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Li L, Chen R, Zhang H, Li J, Huang H, Weng J, Tan H, Guo T, Wang M, Xie J. The epigenetic modification of DNA methylation in neurological diseases. Front Immunol 2024; 15:1401962. [PMID: 39376563 PMCID: PMC11456496 DOI: 10.3389/fimmu.2024.1401962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 09/03/2024] [Indexed: 10/09/2024] Open
Abstract
Methylation, a key epigenetic modification, is essential for regulating gene expression and protein function without altering the DNA sequence, contributing to various biological processes, including gene transcription, embryonic development, and cellular functions. Methylation encompasses DNA methylation, RNA methylation and histone modification. Recent research indicates that DNA methylation is vital for establishing and maintaining normal brain functions by modulating the high-order structure of DNA. Alterations in the patterns of DNA methylation can exert significant impacts on both gene expression and cellular function, playing a role in the development of numerous diseases, such as neurological disorders, cardiovascular diseases as well as cancer. Our current understanding of the etiology of neurological diseases emphasizes a multifaceted process that includes neurodegenerative, neuroinflammatory, and neurovascular events. Epigenetic modifications, especially DNA methylation, are fundamental in the control of gene expression and are critical in the onset and progression of neurological disorders. Furthermore, we comprehensively overview the role and mechanism of DNA methylation in in various biological processes and gene regulation in neurological diseases. Understanding the mechanisms and dynamics of DNA methylation in neural development can provide valuable insights into human biology and potentially lead to novel therapies for various neurological diseases.
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Affiliation(s)
- Linke Li
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Rui Chen
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, China
- Department of Stomatology, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Hui Zhang
- Department of Stomatology, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Jinsheng Li
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Hao Huang
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Jie Weng
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Huan Tan
- College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Tailin Guo
- College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Mengyuan Wang
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, China
- Department of Stomatology, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Jiang Xie
- Key Laboratory of Drug Targeting and Drug Delivery of Ministry of Education (MOE), Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, West China School of Pharmacy, Sichuan University, Chengdu, China
- Department of Pediatrics, Chengdu Third People’s Hospital, Chengdu, China
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Jiang Y, Pan Y, Long T, Qi J, Liu J, Zhang M. Significance of RNA N6-methyladenosine regulators in the diagnosis and subtype classification of coronary heart disease using the Gene Expression Omnibus database. Front Cardiovasc Med 2023; 10:1185873. [PMID: 37928762 PMCID: PMC10621741 DOI: 10.3389/fcvm.2023.1185873] [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: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 11/07/2023] Open
Abstract
Background Many investigations have revealed that alterations in m6A modification levels may be linked to coronary heart disease (CHD). However, the specific link between m6A alteration and CHD warrants further investigation. Methods Gene expression profiles from the Gene Expression Omnibus (GEO) databases. We began by constructing a Random Forest model followed by a Nomogram model, both aimed at enhancing our predictive capabilities on specific m6A markers. We then shifted our focus to identify distinct molecular subtypes based on the key m6A regulators and to discern differentially expressed genes between the unique m6A clusters. Following this molecular exploration, we embarked on an in-depth analysis of the biological characteristics associated with each m6A cluster, revealing profound differences between them. Finally, we delved into the identification and correlation analysis of immune cell infiltration across these clusters, emphasizing the potential interplay between m6A modification and the immune system. Results In this research, 37 important m6Aregulators were identified by comparing non-CHD and CHD patients from the GSE20680, GSE20681, and GSE71226 datasets. To predict the risk of CHD, seven candidate m6A regulators (CBLL1, HNRNPC, YTHDC2, YTHDF1, YTHDF2, YTHDF3, ZC3H13) were screened using the logistic regression model. Based on the seven possible m6A regulators, a nomogram model was constructed. An examination of decision curves revealed that CHD patients could benefit from the nomogram model. On the basis of the selected relevant m6A regulators, patients with CHD were separated into two m6A clusters (cluster1 and cluster2) using the consensus clustering approach. The Single Sample Gene Set Enrichment Analysis (ssGSEA) and CIBERSORT methods were used to estimate the immunological characteristics of two separate m6A Gene Clusters; the results indicated a close association between seven candidate genes and immune cell composition. The drug sensitivity of seven candidate regulators was predicted, and these seven regulators appeared in numerous diseases as pharmacological targets while displaying strong drug sensitivity. Conclusion m6A regulators play crucial roles in the development of CHD. Our research of m6A clusters may facilitate the development of novel molecular therapies and inform future immunotherapeutic methods for CHD.
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Affiliation(s)
- Yu Jiang
- Department of Cardiovascular Surgery, Yan'an Hospital affiliated to Kunming Medical University, Yunnan, China
| | - Yaqiang Pan
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Tao Long
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Junqing Qi
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Jianchao Liu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Mengya Zhang
- Department of Cardiology, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School of Nanjing Medical University, Suzhou, China
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Yadav NS, Titov V, Ayemere I, Byeon B, Ilnytskyy Y, Kovalchuk I. Multigenerational Exposure to Heat Stress Induces Phenotypic Resilience, and Genetic and Epigenetic Variations in Arabidopsis thaliana Offspring. FRONTIERS IN PLANT SCIENCE 2022; 13:728167. [PMID: 35419019 PMCID: PMC8996174 DOI: 10.3389/fpls.2022.728167] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Plants are sedentary organisms that constantly sense changes in their environment and react to various environmental cues. On a short-time scale, plants respond through alterations in their physiology, and on a long-time scale, plants alter their development and pass on the memory of stress to the progeny. The latter is controlled genetically and epigenetically and allows the progeny to be primed for future stress encounters, thus increasing the likelihood of survival. The current study intended to explore the effects of multigenerational heat stress in Arabidopsis thaliana. Twenty-five generations of Arabidopsis thaliana were propagated in the presence of heat stress. The multigenerational stressed lineage F25H exhibited a higher tolerance to heat stress and elevated frequency of homologous recombination, as compared to the parallel control progeny F25C. A comparison of genomic sequences revealed that the F25H lineage had a three-fold higher number of mutations [single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs)] as compared control lineages, suggesting that heat stress induced genetic variations in the heat-stressed progeny. The F25H stressed progeny showed a 7-fold higher number of non-synonymous mutations than the F25C line. Methylome analysis revealed that the F25H stressed progeny showed a lower global methylation level in the CHH context than the control progeny. The F25H and F25C lineages were different from the parental control lineage F2C by 66,491 and 80,464 differentially methylated positions (DMPs), respectively. F25H stressed progeny displayed higher frequency of methylation changes in the gene body and lower in the body of transposable elements (TEs). Gene Ontology analysis revealed that CG-DMRs were enriched in processes such as response to abiotic and biotic stimulus, cell organizations and biogenesis, and DNA or RNA metabolism. Hierarchical clustering of these epimutations separated the heat stressed and control parental progenies into distinct groups which revealed the non-random nature of epimutations. We observed an overall higher number of epigenetic variations than genetic variations in all comparison groups, indicating that epigenetic variations are more prevalent than genetic variations. The largest difference in epigenetic and genetic variations was observed between control plants comparison (F25C vs. F2C), which clearly indicated that the spontaneous nature of epigenetic variations and heat-inducible nature of genetic variations. Overall, our study showed that progenies derived from multigenerational heat stress displayed a notable adaption in context of phenotypic, genotypic and epigenotypic resilience.
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Ben Maamar M, Beck D, Nilsson E, McCarrey JR, Skinner MK. Developmental alterations in DNA methylation during gametogenesis from primordial germ cells to sperm. iScience 2022; 25:103786. [PMID: 35146397 PMCID: PMC8819394 DOI: 10.1016/j.isci.2022.103786] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 02/08/2023] Open
Abstract
Because epigenetics is a critical component for gene expression, the hypothesis was tested that DNA methylation alterations are dynamic and continually change throughout gametogenesis to generate the mature sperm. Developmental alterations and stage-specific DNA methylation during gametogenesis from primordial germ cells (PGCs) to mature sperm are investigated. Individual developmental stage germ cells were isolated and analyzed for differential DNA methylation regions (DMRs). The number of DMRs was highest in the first three comparisons with mature PGCs, prospermatogonia, and spermatogonia. The most statistically significant DMRs were present at all stages of development and had variations involving both increases or decreases in DNA methylation. DMR-associated genes were identified and correlated with gene functional categories, pathways, and cellular processes. Observations identified a dynamic cascade of epigenetic changes during development that is dramatic during the early developmental stages. Complex epigenetic alterations are required to regulate genome biology and gene expression during gametogenesis. A dynamic cascade of epigenetic change throughout gametogenesis from PGC to sperm Most dramatic epigenetic alterations in PGC and spermatogenic stem cell stages Different DNA methylation regions between and within stages were identified Complex epigenetic alterations required for gene expression during gametogenesis
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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Nilsson EE, Ben Maamar M, Skinner MK. Role of epigenetic transgenerational inheritance in generational toxicology. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac001. [PMID: 35186326 PMCID: PMC8848501 DOI: 10.1093/eep/dvac001] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/04/2021] [Accepted: 02/03/2022] [Indexed: 05/27/2023]
Abstract
Many environmental toxicants have been shown to be associated with the transgenerational inheritance of increased disease susceptibility. This review describes the generational toxicity of some of these chemicals and their role in the induction of epigenetic transgenerational inheritance of disease. Epigenetic factors include DNA methylation, histone modifications, retention of histones in sperm, changes to chromatin structure, and expression of non-coding RNAs. For toxicant-induced epigenetic transgenerational inheritance to occur, exposure to a toxicant must result in epigenetic changes to germ cells (sperm or eggs) since it is the germ cells that carry molecular information to subsequent generations. In addition, the epigenetic changes induced in transgenerational generation animals must cause alterations in gene expression in these animals' somatic cells. In some cases of generational toxicology, negligible changes are seen in the directly exposed generations, but increased disease rates are seen in transgenerational descendants. Governmental policies regulating toxicant exposure should take generational effects into account. A new approach that takes into consideration generational toxicity will be needed to protect our future populations.
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Affiliation(s)
- Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K Skinner
- **Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +509-335-1524; E-mail:
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Garrido N, Cruz F, Egea RR, Simon C, Sadler-Riggleman I, Beck D, Nilsson E, Ben Maamar M, Skinner MK. Sperm DNA methylation epimutation biomarker for paternal offspring autism susceptibility. Clin Epigenetics 2021; 13:6. [PMID: 33413568 PMCID: PMC7789568 DOI: 10.1186/s13148-020-00995-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/17/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) has increased over tenfold over the past several decades and appears predominantly associated with paternal transmission. Although genetics is anticipated to be a component of ASD etiology, environmental epigenetics is now also thought to be an important factor. Epigenetic alterations, such as DNA methylation, have been correlated with ASD. The current study was designed to identify a DNA methylation signature in sperm as a potential biomarker to identify paternal offspring autism susceptibility. METHODS AND RESULTS Sperm samples were obtained from fathers that have children with or without autism, and the sperm then assessed for alterations in DNA methylation. A genome-wide analysis (> 90%) for differential DNA methylation regions (DMRs) was used to identify DMRs in the sperm of fathers (n = 13) with autistic children in comparison with those (n = 13) without ASD children. The 805 DMR genomic features such as chromosomal location, CpG density and length of the DMRs were characterized. Genes associated with the DMRs were identified and found to be linked to previously known ASD genes, as well as other neurobiology-related genes. The potential sperm DMR biomarkers/diagnostic was validated with blinded test sets (n = 8-10) of individuals with an approximately 90% accuracy. CONCLUSIONS Observations demonstrate a highly significant set of 805 DMRs in sperm that can potentially act as a biomarker for paternal offspring autism susceptibility. Ancestral or early-life paternal exposures that alter germline epigenetics are anticipated to be a molecular component of ASD etiology.
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Affiliation(s)
- Nicolás Garrido
- IVI-RMA València, and IVI Foundation, Health Research Institute La Fe, València, Spain
| | - Fabio Cruz
- IVI-RMA València, and IVI Foundation, Health Research Institute La Fe, València, Spain
| | - Rocio Rivera Egea
- IVI-RMA València, and IVI Foundation, Health Research Institute La Fe, València, Spain
| | - Carlos Simon
- Dept Ob/Gyn, València University/Instituto de Investigacion Clinica, Hospital Clinico de Valencia (INCLIVA), and Igenomix Foundation, València, Spain
- Beth Israel Deaconess Medical Center, Harvard University, Boston, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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Nilsson E, Sadler-Riggleman I, Beck D, Skinner MK. Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab002. [PMID: 34040807 PMCID: PMC8132314 DOI: 10.1093/eep/dvab002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/09/2021] [Accepted: 03/01/2021] [Indexed: 05/06/2023]
Abstract
Environmental factors such as nutrition, stress, and toxicants can influence epigenetic programming and phenotypes of a wide variety of species from plants to humans. The current study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) vs the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth (2 years) and fast growth (1 year) hatchery trout were investigated. The sperm and red blood cells (RBC) from adult male slow growth/maturation hatchery steelhead, fast growth/maturation hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs) and genetic mutations, involving copy number variations (CNVs). The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery vs wild steelhead trout populations. The DMRs were cell type specific with negligible overlap. Slow growth/maturation compared to fast growth/maturation steelhead also had a larger number of DMRs in the RBC samples. A number of the DMRs had associated genes that were correlated to various biological processes and pathologies. Observations demonstrate a major epigenetic programming difference between the hatchery and wild natural-origin fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth/maturation rate can alter the epigenetic developmental programming of the steelhead trout. Interestingly, epigenetic alterations in the sperm allow for potential epigenetic transgenerational inheritance of phenotypic variation to future generations. The impacts of hatchery exposures are not only important to consider on the fish exposed, but also on future generations and evolutionary trajectory of fish in the river populations.
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Affiliation(s)
- Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
- Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1-509-335-1524; E-mail:
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Lehle JD, McCarrey JR. Differential susceptibility to endocrine disruptor-induced epimutagenesis. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa016. [PMID: 33324495 PMCID: PMC7722801 DOI: 10.1093/eep/dvaa016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 05/08/2023]
Abstract
There is now considerable evidence indicating the potential for endocrine disrupting chemicals to alter the epigenome and for subsets of these epigenomic changes or "epimutations" to be heritably transmitted to offspring in subsequent generations. While there have been many studies indicating how exposure to endocrine disrupting chemicals can disrupt various organs associated with the body's endocrine systems, there is relatively limited information regarding the relative susceptibility of different specific organs, tissues, or cell types to endocrine disrupting chemical-induced epimutagenesis. Here we review available information about different organs, tissues, cell types, and/or cell lines which have been shown to be susceptible to specific endocrine disrupting chemical-induced epimutations. In addition, we discuss possible mechanisms that may be involved, or impacted by this tissue- or cell type-specific, differential susceptibility to different endocrine disrupting chemicals. Finally, we summarize available information indicating that certain periods of development display elevated susceptibility to endocrine disrupting chemical exposure and we describe how this may affect the extent to which germline epimutations can be transmitted inter- or transgenerationally. We conclude that cell type-specific differential susceptibility to endocrine disrupting chemical-induced epimutagenesis is likely to directly impact the extent to, or manner in, which endocrine disrupting chemical exposure initially induces epigenetic changes to DNA methylation and/or histone modifications, and how these endocrine disrupting chemical-induced epimutations can then subsequently impact gene expression, potentially leading to the development of heritable disease states.
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Affiliation(s)
- Jake D Lehle
- Department of Biology, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
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Gagliardi A, Dugué PA, Nøst TH, Southey MC, Buchanan DD, Schmidt DF, Makalic E, Hodge AM, English DR, Doo NW, Hopper JL, Severi G, Baglietto L, Naccarati A, Tarallo S, Pace L, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Lund E, Giles GG, Pardini B, Sandanger TM, Milne RL, Vineis P, Polidoro S, Fiorito G. Stochastic Epigenetic Mutations Are Associated with Risk of Breast Cancer, Lung Cancer, and Mature B-cell Neoplasms. Cancer Epidemiol Biomarkers Prev 2020; 29:2026-2037. [PMID: 32788174 DOI: 10.1158/1055-9965.epi-20-0451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Age-related epigenetic dysregulations are associated with several diseases, including cancer. The number of stochastic epigenetic mutations (SEM) has been suggested as a biomarker of life-course accumulation of exposure-related DNA damage; however, the predictive role of SEMs in cancer has seldom been investigated. METHODS A SEM, at a given CpG site, was defined as an extreme outlier of DNA methylation value distribution across individuals. We investigated the association of the total number of SEMs with the risk of eight cancers in 4,497 case-control pairs nested in three prospective cohorts. Furthermore, we investigated whether SEMs were randomly distributed across the genome or enriched in functional genomic regions. RESULTS In the three-study meta-analysis, the estimated ORs per one-unit increase in log(SEM) from logistic regression models adjusted for age and cancer risk factors were 1.25; 95% confidence interval (CI), 1.11-1.41 for breast cancer, and 1.23; 95% CI, 1.07-1.42 for lung cancer. In the Melbourne Collaborative Cohort Study, the OR for mature B-cell neoplasm was 1.46; 95% CI, 1.25-1.71. Enrichment analyses indicated that SEMs frequently occur in silenced genomic regions and in transcription factor binding sites regulated by EZH2 and SUZ12 (P < 0.0001 and P = 0.0005, respectively): two components of the polycomb repressive complex 2 (PCR2). Finally, we showed that PCR2-specific SEMs are generally more stable over time compared with SEMs occurring in the whole genome. CONCLUSIONS The number of SEMs is associated with a higher risk of different cancers in prediagnostic blood samples. IMPACT We identified a candidate biomarker for cancer early detection, and we described a carcinogenesis mechanism involving PCR2 complex proteins worthy of further investigations.
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Affiliation(s)
- Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy.
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Therese H Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Department of Clinical Pathology | Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research Level 10, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicole W Doo
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Concord Repatriation General Hospital, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Concord Clinical School, University of Sydney, Concord, New South Wales, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
| | - Laura Baglietto
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Luigia Pace
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Vittorio Krogh
- Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - Domenico Palli
- Institute for Cancer Research, Prevention and Clinical Network - ISPRO, Villa delle Rose, Via Cosimo il Vecchio, Florence, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Corso Umberto I, Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Department of Cancer Registry and Histopathology, Provincial Health Authority (ASP 7) Ragusa, Piazza Igea, Ragusa, Italy
| | - Eiliv Lund
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- The Cancer Registry of Norway, Oslo, Norway
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Torkjel M Sandanger
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Paolo Vineis
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Giovanni Fiorito
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Department of Biomedical Sciences, Laboratory of Biostatistics, University of Sassari, Sassari, Italy
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10
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Fiorito G, McCrory C, Robinson O, Carmeli C, Ochoa-Rosales C, Zhang Y, Colicino E, Dugué PA, Artaud F, McKay GJ, Jeong A, Mishra PP, Nøst TH, Krogh V, Panico S, Sacerdote C, Tumino R, Palli D, Matullo G, Guarrera S, Gandini M, Bochud M, Dermitzakis E, Muka T, Schwartz J, Vokonas PS, Just A, Hodge AM, Giles GG, Southey MC, Hurme MA, Young I, McKnight AJ, Kunze S, Waldenberger M, Peters A, Schwettmann L, Lund E, Baccarelli A, Milne RL, Kenny RA, Elbaz A, Brenner H, Kee F, Voortman T, Probst-Hensch N, Lehtimäki T, Elliot P, Stringhini S, Vineis P, Polidoro S. Socioeconomic position, lifestyle habits and biomarkers of epigenetic aging: a multi-cohort analysis. Aging (Albany NY) 2020; 11:2045-2070. [PMID: 31009935 PMCID: PMC6503871 DOI: 10.18632/aging.101900] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/31/2019] [Indexed: 12/12/2022]
Abstract
Differences in health status by socioeconomic position (SEP) tend to be more evident at older ages, suggesting the involvement of a biological mechanism responsive to the accumulation of deleterious exposures across the lifespan. DNA methylation (DNAm) has been proposed as a biomarker of biological aging that conserves memory of endogenous and exogenous stress during life. We examined the association of education level, as an indicator of SEP, and lifestyle-related variables with four biomarkers of age-dependent DNAm dysregulation: the total number of stochastic epigenetic mutations (SEMs) and three epigenetic clocks (Horvath, Hannum and Levine), in 18 cohorts spanning 12 countries. The four biological aging biomarkers were associated with education and different sets of risk factors independently, and the magnitude of the effects differed depending on the biomarker and the predictor. On average, the effect of low education on epigenetic aging was comparable with those of other lifestyle-related risk factors (obesity, alcohol intake), with the exception of smoking, which had a significantly stronger effect. Our study shows that low education is an independent predictor of accelerated biological (epigenetic) aging and that epigenetic clocks appear to be good candidates for disentangling the biological pathways underlying social inequalities in healthy aging and longevity.
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Affiliation(s)
- Giovanni Fiorito
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy.,Equal contribution
| | - Cathal McCrory
- The Irish Longitudinal Study on Ageing, Trinity College Dublin, Dublin, Ireland.,Equal contribution
| | - Oliver Robinson
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.,Equal contribution
| | - Cristian Carmeli
- Institute of Social and Preventive Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland.,Equal contribution
| | - Carolina Ochoa-Rosales
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Centro de Vida Saludable de la Universidad de Concepción, Concepción, Chile.,Equal contribution
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Equal contribution
| | - Elena Colicino
- Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA.,Equal contribution
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Victoria, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Equal contribution
| | - Fanny Artaud
- CESP, Faculté de Médecine - Université Paris-Sud, Faculté de Médecine, UVSQ, Institut National de la Santé et de la Recherche Médicale, -, Université Paris, Saclay, France.,Equal contribution
| | - Gareth J McKay
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland.,Equal contribution
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Equal contribution
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland.,Equal contribution
| | - Therese H Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.,NILU Norwegian Institute for Air Research, The Fram Centre, Tromsø, Norway.,Equal contribution
| | - Vittorio Krogh
- Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Department, 'Civic - M. P. Arezzo' Hospital, ASP Ragusa, Ragusa, Italy
| | - Domenico Palli
- Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO Toscana), Florence, Italy
| | - Giuseppe Matullo
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Martina Gandini
- Environmental Epidemiological Unit, Regional Environmental Protection Agency, Piedmont Region, Torino, Italy
| | - Murielle Bochud
- Institute of Social and Preventive Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Emmanouil Dermitzakis
- Institute of Social and Preventive Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Taulant Muka
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Joel Schwartz
- Department of Environmental Health and Department of Epidemiology, Harvard T.H. School of Public Health, Boston, MA 02115, USA
| | - Pantel S Vokonas
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02115, USA
| | - Allan Just
- Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Victoria, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Australia
| | - Mikko A Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Ian Young
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Munich, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Munich, Germany.,Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lars Schwettmann
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, D-85764, Germany.,Department of Economics, Martin Luther University Halle-Wittenberg, Halle, Germany.,Equal senior researcher
| | - Eiliv Lund
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.,Equal senior researcher
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA.,Equal senior researcher
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Victoria, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Equal senior researcher
| | - Rose A Kenny
- The Irish Longitudinal Study on Ageing, Trinity College Dublin, Dublin, Ireland.,Equal senior researcher
| | - Alexis Elbaz
- CESP, Faculté de Médecine - Université Paris-Sud, Faculté de Médecine, UVSQ, Institut National de la Santé et de la Recherche Médicale, -, Université Paris, Saclay, France.,Equal senior researcher
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Network Aging Research, University of Heidelberg, Heidelberg, Germany.,Equal senior researcher
| | - Frank Kee
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland.,Equal senior researcher
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Equal senior researcher
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Equal senior researcher
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland.,Equal senior researcher
| | - Paul Elliot
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.,Equal senior researcher
| | - Silvia Stringhini
- Institute of Social and Preventive Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland.,Unit of Population Epidemiology, Primary Care Division, Geneva University Hospitals, Geneva, Switzerland.,Equal senior researcher
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.,Equal senior researcher
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy.,Equal senior researcher
| | | | -
- See ACKNOWLEDGMENTS AND FUNDING
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11
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Cheung AC, Walker DI, Juran BD, Miller GW, Lazaridis KN. Studying the Exposome to Understand the Environmental Determinants of Complex Liver Diseases. Hepatology 2020; 71:352-362. [PMID: 31701542 PMCID: PMC7329010 DOI: 10.1002/hep.31028] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Angela C. Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Douglas I. Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Brian D. Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Gary W. Miller
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY
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12
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Abstract
Ewing sarcoma is a rare tumor developed in bone and soft tissues of children and teenagers. This entity is biologically led by a chromosomal translocation, typically including EWS and FLI1 genes. Little is known about Ewing sarcoma predisposition, although the role of environmental factors, ethnicity and certain polymorphisms on Ewing sarcoma susceptibility has been studied during the last few years. Its prevalence among cancer predisposition syndromes has also been thoroughly examined. This review summarizes the available evidence on predisposing factors involved in Ewing sarcoma susceptibility. On the basis of these data, an integrated approach of the most influential factors on Ewing sarcoma predisposition is proposed.
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13
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Cleary JA, Tillitt DE, Vom Saal FS, Nicks DK, Claunch RA, Bhandari RK. Atrazine induced transgenerational reproductive effects in medaka (Oryzias latipes). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 251:639-650. [PMID: 31108297 DOI: 10.1016/j.envpol.2019.05.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/23/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
Atrazine is presently one of the most abundantly used herbicides in the United States, and a common contaminant of natural water bodies and drinking waters in high-use areas. Dysregulation of reproductive processes has been demonstrated in atrazine exposed fish, including alteration of key endocrine pathways on hypothalamic-pituitary-gonadal (HPG) axis. However, the potential for atrazine-induced transgenerational inheritance of reproductive effects in fish has not been investigated. The present study examined the effects of early developmental atrazine exposure on transgenerational reproductive dysregulation in Japanese medaka (Oryzias latipes). F0 medaka were exposed to atrazine (ATZ, 5 or 50 μg/L), 17α-ethinylestradiol (EE2, 0.002 or 0.05 μg/L), or solvent control during the first twelve days of development with no subsequent exposure over three generations. This exposure overlapped with the critical developmental window for embryonic germ cell development, gonadogenesis, and sex determination. Exposed males and females of the F0 generation were bred to produce an F1 generation, and this was continued until the F2 generation. Sperm count and motility were not affected in F0 males; however, both parameters were significantly reduced in the males from F2 Low EE2 (0.002 μg/L), Low ATZ (5 μg/L), and High ATZ (50 μg/L) lineages. Fecundity was unaffected by atrazine or EE2 in F0 through F2 generations; however, fertilization rate was decreased in low atrazine and EE2 exposure lineages in the F2 generation. There were significant transgenerational differences in expression of the genes involved in steroidogenesis and DNA methylation. These results suggest that although early life exposure to atrazine did not cause significant phenotypes in the directly exposed F0 generation, subsequent generations of fish were at greater risk of reproductive dysfunction.
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Affiliation(s)
- Jacob A Cleary
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA
| | - Donald E Tillitt
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO 65201, USA
| | - Frederick S Vom Saal
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Diane K Nicks
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO 65201, USA
| | - Rachel A Claunch
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO 65201, USA
| | - Ramji K Bhandari
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA.
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14
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Lee MK, Blumberg B. Transgenerational effects of obesogens. Basic Clin Pharmacol Toxicol 2019; 125 Suppl 3:44-57. [PMID: 30801972 PMCID: PMC6708505 DOI: 10.1111/bcpt.13214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/08/2019] [Indexed: 02/06/2023]
Abstract
Obesity and associated disorders are now a global pandemic. The prevailing clinical model for obesity is overconsumption of calorie-dense food and diminished physical activity (the calories in-calories out model). However, this explanation does not account for numerous recent research findings demonstrating that a variety of environmental factors can be superimposed on diet and exercise to influence the development of obesity. The environmental obesogen model proposes that exposure to chemical obesogens during in utero and/or early life can strongly influence later predisposition to obesity. Obesogens are chemicals that inappropriately stimulate adipogenesis and fat storage, in vivo either directly or indirectly. Numerous obesogens have been identified in recent years and some of these elicit transgenerational effects on obesity as well as a variety of health end-points after exposure of pregnant F0 females. Prenatal exposure to environmental obesogens can produce lasting effects on the exposed animals and their offspring to at least the F4 generation. Recent results show that some of these transgenerational effects of obesogen exposure can be carried across the generations via alterations in chromatin structure and accessibility. That some chemicals can have permanent effects on the offspring of exposed animals suggests increased caution in the debate about whether and to what extent exposure to endocrine-disrupting chemicals and obesogens should be regulated.
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Affiliation(s)
- Michelle Kira Lee
- Department of Developmental and Cell Biology, 2011 BioSci
3, University of California, Irvine, CA 926970-2300
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 BioSci
3, University of California, Irvine, CA 926970-2300
- Department of Pharmaceutical Sciences, University of
California, Irvine
- Dept of Biomedical Engineering, University of California,
Irvine
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15
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Kubsad D, Nilsson EE, King SE, Sadler-Riggleman I, Beck D, Skinner MK. Assessment of Glyphosate Induced Epigenetic Transgenerational Inheritance of Pathologies and Sperm Epimutations: Generational Toxicology. Sci Rep 2019; 9:6372. [PMID: 31011160 PMCID: PMC6476885 DOI: 10.1038/s41598-019-42860-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/09/2019] [Indexed: 12/28/2022] Open
Abstract
Ancestral environmental exposures to a variety of factors and toxicants have been shown to promote the epigenetic transgenerational inheritance of adult onset disease. One of the most widely used agricultural pesticides worldwide is the herbicide glyphosate (N-(phosphonomethyl)glycine), commonly known as Roundup. There are an increasing number of conflicting reports regarding the direct exposure toxicity (risk) of glyphosate, but no rigorous investigations on the generational actions. The current study using a transient exposure of gestating F0 generation female rats found negligible impacts of glyphosate on the directly exposed F0 generation, or F1 generation offspring pathology. In contrast, dramatic increases in pathologies in the F2 generation grand-offspring, and F3 transgenerational great-grand-offspring were observed. The transgenerational pathologies observed include prostate disease, obesity, kidney disease, ovarian disease, and parturition (birth) abnormalities. Epigenetic analysis of the F1, F2 and F3 generation sperm identified differential DNA methylation regions (DMRs). A number of DMR associated genes were identified and previously shown to be involved in pathologies. Therefore, we propose glyphosate can induce the transgenerational inheritance of disease and germline (e.g. sperm) epimutations. Observations suggest the generational toxicology of glyphosate needs to be considered in the disease etiology of future generations.
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Affiliation(s)
- Deepika Kubsad
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Stephanie E King
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | | | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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16
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Zhang H, Xu P, Jiang Y, Zhao Z, Feng J, Tai R, Dong C, Xu J. Genomic, Transcriptomic, and Epigenomic Features Differentiate Genes That Are Relevant for Muscular Polyunsaturated Fatty Acids in the Common Carp. Front Genet 2019; 10:217. [PMID: 30930941 PMCID: PMC6428711 DOI: 10.3389/fgene.2019.00217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Polyunsaturated fatty acids (PUFAs) are a set of important nutrients that mainly include arachidonic acid (ARA4), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and α-linolenic acid (ALA). Recently, fish-derived PUFAs have been associated with cardiovascular health, fetal development, and improvement of brain functions. Studies have shown that fish muscular tissues are rich in PUFAs, which are influenced by various factors, including genetic variations, regulatory profiles, and methylation status of desaturase genes during fatty acid desaturation and elongation processes. However, the genetic mechanism and the pathways involved in fatty acid metabolism in fishes remain unclear. The overall aim of this study was to assess differences in gene expression responses among fishes with different fatty acid levels. To achieve this goal, we conducted genome-wide association analysis (GWAS) using a 250K SNP array in a population of 203 samples of common carp (Cyprinus carpio) and identified nine SNPs and 15 genes associated with muscular PUFA content. Then, RNA-Seq and whole genome bisulfite sequencing (WGBS) of different groups with high and low EPA, DHA, ARA4, and ALA contents in muscle, liver and brain tissues were conducted, resulting in 6,750 differentially expressed genes and 5,631 genes with differentially methylated promoters. Gene ontology and KEGG pathway enrichment analyses of RNA-Seq and WGBS results identified enriched pathways for fatty acid metabolism, which included the adipocytokine signaling pathway, ARA4 and linoleic acid metabolism pathway, and insulin signaling pathway. Integrated analysis indicated significant correlations between gene expression and methylation status among groups with high and low PUFA contents in muscular tissues. Taken together, these multi-level results uncovered candidate genes and pathways that are associated with fatty acid metabolism and paved the way for further genomic selection and carp breeding for PUFA traits.
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Affiliation(s)
- Hanyuan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Peng Xu
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, China
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Zixia Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Jianxin Feng
- Henan Academy of Fishery Science, Zhengzhou, China
| | - Ruyu Tai
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Chuanju Dong
- College of Fishery, Henan Normal University, Xinxiang, China
| | - Jian Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
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17
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Klukovich R, Nilsson E, Sadler-Riggleman I, Beck D, Xie Y, Yan W, Skinner MK. Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Prostate Pathology and Stromal-Epithelial Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Prostate Disease. Sci Rep 2019; 9:2209. [PMID: 30778168 PMCID: PMC6379561 DOI: 10.1038/s41598-019-38741-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/09/2019] [Indexed: 12/15/2022] Open
Abstract
Prostate diseases include prostate cancer, which is the second most common male neoplasia, and benign prostatic hyperplasia (BPH), which affects approximately 50% of men. The incidence of prostate disease is increasing, and some of this increase may be attributable to ancestral exposure to environmental toxicants and epigenetic transgenerational inheritance mechanisms. The goal of the current study was to determine the effects that exposure of gestating female rats to vinclozolin has on the epigenetic transgenerational inheritance of prostate disease, and to characterize by what molecular epigenetic mechanisms this has occurred. Gestating female rats (F0 generation) were exposed to vinclozolin during E8-E14 of gestation. F1 generation offspring were bred to produce the F2 generation, which were bred to produce the transgenerational F3 generation. The transgenerational F3 generation vinclozolin lineage males at 12 months of age had an increased incidence of prostate histopathology and abnormalities compared to the control lineage. Ventral prostate epithelial and stromal cells were isolated from F3 generation 20-day old rats, prior to the onset of pathology, and used to obtain DNA and RNA for analysis. Results indicate that there were transgenerational changes in gene expression, noncoding RNA expression, and DNA methylation in both cell types. Our results suggest that ancestral exposure to vinclozolin at a critical period of gestation induces the epigenetic transgenerational inheritance of prostate stromal and epithelial cell changes in both the epigenome and transcriptome that ultimately lead to prostate disease susceptibility and may serve as a source of the increased incidence of prostate pathology observed in recent years.
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Affiliation(s)
- Rachel Klukovich
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA.
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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18
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Chamorro-Garcia R, Blumberg B. Current Research Approaches and Challenges in the Obesogen Field. Front Endocrinol (Lausanne) 2019; 10:167. [PMID: 30967838 PMCID: PMC6438851 DOI: 10.3389/fendo.2019.00167] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/28/2019] [Indexed: 01/02/2023] Open
Abstract
Obesity is a worldwide pandemic that also contributes to the increased incidence of other diseases such as type 2 diabetes. Increased obesity is generally ascribed to positive energy balance. However, recent findings suggest that exposure to endocrine-disrupting chemicals such as obesogens during critical windows of development, may play an important role in the current obesity trends. Several experimental approaches, from in vitro cell cultures to transgenerational in vivo studies, are used to better understand the mechanisms of action of obesogens, each of which contributes to answer different questions. In this review, we discuss current knowledge in the obesogen field and the existing tools developed in research laboratories using tributyltin as a model obesogen. By understanding the advantages and limitations of each of these tools, we will better focus and design experimental approaches that will help expanding the obesogen field with the objective of finding potential therapeutic targets in human populations.
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Affiliation(s)
- Raquel Chamorro-Garcia
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- *Correspondence: Bruce Blumberg
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19
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Kamstra JH, Hurem S, Martin LM, Lindeman LC, Legler J, Oughton D, Salbu B, Brede DA, Lyche JL, Aleström P. Ionizing radiation induces transgenerational effects of DNA methylation in zebrafish. Sci Rep 2018; 8:15373. [PMID: 30337673 PMCID: PMC6193964 DOI: 10.1038/s41598-018-33817-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/06/2018] [Indexed: 01/08/2023] Open
Abstract
Ionizing radiation is known to cause DNA damage, yet the mechanisms underlying potential transgenerational effects of exposure have been scarcely studied. Previously, we observed effects in offspring of zebrafish exposed to gamma radiation during gametogenesis. Here, we hypothesize that these effects are accompanied by changes of DNA methylation possibly inherited by subsequent generations. We assessed DNA methylation in F1 embryos (5.5 hours post fertilization) with whole genome bisulfite sequencing following parental exposure to 8.7 mGy/h for 27 days and found 5658 differentially methylated regions (DMRs). DMRs were predominantly located at known regulatory regions, such as gene promoters and enhancers. Pathway analysis indicated the involvement of DMRs related to similar pathways found with gene expression analysis, such as development, apoptosis and cancers, which could be linked to previous observed developmental defects and genomic instability in the offspring. Follow up of 19 F1 DMRs in F2 and F3 embryos revealed persistent effects up to the F3 generation at 5 regions. These results indicate that ionizing radiation related effects in offspring can be linked to DNA methylation changes that partly can persist over generations. Monitoring DNA methylation could serve as a biomarker to provide an indication of ancestral exposures to ionizing radiation.
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Affiliation(s)
- Jorke H Kamstra
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway.
| | - Selma Hurem
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway
| | - Leonardo Martin Martin
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway.,University of Camagüey, Faculty of Agropecuary Sciences, Camagüey, 70100, Cuba
| | - Leif C Lindeman
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway.,Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1433, Ås, Norway
| | - Juliette Legler
- Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.,Utrecht University, Institute for Risk Assessment Sciences, 3508, TD, Utrecht, The Netherlands
| | - Deborah Oughton
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1433, Ås, Norway
| | - Brit Salbu
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1433, Ås, Norway
| | - Dag Anders Brede
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1433, Ås, Norway
| | - Jan Ludvig Lyche
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway
| | - Peter Aleström
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway
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20
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Nilsson E, Klukovich R, Sadler-Riggleman I, Beck D, Xie Y, Yan W, Skinner MK. Environmental toxicant induced epigenetic transgenerational inheritance of ovarian pathology and granulosa cell epigenome and transcriptome alterations: ancestral origins of polycystic ovarian syndrome and primary ovarian insufiency. Epigenetics 2018; 13:875-895. [PMID: 30207508 PMCID: PMC6224216 DOI: 10.1080/15592294.2018.1521223] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/23/2018] [Accepted: 08/30/2018] [Indexed: 12/30/2022] Open
Abstract
Two of the most prevalent ovarian diseases affecting women's fertility and health are Primary Ovarian Insufficiency (POI) and Polycystic Ovarian Syndrome (PCOS). Previous studies have shown that exposure to a number of environmental toxicants can promote the epigenetic transgenerational inheritance of ovarian disease. In the current study, transgenerational changes to the transcriptome and epigenome of ovarian granulosa cells are characterized in F3 generation rats after ancestral vinclozolin or DDT exposures. In purified granulosa cells from 20-day-old F3 generation females, 164 differentially methylated regions (DMRs) (P < 1 x 10-6) were found in the F3 generation vinclozolin lineage and 293 DMRs (P < 1 x 10-6) in the DDT lineage, compared to controls. Long noncoding RNAs (lncRNAs) and small noncoding RNAs (sncRNAs) were found to be differentially expressed in both the vinclozolin and DDT lineage granulosa cells. There were 492 sncRNAs (P < 1 x 10-4) in the vinclozolin lineage and 1,085 sncRNAs (P < 1 x 10-4) in the DDT lineage. There were 123 lncRNAs and 51 lncRNAs in the vinclozolin and DDT lineages, respectively (P < 1 x 10-4). Differentially expressed mRNAs were also found in the vinclozolin lineage (174 mRNAs at P < 1 x 10-4) and the DDT lineage (212 mRNAs at P < 1 x 10-4) granulosa cells. Comparisons with known ovarian disease associated genes were made. These transgenerational epigenetic changes appear to contribute to the dysregulation of the ovary and disease susceptibility that can occur in later life. Observations suggest that ancestral exposure to toxicants is a risk factor that must be considered in the molecular etiology of ovarian disease.
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Affiliation(s)
- Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Rachel Klukovich
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
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21
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Abstract
Obesity is a worldwide pandemic in adults as well as children and adds greatly to health care costs through its association with type 2 diabetes, metabolic syndrome, cardiovascular disease, and cancers. The prevailing medical view of obesity is that it results from a simple imbalance between caloric intake and energy expenditure. However, numerous other factors are important in the etiology of obesity. The obesogen hypothesis proposes that environmental chemicals termed obesogens promote obesity by acting to increase adipocyte commitment, differentiation, and size by altering metabolic set points or altering the hormonal regulation of appetite and satiety. Many obesogens are endocrine disrupting chemicals that interfere with normal endocrine regulation. Endocrine disrupting obesogens are abundant in our environment, used in everyday products from food packaging to fungicides. In this review, we explore the evidence supporting the obesogen hypothesis, as well as the gaps in our knowledge that are currently preventing a complete understanding of the extent to which obesogens contribute to the obesity pandemic.
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Affiliation(s)
- Jerrold J Heindel
- Program on Endocrine Disruption Strategies, Commonweal, Bolinas, California 94924, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, and Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
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22
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Nilsson EE, Sadler-Riggleman I, Skinner MK. Environmentally induced epigenetic transgenerational inheritance of disease. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy016. [PMID: 30038800 PMCID: PMC6051467 DOI: 10.1093/eep/dvy016] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/01/2018] [Accepted: 05/15/2018] [Indexed: 05/21/2023]
Abstract
Ancestral environmental exposures such as toxicants, abnormal nutrition or stress can promote the epigenetic transgenerational inheritance of disease and phenotypic variation. These environmental factors induce the epigenetic reprogramming of the germline (sperm and egg). The germline epimutations can in turn increase disease susceptibility of subsequent generations of the exposed ancestors. A variety of environmental factors, species and exposure specificity of this induced epigenetic transgenerational inheritance of disease is discussed with a consideration of generational toxicology. The molecular mechanisms and processes involved in the ability of these inherited epimutations to increase disease susceptibility are discussed. In addition to altered disease susceptibility, the potential impact of the epigenetic inheritance on phenotypic variation and evolution is considered. Observations suggest environmentally induced epigenetic transgenerational inheritance of disease is a critical aspect of disease etiology, toxicology and evolution that needs to be considered.
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Affiliation(s)
- Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
- Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1-509-335-1524; Fax: +1-509-335-2176; E-mail:
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23
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Skinner MK, Ben Maamar M, Sadler-Riggleman I, Beck D, Nilsson E, McBirney M, Klukovich R, Xie Y, Tang C, Yan W. Alterations in sperm DNA methylation, non-coding RNA and histone retention associate with DDT-induced epigenetic transgenerational inheritance of disease. Epigenetics Chromatin 2018; 11:8. [PMID: 29482626 PMCID: PMC5827984 DOI: 10.1186/s13072-018-0178-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/16/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Environmental toxicants such as DDT have been shown to induce the epigenetic transgenerational inheritance of disease (e.g., obesity) through the germline. The current study was designed to investigate the DDT-induced concurrent alterations of a number of different epigenetic processes including DNA methylation, non-coding RNA (ncRNA) and histone retention in sperm. METHODS Gestating females were exposed transiently to DDT during fetal gonadal development, and then, the directly exposed F1 generation, the directly exposed germline F2 generation and the transgenerational F3 generation sperm were investigated. RESULTS DNA methylation and ncRNA were altered in each generation sperm with the direct exposure F1 and F2 generations being predominantly distinct from the F3 generation epimutations. The piRNA and small tRNA were the most predominant classes of ncRNA altered. A highly conserved set of histone retention sites were found in the control lineage generations which was not significantly altered between generations, but a large number of new histone retention sites were found only in the transgenerational generation DDT lineage sperm. CONCLUSIONS Therefore, all three different epigenetic processes were concurrently altered as DDT induced the epigenetic transgenerational inheritance of sperm epimutations. The direct exposure generations sperm epigenetic alterations were distinct from the transgenerational sperm epimutations. The genomic features and gene associations with the epimutations were investigated to help elucidate the integration of these different epigenetic processes. Observations demonstrate all three epigenetic processes are involved in transgenerational inheritance. The different epigenetic processes appear to be integrated in mediating the epigenetic transgenerational inheritance phenomenon.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Margaux McBirney
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Rachel Klukovich
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Chong Tang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
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24
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Giannese F, Luchetti A, Barbiera G, Lampis V, Zanettini C, Knudsen GP, Scaini S, Lazarevic D, Cittaro D, D'Amato FR, Battaglia M. Conserved DNA Methylation Signatures in Early Maternal Separation and in Twins Discordant for CO 2 Sensitivity. Sci Rep 2018; 8:2258. [PMID: 29396481 PMCID: PMC5797081 DOI: 10.1038/s41598-018-20457-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/18/2018] [Indexed: 01/07/2023] Open
Abstract
Respiratory and emotional responses to blood-acidifying inhalation of CO2 are markers of some human anxiety disorders, and can be enhanced by repeatedly cross-fostering (RCF) mouse pups from their biological mother to unrelated lactating females. Yet, these dynamics remain poorly understood. We show RCF-associated intergenerational transmission of CO2 sensitivity in normally-reared mice descending from RCF-exposed females, and describe the accompanying alterations in brain DNA methylation patterns. These epigenetic signatures were compared to DNA methylation profiles of monozygotic twins discordant for emotional reactivity to a CO2 challenge. Altered methylation was consistently associated with repeated elements and transcriptional regulatory regions among RCF-exposed animals, their normally-reared offspring, and humans with CO2 hypersensitivity. In both species, regions bearing differential methylation were associated with neurodevelopment, circulation, and response to pH acidification processes, and notably included the ASIC2 gene. Our data show that CO2 hypersensitivity is associated with specific methylation clusters and genes that subserve chemoreception and anxiety. The methylation status of genes implicated in acid-sensing functions can inform etiological and therapeutic research in this field.
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Affiliation(s)
- Francesca Giannese
- Centre for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Luchetti
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
| | - Giulia Barbiera
- Centre for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Milan, Italy
| | | | - Claudio Zanettini
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy.,National Institute on Drug Abuse, Medication Development Program Molecular Targets and Medications Discovery Branch, Intramural Research Program, NIH, Baltimore, USA
| | - Gun Peggy Knudsen
- The Norwegian Institute of Public Health Department of Genetics, Environment and Mental Health, Oslo, Norway
| | - Simona Scaini
- Department of Psychology, Sigmund Freud University, Milan, Italy
| | - Dejan Lazarevic
- Centre for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cittaro
- Centre for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Milan, Italy
| | - Francesca R D'Amato
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy.
| | - Marco Battaglia
- Department of Psychiatry, the University of Toronto, Toronto, Canada. .,Division of Child, Youth and Emerging Adulthood, Centre for Addiction and Mental Health, Toronto, Canada.
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25
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McBirney M, King SE, Pappalardo M, Houser E, Unkefer M, Nilsson E, Sadler-Riggleman I, Beck D, Winchester P, Skinner MK. Atrazine induced epigenetic transgenerational inheritance of disease, lean phenotype and sperm epimutation pathology biomarkers. PLoS One 2017; 12:e0184306. [PMID: 28931070 PMCID: PMC5606923 DOI: 10.1371/journal.pone.0184306] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/21/2017] [Indexed: 01/09/2023] Open
Abstract
Ancestral environmental exposures to a variety of environmental toxicants and other factors have been shown to promote the epigenetic transgenerational inheritance of adult onset disease. The current study examined the potential transgenerational actions of the herbicide atrazine. Atrazine is one of the most commonly used herbicides in the agricultural industry, in particular with corn and soy crops. Outbred gestating female rats were transiently exposed to a vehicle control or atrazine. The F1 generation offspring were bred to generate the F2 generation and then the F2 generation bred to generate the F3 generation. The F1, F2 and F3 generation control and atrazine lineage rats were aged and various pathologies investigated. The male sperm were collected to investigate DNA methylation differences between the control and atrazine lineage sperm. The F1 generation offspring (directly exposed as a fetus) did not develop disease, but weighed less compared to controls. The F2 generation (grand-offspring) was found to have increased frequency of testis disease and mammary tumors in males and females, early onset puberty in males, and decreased body weight in females compared to controls. The transgenerational F3 generation rats were found to have increased frequency of testis disease, early onset puberty in females, behavioral alterations (motor hyperactivity) and a lean phenotype in males and females. The frequency of multiple diseases was significantly higher in the transgenerational F3 generation atrazine lineage males and females. The transgenerational transmission of disease requires germline (egg or sperm) epigenetic alterations. The sperm differential DNA methylation regions (DMRs), termed epimutations, induced by atrazine were identified in the F1, F2 and F3 generations. Gene associations with the DMRs were identified. For the transgenerational F3 generation sperm, unique sets of DMRs (epimutations) were found to be associated with the lean phenotype or testis disease. These DMRs provide potential biomarkers for transgenerational disease. The etiology of disease appears to be in part due to environmentally induced epigenetic transgenerational inheritance, and epigenetic biomarkers may facilitate the diagnosis of the ancestral exposure and disease susceptibility. Observations indicate that although atrazine does not promote disease in the directly exposed F1 generation, it does have the capacity to promote the epigenetic transgenerational inheritance of disease.
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Affiliation(s)
- Margaux McBirney
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Stephanie E. King
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michelle Pappalardo
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Elizabeth Houser
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Margaret Unkefer
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Paul Winchester
- Indiana University, School of Medicine, Department of Pediatrics, Indianapolis, Indiana, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
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26
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Rothstein MA, Harrell HL, Marchant GE. Transgenerational epigenetics and environmental justice. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx011. [PMID: 29492313 PMCID: PMC5804551 DOI: 10.1093/eep/dvx011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/15/2017] [Accepted: 06/19/2017] [Indexed: 05/20/2023]
Abstract
Human transmission to offspring and future generations of acquired epigenetic modifications has not been definitively established, although there are several environmental exposures with suggestive evidence. This article uses three examples of hazardous substances with greater exposures in vulnerable populations: pesticides, lead, and diesel exhaust. It then considers whether, if there were scientific evidence of transgenerational epigenetic inheritance, there would be greater attention given to concerns about environmental justice in environmental laws, regulations, and policies at all levels of government. To provide a broader perspective on environmental justice the article discusses two of the most commonly cited approaches to environmental justice. John Rawls's theory of justice as fairness, a form of egalitarianism, is frequently invoked for the principle that differential treatment of individuals is justified only if actions are designed to benefit those with the greatest need. Another theory, the capabilities approach of Amartya Sen and Martha Nussbaum, focuses on whether essential capabilities of society, such as life and health, are made available to all individuals. In applying principles of environmental justice the article considers whether there is a heightened societal obligation to protect the most vulnerable individuals from hazardous exposures that could adversely affect their offspring through epigenetic mechanisms. It concludes that unless there were compelling evidence of transgenerational epigenetic harms, it is unlikely that there would be a significant impetus to adopt new policies to prevent epigenetic harms by invoking principles of environmental justice.
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Affiliation(s)
- Mark A. Rothstein
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, 501 East Broadway #310, Louisville, KY 40202, USA
| | - Heather L. Harrell
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Gary E. Marchant
- Center for Law, Science & Innovation, Sandra Day O'Connor College of Law, Arizona State University, Phoenix, AZ 85004, USA
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27
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Abstract
Pharmacogenomics (PGx), a substantial component of "personalized medicine", seeks to understand each individual's genetic composition to optimize drug therapy -- maximizing beneficial drug response, while minimizing adverse drug reactions (ADRs). Drug responses are highly variable because innumerable factors contribute to ultimate phenotypic outcomes. Recent genome-wide PGx studies have provided some insight into genetic basis of variability in drug response. These can be grouped into three categories. [a] Monogenic (Mendelian) traits include early examples mostly of inherited disorders, and some severe (idiosyncratic) ADRs typically influenced by single rare coding variants. [b] Predominantly oligogenic traits represent variation largely influenced by a small number of major pharmacokinetic or pharmacodynamic genes. [c] Complex PGx traits resemble most multifactorial quantitative traits -- influenced by numerous small-effect variants, together with epigenetic effects and environmental factors. Prediction of monogenic drug responses is relatively simple, involving detection of underlying mutations; due to rarity of these events and incomplete penetrance, however, prospective tests based on genotype will have high false-positive rates, plus pharmacoeconomics will require justification. Prediction of predominantly oligogenic traits is slowly improving. Although a substantial fraction of variation can be explained by limited numbers of large-effect genetic variants, uncertainty in successful predictions and overall cost-benefit ratios will make such tests elusive for everyday clinical use. Prediction of complex PGx traits is almost impossible in the foreseeable future. Genome-wide association studies of large cohorts will continue to discover relevant genetic variants; however, these small-effect variants, combined, explain only a small fraction of phenotypic variance -- thus having limited predictive power and clinical utility.
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Affiliation(s)
- Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, United States.
| | - Daniel W Nebert
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, United States; Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati School of Medicine, Cincinnati, OH 45267-0056, United States.
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28
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Beck D, Sadler-Riggleman I, Skinner MK. Generational comparisons (F1 versus F3) of vinclozolin induced epigenetic transgenerational inheritance of sperm differential DNA methylation regions (epimutations) using MeDIP-Seq. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx016. [PMID: 29147574 PMCID: PMC5685552 DOI: 10.1093/eep/dvx016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation has been shown to involve DNA methylation alterations in the germline (e.g. sperm). These differential DNA methylation regions (DMRs) are termed epimutations and in part transmit the transgenerational phenotypes. The agricultural fungicide vinclozolin exposure of a gestating female rat has previously been shown to promote transgenerational disease and epimutations in F3 generation (great-grand-offspring) animals. The current study was designed to investigate the actions of direct fetal exposure on the F1 generation rat sperm DMRs compared to the F3 transgenerational sperm DMRs. A protocol involving methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (Seq) was used in the current study. Bioinformatics analysis of the MeDIP-Seq data was developed and several different variations in the bioinformatic analysis were evaluated. Observations indicate needs to be considered. Interestingly, the F1 generation DMRs were found to be fewer in number and for the most part distinct from the F3 generation epimutations. Observations suggest the direct exposure induced F1 generation sperm DMRs appear to promote in subsequent generations alterations in the germ cell developmental programming that leads to the distinct epimutations in the F3 generation. This may help explain the differences in disease and phenotypes between the direct exposure F1 generation and transgenerational F3 generation. Observations demonstrate a distinction between the direct exposure versus transgenerational epigenetic programming induced by environmental exposures and provide insights into the molecular mechanisms involved in the epigenetic transgenerational inheritance phenomenon.
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Affiliation(s)
- Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
- Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1-509-335-1524; Fax: +1-509-335-2176; E-mail:
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