome-wide DNA methylation analysis was performed using Infinium MethylationEPIC BeadChip on spermatozoal DNA from 20 male patients. Differentially methylated regions (DMRs) were identified and validated using targeted bisulfite amplicon sequencing in spermatozoal DNA from 266 males. RESULT(S) Unsupervised hierarchical clustering analysis revealed three main clusters corresponding to sperm DFI levels (low, medium, or high). Between-cluster comparisons identified 959 (medium-low), 738 (high-medium), and 937 (high-low) DMRs. Sixty-six DMRs were validated in the 266-sample cohort, of which nine CpG fragments corresponding to nine genes (BLCAP, DIRAS3, FAM50B, GNAS, MEST, TSPAN32, PSMA8, SYCP1, and TEX12) exhibited significantly altered methylation in those with high DFI (≥25%) compared with those with low DFI (<25%). CONCLUSION(S) We identified and validated a distinct DNA methylation signature associated with sperm DNA damage in a large, unselected cohort. These results indicate that sperm DNA damage may affect DNA methylation patterns in human sperm.
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Affiliation(s)
- Weijian Zhu
- Central Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Lei Jiang
- Central Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Chengshuang Pan
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Junhui Sun
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xuefeng Huang
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Wuhua Ni
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
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Laqqan MM, Yassin MM. Potential effect of tobacco cigarettes smoking on global DNA methylation status and protamines transcripts in human spermatozoa. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2021. [DOI: 10.1186/s43043-021-00066-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Background
Epigenetics refers to an alteration in gene expression without alteration in the sequence of DNA and this process may be affected by environmental factors and lifestyle like cigarette smoking. This study was designed to evaluate the potential effect of cigarette smoking on the global DNA methylation status and the transcription level of protamine 1 and protamine 2 in human spermatozoa. A total of 188 semen samples were collected from men with a mean age of 34.9 ± 5.8 years old (98 heavy smokers and 90 non-smokers). The DNA and RNA were isolated from purified spermatozoa, then the status of global DNA methylation and the transcription level of protamine 1 and protamine 2 were evaluated using ELISA and qPCR, respectively. The chromatin non-condensation and DNA fragmentation in human spermatozoa were evaluated using chromomycin A3 staining and TUNEL assay, respectively.
Results
A significant increase has been found in the status of global DNA methylation in spermatozoa of heavy smokers compared to non-smokers (7.69 ± 0.69 ng/μl vs. 4.90 ± 0.40 ng/μl, P < 0.001). Additionally, a significant reduction has been found in transcription level of protamine 1 (25.49 ± 0.31 vs. 23.94 ± 0.40, P < 0.001) and protamine 2 (28.27 ± 0.39 vs. 23.45 ± 0.30, P < 0.001) in heavy smokers. A downregulation has been found in the transcription level of protamine 1 and protamine 2 with a fold change of 0.497 and 0.047, respectively. A significant increase has been shown in the level of DNA fragmentation and chromatin non-condensation in heavy smokers compared to non-smokers (P < 0.001). On the other hand, a significant positive correlation has been found between sperm chromatin non-condensation, sperm DNA fragmentation, transcription level of protamine 1, transcription level of protamine 2, and global DNA methylation status (r = 0.304, P < 0.001; r = 0.399, P < 0.001; r = 0.216, P = 0.003; r = 0.494, P < 0.001, respectively).
Conclusion
Tobacco cigarette smoking has a potential influence on the global DNA methylation and the transcription level of protamine genes in human spermatozoa, and consequently, affect negatively on the semen parameters.
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Altintaş A, Liu J, Fabre O, Chuang TD, Wang Y, Sakurai R, Chehabi GN, Barrès R, Rehan VK. Perinatal exposure to nicotine alters spermatozoal DNA methylation near genes controlling nicotine action. FASEB J 2021; 35:e21702. [PMID: 34153130 PMCID: PMC9231556 DOI: 10.1096/fj.202100215r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022]
Abstract
Perinatal smoke/nicotine exposure alters lung development and causes asthma in exposed offspring, transmitted transgenerationally. The mechanism underlying the transgenerational inheritance of perinatal smoke/nicotine-induced asthma remains unknown, but germline epigenetic modulations may play a role. Using a well-established rat model of perinatal nicotine-induced asthma, we determined the DNA methylation pattern of spermatozoa of F1 rats exposed perinatally to nicotine in F0 gestation. To identify differentially methylated regions (DMRs), reduced representation bisulfite sequencing was performed on spermatozoa of F1 litters. The top regulated gene body and promoter DMRs were tested for lung gene expression levels, and key proteins involved in lung development and repair were determined. The overall CpG methylation in F1 sperms across gene bodies, promoters, 5'-UTRs, exons, introns, and 3'-UTRs was not affected by nicotine exposure. However, the methylation levels were different between the different genomic regions. Eighty one CpG sites, 16 gene bodies, and 3 promoter regions were differentially methylated. Gene enrichment analysis of DMRs revealed pathways involved in oxidative stress, nicotine response, alveolar and brain development, and cellular signaling. Among the DMRs, Dio1 and Nmu were the most hypermethylated and hypomethylated genes, respectively. Gene expression analysis showed that the mRNA expression and DNA methylation were incongruous. Key proteins involved in lung development and repair were significantly different (FDR < 0.05) between the nicotine and placebo-treated groups. Our data show that DNA methylation is remodeled in offspring spermatozoa upon perinatal nicotine exposure. These epigenetic alterations may play a role in transgenerational inheritance of perinatal smoke/nicotine induced asthma.
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Affiliation(s)
- Ali Altintaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jie Liu
- Lundquist Institute for Biomedical Innovation at Harbor-ULCA Medical Center, David Geffen School of Medicine at UCLA, Torrance, CA, USA
| | - Odile Fabre
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Tsai-Der Chuang
- Lundquist Institute for Biomedical Innovation at Harbor-ULCA Medical Center, David Geffen School of Medicine at UCLA, Torrance, CA, USA
| | - Ying Wang
- Lundquist Institute for Biomedical Innovation at Harbor-ULCA Medical Center, David Geffen School of Medicine at UCLA, Torrance, CA, USA
| | - Reiko Sakurai
- Lundquist Institute for Biomedical Innovation at Harbor-ULCA Medical Center, David Geffen School of Medicine at UCLA, Torrance, CA, USA
| | - Galal Nazih Chehabi
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Virender K. Rehan
- Lundquist Institute for Biomedical Innovation at Harbor-ULCA Medical Center, David Geffen School of Medicine at UCLA, Torrance, CA, USA
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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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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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42
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Escher J. How Family Histories Can Inform Research About Germ Cell Exposures: The Example of Autism. Biol Reprod 2021; 105:767-773. [PMID: 33959752 DOI: 10.1093/biolre/ioab092] [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: 03/02/2021] [Revised: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 12/19/2022] Open
Abstract
Throughout the scientific literature, heritable traits are routinely presumed to be genetic in origin. However, as emerging evidence from the realms of genetic toxicology and epigenomics demonstrate, heritability may be better understood as encompassing not only DNA sequence passed down through generations, but also disruptions to the parental germ cells causing de novo mutations or epigenetic alterations, with subsequent shifts in gene expression and functions in offspring. The Beyond Genes conference highlighted advances in understanding these aspects at molecular, experimental and epidemiological levels. In this commentary I suggest that future research on this topic could be inspired by collecting parents' germ cell exposure histories, with particular attention to cases of families with multiple children suffering idiopathic disorders. In so doing I focus on the endpoint of autism spectrum disorders (ASD). Rates of this serious neurodevelopment disability have climbed around the world, a growing crisis that cannot be explained by diagnostic shifts. ASD's strong heritability has prompted a research program largely focused on DNA sequencing to locate rare and common variants, but decades of this gene-focused research have revealed surprisingly little about the molecular origins of the disorder. Based on my experience as the mother of two children with idiopathic autism, and as a research philanthropist and autism advocate, I suggest ways researchers might probe parental germ cell exposure histories to develop new hypotheses that may ultimately reveal sources of non-genetic heritability in a subset of idiopathic heritable pathologies.
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Quan Y, Liang F, Deng SM, Zhu Y, Chen Y, Xiong J. Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations With Phenotype. Front Mol Biosci 2021; 8:597513. [PMID: 33842534 PMCID: PMC8034267 DOI: 10.3389/fmolb.2021.597513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlaps of identified phenotype-related DNA methylation sites between various studies are often quite small, and it might be due to the fact that methylation remodeling has a certain degree of randomness within the genome. Thus, the identification of robust gene-phenotype associations is crucial to interpreting pathogenesis. How to integrate the methylation values of different sites on the same gene and to mine the DNA methylation at the gene level remains a challenge. A recent study found that the DNA methylation difference of the gene body and promoter region has a strong correlation with gene expression. In this study, we proposed a Statistical difference of DNA Methylation between Promoter and Other Body Region (SIMPO) algorithm to extract DNA methylation values at the gene level. First, by choosing to smoke as an environmental exposure factor, our method led to significant improvements in gene overlaps (from 5 to 17%) between different datasets. In addition, the biological significance of phenotype-related genes identified by SIMPO algorithm is comparable to that of the traditional probe-based methods. Then, we selected two disease contents (e.g., insulin resistance and Parkinson's disease) to show that the biological efficiency of disease-related gene identification increased from 15.43 to 44.44% (p-value = 1.20e-28). In summary, our results declare that mining the selective remodeling of DNA methylation in promoter regions can identify robust gene-level associations with phenotype, and the characteristic remodeling of a given gene's promoter region can reflect the essence of disease.
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Affiliation(s)
- Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
| | - Fengji Liang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Si-Min Deng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yuexing Zhu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- Aromability Inc., Beijing, China
| | - Ying Chen
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
| | - Jianghui Xiong
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- Aromability Inc., Beijing, China
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, Jiangsu, China
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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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Pelzman DL, Hwang K. Genetic testing for men with infertility: techniques and indications. Transl Androl Urol 2021; 10:1354-1364. [PMID: 33850771 PMCID: PMC8039607 DOI: 10.21037/tau-19-725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetic testing is an integral component in the workup of male infertility as genetic conditions may be responsible for up to 15% of all cases. Currently, three genetic tests are commonly performed and recommended by major urologic associations: karyotype analysis (KA), Y-chromosome microdeletion testing, and CFTR mutation testing. Despite widespread adoption of these tests, an etiology for infertility remains elusive in up to 80% of cases. Recent work has identified intriguing new targets for genetic testing which may soon see clinical relevance. This review will discuss the indications and techniques for currently offered genetic tests and briefly explore ongoing research directions within this field.
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Affiliation(s)
- Daniel L Pelzman
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kathleen Hwang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Kasman AM, Zhang CA, Li S, Lu Y, Lathi RB, Stevenson DK, Shaw GM, Eisenberg ML. Association between preconception paternal health and pregnancy loss in the USA: an analysis of US claims data. Hum Reprod 2021; 36:785-793. [PMID: 33336240 PMCID: PMC8679308 DOI: 10.1093/humrep/deaa332] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/24/2020] [Indexed: 09/16/2023] Open
Abstract
STUDY QUESTION Is preconception paternal health associated with pregnancy loss? SUMMARY ANSWER Poor preconception paternal health is associated with a higher risk of pregnancy loss as confirmed in sensitivity analyses accounting for maternal age and health. WHAT IS KNOWN ALREADY Preconception paternal health can negatively impact perinatal outcomes. STUDY DESIGN, SIZE, DURATION Retrospective cohort study of US insurance claims database from 2009 to 2016 covering 958 804 pregnancies. PARTICIPANTS/MATERIALS, SETTING, METHODS US insurance claims database including women, men and pregnancies within the USA between 2007 and 2016. Paternal preconception health status (e.g. metabolic syndrome diagnoses (MetS), Charlson comorbidity index (CCI) and individual chronic disease diagnoses) was examined in relation to pregnancy loss (e.g. ectopic pregnancy, miscarriage and stillbirth). MAIN RESULTS AND THE ROLE OF CHANCE In all, 958 804 pregnancies were analyzed. The average paternal age was 35.3 years (SD 5.3) and maternal age was 33.1 years (SD 4.4). Twenty-two percent of all pregnancies ended in a loss. After adjusting for maternal factors, the risk of pregnancy loss increased with increasing paternal comorbidity. For example, compared to men with no components of MetS, the risk of pregnancy loss increased for men with one (relative risk (RR) 1.10, 95% CI 1.09-1.12), two (RR 1.15, 95% CI 1.13-1.17) or three or more (RR 1.19, 95% CI 1.14-1.24) components. Specifically, less healthy men had a higher risk of siring a pregnancy ending in spontaneous abortion, stillbirth and ectopic pregnancies. Similar patterns remained with other measures of paternal health (e.g. CCI, chronic diseases, etc.). When stratifying by maternal age as well as maternal health, a similar pattern of increasing pregnancy loss risk for men with 1, 2 or 3+ MetS was observed. A statistically significant but weak association between timing of pregnancy loss and paternal health was found. LIMITATIONS, REASONS FOR CAUTION Retrospective study design covering only employer insured individuals may limit generalizability. WIDER IMPLICATIONS OF THE FINDINGS Optimization of a father's health may improve pregnancy outcomes. STUDY FUNDING/COMPETING INTERESTS National Institutes of Health National Center for Advancing Translational Science Clinical and Translational Science Award (UL1 TR001085). M.L.E. is an advisor for Sandstone Diagnostics, Dadi, Hannah and Underdog. No other competing interests were declared. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Alex M Kasman
- Department of Urology, Stanford University School of
Medicine, Stanford, CA 94305-5118, USA
| | - Chiyuan A Zhang
- Department of Urology, Stanford University School of
Medicine, Stanford, CA 94305-5118, USA
| | - Shufeng Li
- Department of Urology, Stanford University School of
Medicine, Stanford, CA 94305-5118, USA
| | - Ying Lu
- Department of Biomedical Data Science, Stanford
University School of Medicine, Stanford, CA 94305-5118, USA
| | - Ruth B Lathi
- Department of Pediatrics, Stanford University School
of Medicine, Stanford, CA 94305-5118, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School
of Medicine, Stanford, CA 94305-5118, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School
of Medicine, Stanford, CA 94305-5118, USA
| | - Michael L Eisenberg
- Department of Urology, Stanford University School of
Medicine, Stanford, CA 94305-5118, USA
- Department of Obstetrics and Gynecology, Stanford
University School of Medicine, Stanford, CA 94305-5118, USA
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Genome-wide DNA methylation differences in nucleus accumbens of smokers vs. nonsmokers. Neuropsychopharmacology 2021; 46:554-560. [PMID: 32731254 PMCID: PMC8027202 DOI: 10.1038/s41386-020-0782-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022]
Abstract
Numerous DNA methylation (DNAm) biomarkers of cigarette smoking have been identified in peripheral blood studies, but because of tissue specificity, blood-based studies may not detect brain-specific smoking-related DNAm differences that may provide greater insight as neurobiological indicators of smoking and its exposure effects. We report the first epigenome-wide association study (EWAS) of smoking in human postmortem brain, focusing on nucleus accumbens (NAc) as a key brain region in developing and reinforcing addiction. Illumina HumanMethylation EPIC array data from 221 decedents (120 European American [23% current smokers], 101 African American [26% current smokers]) were analyzed. DNAm by smoking (current vs. nonsmoking) was tested within each ancestry group using robust linear regression models adjusted for age, sex, cell-type proportion, DNAm-derived negative control principal components (PCs), and genotype-derived PCs. The resulting ancestry-specific results were combined via meta-analysis. We extended our NAc findings, using published smoking EWAS results in blood, to identify DNAm smoking effects that are unique (tissue-specific) vs. shared between tissues (tissue-shared). We identified seven CpGs (false discovery rate < 0.05), of which three CpGs are located near genes previously indicated with blood-based smoking DNAm biomarkers: ZIC1, ZCCHC24, and PRKDC. The other four CpGs are novel for smoking-related DNAm changes: ABLIM3, APCDD1L, MTMR6, and CTCF. None of the seven smoking-related CpGs in NAc are driven by genetic variants that share association signals with predisposing genetic risk variants for smoking, suggesting that the DNAm changes reflect consequences of smoking. Our results provide the first evidence for smoking-related DNAm changes in human NAc, highlighting CpGs that were undetected as peripheral biomarkers and may reflect brain-specific responses to smoking exposure.
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Saintilnord WN, Tenlep SYN, Preston JD, Duregon E, DeRouchey JE, Unrine JM, de Cabo R, Pearson KJ, Fondufe-Mittendorf YN. Chronic Exposure to Cadmium Induces Differential Methylation in Mice Spermatozoa. Toxicol Sci 2021; 180:262-276. [PMID: 33483743 PMCID: PMC8041459 DOI: 10.1093/toxsci/kfab002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cadmium exposure is ubiquitous and has been linked to diseases including cancers and reproductive defects. Since cadmium is nonmutagenic, it is thought to exert its gene dysregulatory effects through epigenetic reprogramming. Several studies have implicated germline exposure to cadmium in developmental reprogramming. However, most of these studies have focused on maternal exposure, while the impact on sperm fertility and disease susceptibility has received less attention. In this study, we used reduced representation bisulfite sequencing to comprehensively investigate the impact of chronic cadmium exposure on mouse spermatozoa DNA methylation. Adult male C57BL/J6 mice were provided water with or without cadmium chloride for 9 weeks. Sperm, testes, liver, and kidney tissues were collected at the end of the treatment period. Cadmium exposure was confirmed through gene expression analysis of metallothionein-1 and 2, 2 well-known cadmium-induced genes. Analysis of sperm DNA methylation changes revealed 1788 differentially methylated sites present at regulatory regions in sperm of mice exposed to cadmium compared with vehicle (control) mice. Furthermore, most of these differential methylation changes positively correlated with changes in gene expression at both the transcription initiation stage as well as the splicing levels. Interestingly, the genes targeted by cadmium exposure are involved in several critical developmental processes. Our results present a comprehensive analysis of the sperm methylome in response to chronic cadmium exposure. These data, therefore, highlight a foundational framework to study gene expression patterns that may affect fertility in the exposed individual as well as their offspring, through paternal inheritance.
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Affiliation(s)
- Wesley N Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Sara Y N Tenlep
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Joshua D Preston
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA,Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Eleonora Duregon
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 20892, USA
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 20892, USA
| | - Kevin J Pearson
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA,To whom correspondence should be addressed at Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536-0509, USA. E-mail: ; Department of Molecular and Cellular Biochemistry, University of Kentucky, 800 Rose Street, 273 BBSRB, Lexington, KY 40536-0509, USA. E-mail:
| | - Yvonne N Fondufe-Mittendorf
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0509, USA,To whom correspondence should be addressed at Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536-0509, USA. E-mail: ; Department of Molecular and Cellular Biochemistry, University of Kentucky, 800 Rose Street, 273 BBSRB, Lexington, KY 40536-0509, USA. E-mail:
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Chronopoulou E, Seifalian A, Stephenson J, Serhal P, Saab W, Seshadri S. Preconceptual care for couples seeking fertility treatment, an evidence-based approach. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.xfnr.2020.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Wang L, Chen M, Yan G, Zhao S. DNA Methylation Differences Between Zona Pellucida-Bound and Manually Selected Spermatozoa Are Associated With Autism Susceptibility. Front Endocrinol (Lausanne) 2021; 12:774260. [PMID: 34858344 PMCID: PMC8630694 DOI: 10.3389/fendo.2021.774260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/25/2021] [Indexed: 01/20/2023] Open
Abstract
Children conceived through intracytoplasmic sperm injection (ICSI) have been reported to have a higher risk of many abnormalities and disorders, including autism and intellectual disability, which may be due to bypassing of the natural sperm selection process during ICSI. Zona pellucida (ZP)-bound spermatozoa (ZPBS) have normal morphology and nuclear DNA. Using these spermatozoa for ICSI results in better outcomes compared with conventional ICSI. However, differences besides morphology that exist between sperm selected by ZP and by an embryologist and whether these differences affect the risk of autism in offspring after ICSI are unclear. To explore these questions, we compared genome-wide DNA methylation profiles between ZPBS and manually selected spermatozoa (MSS)using single-cell bisulfite sequencing. Global DNA methylation levels were significantly lower in ZPBS than in MSS. Using gene ontology (GO) analysis, genes overlapping differentially methylated regions (DMRs) were enriched in biological processes involving neurogenesis. Furthermore, we found that 47.8% of autism candidate genes were associated with DMRs, compared with 37.1% of matched background genes (P<0.001). This was mainly because of the high proportion of autism candidate genes with bivalent chromatin structure. In conclusion, bivalent chromatin structure results in large differences in the methylation of autism genes between MSS and ZPBS. ICSI using MSS, which increases the risk of methylation mutations compared with ZPBS, may lead to a higher risk of autism in offspring.
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Affiliation(s)
- Longda Wang
- Department of Reproduction and Genetics, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Mengxiang Chen
- Department of Reproduction and Genetics, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Gaofeng Yan
- Department of Reproduction and Genetics, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shuhua Zhao
- Department of Reproduction and Genetics, First Affiliated Hospital of Kunming Medical University, Kunming, China
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