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Tatemoto P, Pértille F, Bernardino T, Zanella R, Guerrero-Bosagna C, Zanella AJ. An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets. Epigenetics 2023; 18:2196656. [PMID: 37192378 DOI: 10.1080/15592294.2023.2196656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 02/15/2023] [Accepted: 03/08/2023] [Indexed: 05/18/2023] Open
Abstract
Epigenetic mechanisms are important modulators of neurodevelopmental outcomes in the offspring of animals challenged during pregnancy. Pregnant sows living in a confined environment are challenged with stress and lack of stimulation which may result in the expression of stereotypies (repetitive behaviours without an apparent function). Little attention has been devoted to the postnatal effects of maternal stereotypies in the offspring. We investigated how the environment and stereotypies of pregnant sows affected the neuro-epigenome of their piglets. We focused on the amygdala, frontal cortex, and hippocampus, brain regions related to emotionality, learning, memory, and stress response. Differentially methylated regions (DMRs) were investigated in these brain regions of male piglets born from sows kept in an enriched vs a barren environment. Within the latter group of piglets, we compared the brain methylomes of piglets born from sows expressing stereotypies vs sows not expressing stereotypies. DMRs emerged in each comparison. While the epigenome of the hippocampus and frontal cortex of piglets is mainly affected by the maternal environment, the epigenome of the amygdala is mainly affected by maternal stereotypies. The molecular pathways and mechanisms triggered in the brains of piglets by maternal environment or stereotypies are different, which is reflected on the differential gene function associated to the DMRs found in each piglets' brain region . The present study is the first to investigate the neuro-epigenomic effects of maternal enrichment in pigs' offspring and the first to investigate the neuro-epigenomic effects of maternal stereotypies in the offspring of a mammal.
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Affiliation(s)
- Patricia Tatemoto
- Center for Comparative Studies in Sustainability, Health and Welfare, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, FMVZ, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Fábio Pértille
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo - Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Thiago Bernardino
- Center for Comparative Studies in Sustainability, Health and Welfare, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, FMVZ, University of São Paulo, Pirassununga, São Paulo, Brazil
- Graduation Program in One Health, University of Santo Amaro, São Paulo Brazil
| | - Ricardo Zanella
- Faculty of Agronomy and Veterinary Medicine, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Adroaldo José Zanella
- Center for Comparative Studies in Sustainability, Health and Welfare, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, FMVZ, University of São Paulo, Pirassununga, São Paulo, Brazil
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Wegmann B, Tatemoto P, Miemczyk S, Ludvigsson J, Guerrero-Bosagna C. Identification of potentially relevant metals for the etiology of autism by using a Bayesian multivariate approach for partially censored values. Sci Rep 2023; 13:12622. [PMID: 37537167 PMCID: PMC10400650 DOI: 10.1038/s41598-023-38780-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/14/2023] [Indexed: 08/05/2023] Open
Abstract
Heavy metals are known to be able to cross the placental and blood brain barriers to affect critical neurodevelopmental processes in the fetus. We measured metal levels (Al, Cd, Hg, Li, Pb and Zn) in the cord blood of newborns and in the serum of the same children at 5 years of age, and compared between individuals with or without (controls) autism spectrum disorder (ASD) diagnosis. The samples were from a biobank associated with the All Babies in Southeast Sweden (ABIS) registry. We proposed a Bayesian multivariate log-normal model for partially censored values to identify potentially relevant metals for the etiology of ASD. Our results in cord blood suggest prenatal Al levels could be indicative of later ASD incidence, which could also be related to an increased possibility of a high, potentially toxic, exposure to Al and Li during pregnancy. In addition, a larger possibility of a high, potentially beneficial, exposure to Zn could occur during pregnancy in controls. Finally, we found decisive evidence for an average increase of Hg in 5-year-old ASD children compared to only weak evidence for controls. This is concordant with previous research showing an impaired ability for eliminating Hg in the ASD group.
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Affiliation(s)
- Bertil Wegmann
- Division of Statistics and Machine Learning, Department of Computer and Information Science, Linköping University, 581 83, Linköping, Sweden.
| | - Patricia Tatemoto
- Center for Comparative Studies in Sustainability, Health and Welfare, Department of Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, FMVZ, University of São Paulo, Pirassununga, São Paulo, 13635-900, Brazil
| | - Stefan Miemczyk
- Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83, Linköping, Sweden
| | - Johnny Ludvigsson
- Crown Princess Victoria Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 75236, Uppsala, Sweden.
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Videla Rodriguez EA, Pértille F, Guerrero-Bosagna C, Mitchell JBO, Jensen P, Smith VA. Practical application of a Bayesian network approach to poultry epigenetics and stress. BMC Bioinformatics 2022; 23:261. [PMID: 35778683 PMCID: PMC9250184 DOI: 10.1186/s12859-022-04800-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/14/2022] [Indexed: 11/23/2022] Open
Abstract
Background Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide array of possibilities in Bayesian network analysis is limited. Our study aimed to apply a BN approach, while clearly laying out our analysis choices as an example for future researchers, in order to provide further insights into the relationships among epigenetic features and a stressful condition in chickens (Gallus gallus). Results Chickens raised under control conditions (n = 22) and chickens exposed to a social isolation protocol (n = 24) were used to identify differentially methylated regions (DMRs). A total of 60 DMRs were selected by a threshold, after bioinformatic pre-processing and analysis. The treatment was included as a binary variable (control = 0; stress = 1). Thereafter, a BN approach was applied: initially, a pre-filtering test was used for identifying pairs of features that must not be included in the process of learning the structure of the network; then, the average probability values for each arc of being part of the network were calculated; and finally, the arcs that were part of the consensus network were selected. The structure of the BN consisted of 47 out of 61 features (60 DMRs and the stressful condition), displaying 43 functional relationships. The stress condition was connected to two DMRs, one of them playing a role in tight and adhesive intracellular junctions in organs such as ovary, intestine, and brain. Conclusions We clearly explain our steps in making each analysis choice, from discrete BN models to final generation of a consensus network from multiple model averaging searches. The epigenetic BN unravelled functional relationships among the DMRs, as well as epigenetic features in close association with the stressful condition the chickens were exposed to. The DMRs interacting with the stress condition could be further explored in future studies as possible biomarkers of stress in poultry species. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04800-0.
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Affiliation(s)
| | - Fábio Pértille
- Environmental Toxicology Program, Institute of Organismal Biology, Uppsala University, Uppsala, Sweden.,Department of Biomedical & Clinical Sciences (BKV), Linköping University, 58183, Linköping, Sweden.,AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- Environmental Toxicology Program, Institute of Organismal Biology, Uppsala University, Uppsala, Sweden.,AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - John B O Mitchell
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - V Anne Smith
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.
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Rezaei S, Uffenorde J, Gimm O, Hosseinpour Feizi MA, Miemczyk S, Coutinho LL, Jensen P, Guerrero-Bosagna C, Pértille F. GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals. STAR Protoc 2022; 3:101202. [PMID: 35257114 PMCID: PMC8897576 DOI: 10.1016/j.xpro.2022.101202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking. Our protocol combines two well-known techniques, GBS and MeDIP. The GBS-MeDIP allows for parallel interrogation of genetic/methylomic variants. Allows for cost-efficient analysis of reduced genomes from multiple individuals. Ideal for the identification of genetic and/or methylomic markers at reduced cost.
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Affiliation(s)
- Shiva Rezaei
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran
- Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - Julia Uffenorde
- Department of Surgery and Department of Biomedical and Clinical Sciences (BKV), Linköping University, 581 83 Linköping, Sweden
| | - Oliver Gimm
- Department of Surgery and Department of Biomedical and Clinical Sciences (BKV), Linköping University, 581 83 Linköping, Sweden
| | | | - Stefan Miemczyk
- Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - Luiz Lehmann Coutinho
- Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Per Jensen
- Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
- Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
- Corresponding author
| | - Fábio Pértille
- Department of Surgery and Department of Biomedical and Clinical Sciences (BKV), Linköping University, 581 83 Linköping, Sweden
- Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
- Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418-900, Brazil
- Corresponding author
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Olivares-Castro G, Cáceres-Jensen L, Guerrero-Bosagna C, Villagra C. Insect Epigenetic Mechanisms Facing Anthropogenic-Derived Contamination, an Overview. Insects 2021; 12:780. [PMID: 34564220 PMCID: PMC8468710 DOI: 10.3390/insects12090780] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/14/2022]
Abstract
Currently, the human species has been recognized as the primary species responsible for Earth's biodiversity decline. Contamination by different chemical compounds, such as pesticides, is among the main causes of population decreases and species extinction. Insects are key for ecosystem maintenance; unfortunately, their populations are being drastically affected by human-derived disturbances. Pesticides, applied in agricultural and urban environments, are capable of polluting soil and water sources, reaching non-target organisms (native and introduced). Pesticides alter insect's development, physiology, and inheritance. Recently, a link between pesticide effects on insects and their epigenetic molecular mechanisms (EMMs) has been demonstrated. EMMs are capable of regulating gene expression without modifying genetic sequences, resulting in the expression of different stress responses as well as compensatory mechanisms. In this work, we review the main anthropogenic contaminants capable of affecting insect biology and of triggering EMMs. EMMs are involved in the development of several diseases in native insects affected by pesticides (e.g., anomalous teratogenic reactions). Additionally, EMMs also may allow for the survival of some species (mainly pests) under contamination-derived habitats; this may lead to biodiversity decline and further biotic homogenization. We illustrate these patterns by reviewing the effect of neonicotinoid insecticides, insect EMMs, and their ecological consequences.
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Affiliation(s)
- Gabriela Olivares-Castro
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
| | - Lizethly Cáceres-Jensen
- Laboratorio de Físicoquímica Analítica, Departamento de Química, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Santiago 7760197, Chile;
| | - Carlos Guerrero-Bosagna
- Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden;
- Environmental Toxicology Program, Department of Integrative Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Cristian Villagra
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
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Pértille F, Ibelli AMG, Sharif ME, Poleti MD, Fröhlich AS, Rezaei S, Ledur MC, Jensen P, Guerrero-Bosagna C, Coutinho LL. Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes. Front Genet 2020; 11:508809. [PMID: 33240310 PMCID: PMC7667380 DOI: 10.3389/fgene.2020.508809] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 09/11/2020] [Indexed: 12/19/2022] Open
Abstract
Production animals are constantly subjected to early adverse environmental conditions that influence the adult phenotype and produce epigenetic effects. CpG dinucleotide methylation in red blood cells (RBC) could be a useful epigenetic biomarker to identify animals subjected to chronic stress in the production environment. Here we compared a reduced fraction of the RBC methylome of chickens exposed to social isolation to non-exposed. These experiments were performed in two different locations: Brazil and Sweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposed in each facility and their different lineages. Birds were increasingly exposed to a social isolation treatment, combined with food and water deprivation, at random periods of the day from weeks 1-4 after hatching. We then collected the RBC DNA from individuals and compared a reduced fraction of their methylome between the experimental groups using two bioinformatic approaches to identify differentially methylated regions (DMRs): one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P ≤ 0.05, P ≤ 0.005, and P ≤ 0.0005) to identify DMRs between experimental groups, which were then used for different analyses. With both of the approaches more DMRs reached the defined significance thresholds in BR individuals compared to SW. However, more DMRs had higher fold change values in SW compared to BR individuals. Interestingly, ChrZ was enriched above expectancy for the presence of DMRs. Additionally, when analyzing the locations of these DMRs in relation to the transcription starting site (TSS), we found three peaks with high DMR presence: 10 kb upstream, the TSS itself, and 20-40 kb downstream. Interestingly, these peaks had DMRs with a high presence (>50%) of specific transcription factor binding sites. Three overlapping DMRs were found between the BR and SW population using the most relaxed p-value (P ≤ 0.05). With the most stringent p-value (P ≤ 0.0005), we found 7 and 4 DMRs between treatments in the BR and SW populations, respectively. This study is the first approximation to identify epigenetic biomarkers of long-term exposure to stress in different lineages of production animals.
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Affiliation(s)
- Fábio Pértille
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/"Luiz de Queiroz" College of Agriculture (ESALQ), Piracicaba, Brazil.,Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | | | - Maj El Sharif
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Mirele Daiana Poleti
- Animal Science Program, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Anna Sophie Fröhlich
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Shiva Rezaei
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | | | - Per Jensen
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden.,Evolutionary Biology Centre, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/"Luiz de Queiroz" College of Agriculture (ESALQ), Piracicaba, Brazil
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Sundman AS, Pértille F, Lehmann Coutinho L, Jazin E, Guerrero-Bosagna C, Jensen P. DNA methylation in canine brains is related to domestication and dog-breed formation. PLoS One 2020; 15:e0240787. [PMID: 33119634 PMCID: PMC7595415 DOI: 10.1371/journal.pone.0240787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/02/2020] [Indexed: 11/19/2022] Open
Abstract
Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. During domestication, dogs have evolved an unprecedented between-breed variation in morphology and behavior in an evolutionary short period. In the present study, we explore DNA methylation differences in brain, the most relevant tissue with respect to behavior, between wolf and dog breeds. We optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and three wolves was used. GBS and GBS-MeDIP libraries were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 ± 0.4% of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 ± 4,042,106 unique base pairs. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors may have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding but are also useful to further understanding of epigenetic involvement.
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Affiliation(s)
- Ann-Sofie Sundman
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Fábio Pértille
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Carlos Guerrero-Bosagna
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Per Jensen
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- * E-mail:
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Guerrero-Bosagna C. From epigenotype to new genotypes: Relevance of epigenetic mechanisms in the emergence of genomic evolutionary novelty. Semin Cell Dev Biol 2020; 97:86-92. [DOI: 10.1016/j.semcdb.2019.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 11/24/2022]
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9
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Kindgren E, Guerrero-Bosagna C, Ludvigsson J. Heavy metals in fish and its association with autoimmunity in the development of juvenile idiopathic arthritis: a prospective birth cohort study. Pediatr Rheumatol Online J 2019; 17:33. [PMID: 31266504 PMCID: PMC6604193 DOI: 10.1186/s12969-019-0344-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The etiology of Juvenile Idiopathic Arthritis (JIA) is poorly understood. The purpose of this study was to examine the possible influence of early nutrition on later development of JIA. METHODS In a population-based prospective birth cohort of 15,740 children we collected nutritional data, including fish consumption, and biological samples during pregnancy, at birth and at different ages. 16 years after study inclusion we identified 42 children with JIA, of whom 11 were positive for Antinuclear Antibodies (ANA). Heavy metals were analysed in cord blood of all 42 JIA patients and 40 age and sex-matched controls. A multivariable logistic regression model, adjusted for relevant factors, was used as well as Mann-Whitney U-test. RESULTS Fish consumption more than once a week during pregnancy as well as during the child's first year of life was associated with an increased risk of JIA (aOR 4.5 (1.95-10.4); p < 0.001 and aOR 5.1 (2.1-12.4) p < 0.001) and of ANA-positivity (aOR 2.2 (1.4-3.6); p = 0.002 and p < 0.001). Concentrations of Al, Cd, Hg and Li in cord blood were significantly higher in the JIA-group than in controls. The ANA-positive, all of whom had consumed fish >once/week their first year, had significantly higher concentrations of Al (p < 0.001), Cd (p = 0.003), and Li (p < 0.001) in cord blood than controls. Frequency of fish consumption correlated with concentrations of Cd (p = 0.003), Li (p = 0.015) and Hg (p = 0.011). CONCLUSIONS Moderate exposure to heavy metals, associated with fish consumption, during pregnancy and early childhood may cause effects on the immune system of the offspring, resulting in ANA positivity and JIA.
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Affiliation(s)
- Erik Kindgren
- Department of Pediatrics, Västervik Hospital, Västervik, Sweden. .,Division of Pediatrics, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden. .,Department of Pediatrics, Skaraborg Hospital, SE-541 85 Skövde, Skövde, Sweden.
| | - Carlos Guerrero-Bosagna
- 0000 0001 2162 9922grid.5640.7Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Johnny Ludvigsson
- 0000 0001 2162 9922grid.5640.7Division of Pediatrics, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden ,Crown Princess Victoria Children’s Hospital, Region Östergötland, Linköping, Sweden
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Abstract
The incidence of type 1 diabetes (T1D) has increased explained by changes in environment or lifestyle. In modern society dissemination of heavy metals has increased. As the autoimmune process usually starts already, we hypothesized that exposure to toxic metals during fetal life might contribute to development of T1D in children. We analysed arsenic (AS), aluminium (Al), cadmium (Cd), lithium (Li), mercury (Hg), lead (Pb), in cord blood of 20 children who later developed T1D (probands), and in 40 age-and sex-matched controls. Analysis of heavy metals in cord blood was performed by ALS Scandinavia AB (Luleå, Sweden) using the ‘ultrasensitive inductively coupled plasma sector field mass spectrometry method’ (ICP-SFMS) after acid digestion with HNO3. Most children had no increased concentrations of the metals in cord blood. However, children who later developed T1D had more often increased concentrations (above limit of detection; LOD) of aluminium (p = 0.006) in cord blood than the non-diabetic controls, and also more often mercury and arsenic (n.s). Our conclusion is that exposure to toxic metals during pregnancy might be one among several contributing environmental factors to the disease process if confirmed in other birth cohort trials.
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Affiliation(s)
- J Ludvigsson
- Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, Linköping, Sweden
| | - P Andersson-White
- Crown Princess Victoria Children's Hospital, Region Östergötland. Linköping Sweden
| | - C Guerrero-Bosagna
- IFM Biology, Linköping, University; Linköping university, Linköping, Sweden
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Pértille F, Da Silva VH, Johansson AM, Lindström T, Wright D, Coutinho LL, Jensen P, Guerrero-Bosagna C. Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification. Epigenetics 2019; 14:685-707. [PMID: 31070073 PMCID: PMC6557589 DOI: 10.1080/15592294.2019.1609868] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic ‘flexibility’ in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic ‘specificity’ in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.
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Affiliation(s)
- Fábio Pértille
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden.,b Animal Biotechnology Laboratory, Animal Science Department , University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ) , Piracicaba , São Paulo , Brazil
| | - Vinicius H Da Silva
- c Animal Breeding and Genomics Centre , Wageningen University & Research , Wageningen , The Netherlands.,d Department of Animal Ecology (AnE) , Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , The Netherlands.,e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Anna M Johansson
- e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Tom Lindström
- f Division of Theoretical Biology, IFM , Linköping University , Linköping , Sweden
| | - Dominic Wright
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
| | - Luiz L Coutinho
- b Animal Biotechnology Laboratory, Animal Science Department , University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ) , Piracicaba , São Paulo , Brazil
| | - Per Jensen
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
| | - Carlos Guerrero-Bosagna
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
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12
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Frías-Lasserre D, Villagra CA, Guerrero-Bosagna C. Stress in the Educational System as a Potential Source of Epigenetic Influences on Children's Development and Behavior. Front Behav Neurosci 2018; 12:143. [PMID: 30057532 PMCID: PMC6053942 DOI: 10.3389/fnbeh.2018.00143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/25/2018] [Indexed: 11/24/2022] Open
Abstract
Despite current advances on the relevance of environmental cues and epigenetic mechanisms in biological processes, including behavior, little attention has been paid to the potential link between epigenetic influences and educational sciences. For instance, could the learning environment and stress determine epigenetic marking, affecting students' behavior development? Could this have consequences on educational outcomes? So far, it has been shown that environmental stress influences neurological processes and behavior both in humans and rats. Through epigenetic mechanisms, offspring from stressed individuals develop altered behavior without any exposure to traumatizing experiences. Methylated DNA and noncoding RNAs regulate neurological processes such as synaptic plasticity and brain cortex development in children. The malfunctioning of these processes is associated with several neurological disorders, and these findings open up new avenues for the design of enriched environments for education and therapy. In this article, we discuss current cases of stress and behavioral disorders found in youngsters, and highlight the importance of considering epigenetic processes affecting the development of cognitive abilities and learning within the educational environment and for the development of teaching methodologies.
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Affiliation(s)
- Daniel Frías-Lasserre
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
| | - Cristian A. Villagra
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
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13
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Bélteky J, Agnvall B, Bektic L, Höglund A, Jensen P, Guerrero-Bosagna C. Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans. Genet Sel Evol 2018; 50:13. [PMID: 29609558 PMCID: PMC5880090 DOI: 10.1186/s12711-018-0384-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/09/2018] [Indexed: 12/11/2022] Open
Abstract
Background Domestication of animals leads to large phenotypic alterations within a short evolutionary time-period. Such alterations are caused by genomic variations, yet the prevalence of modified traits is higher than expected if they were caused only by classical genetics and mutations. Epigenetic mechanisms may also be important in driving domesticated phenotypes such as behavior traits. Gene expression can be modulated epigenetically by mechanisms such as DNA methylation, resulting in modifications that are not only variable and susceptible to environmental stimuli, but also sometimes transgenerationally stable. To study such mechanisms in early domestication, we used as model two selected lines of red junglefowl (ancestors of modern chickens) that were bred for either high or low fear of humans over five generations, and investigated differences in hypothalamic DNA methylation between the two populations. Results Twenty-two 1-kb windows were differentially methylated between the two selected lines at p < 0.05 after false discovery rate correction. The annotated functions of the genes within these windows indicated epigenetic regulation of metabolic and signaling pathways, which agrees with the changes in gene expression that were previously reported for the same tissue and animals. Conclusions Our results show that selection for an important domestication-related behavioral trait such as tameness can cause divergent epigenetic patterns within only five generations, and that these changes could have an important role in chicken domestication. Electronic supplementary material The online version of this article (10.1186/s12711-018-0384-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johan Bélteky
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Beatrix Agnvall
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Lejla Bektic
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Andrey Höglund
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Per Jensen
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden.
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14
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Guerrero-Bosagna C, Morisson M, Liaubet L, Rodenburg TB, de Haas EN, Košťál Ľ, Pitel F. Transgenerational epigenetic inheritance in birds. Environ Epigenet 2018; 4:dvy008. [PMID: 29732172 PMCID: PMC5920295 DOI: 10.1093/eep/dvy008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 05/04/2023]
Abstract
While it has been shown that epigenetics accounts for a portion of the variability of complex traits linked to interactions with the environment, the real contribution of epigenetics to phenotypic variation remains to be assessed. In recent years, a growing number of studies have revealed that epigenetic modifications can be transmitted across generations in several animal species. Numerous studies have demonstrated inter- or multi-generational effects of changing environment in birds, but very few studies have been published showing epigenetic transgenerational inheritance in these species. In this review, we mention work conducted in parent-to-offspring transmission analyses in bird species, with a focus on the impact of early stressors on behaviour. We then present recent advances in transgenerational epigenetics in birds, which involve germline linked non-Mendelian inheritance, underline the advantages and drawbacks of working on birds in this field and comment on future directions of transgenerational studies in bird species.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - T Bas Rodenburg
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Elske N de Haas
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Ľubor Košťál
- Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
- Correspondence address. GenPhySE, INRA, 31326 Castanet-Tolosan, France. Tel:+33 561 28 54 35. E-mail:
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Pértille F, Brantsæter M, Nordgreen J, Coutinho LL, Janczak AM, Jensen P, Guerrero-Bosagna C. DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions. ACTA ACUST UNITED AC 2017; 220:3579-3587. [PMID: 28784681 DOI: 10.1242/jeb.157891] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/01/2017] [Indexed: 12/30/2022]
Abstract
Stressful conditions are common in the environment where production animals are reared. Stress in animals is usually determined by the levels of stress-related hormones. A big challenge, however, is in determining the history of exposure of an organism to stress, because the release of stress hormones can show an acute (and recent) but not a sustained exposure to stress. Epigenetic tools provide an alternative option to evaluate past exposure to long-term stress. Chickens provide a unique model to study stress effects in the epigenome of red blood cells (RBCs), a cell type of easy access and nucleated in birds. The present study investigated whether two different rearing conditions in chickens can be identified by looking at DNA methylation patterns in their RBCs later in life. These conditions were rearing in open aviaries versus in cages, which are likely to differ regarding the amount of stress they generate. Our comparison revealed 115 genomic windows with significant changes in RBC DNA methylation between experimental groups, which were located around 53 genes and within 22 intronic regions. Our results set the ground for future detection of long-term stress in live production animals by measuring DNA methylation in a cell type of easy accessibility.
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Affiliation(s)
- Fábio Pértille
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, SE-58 183 Linköping, Sweden.,Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), 13418-900 Piracicaba, São Paulo, Brazil
| | - Margrethe Brantsæter
- Animal Welfare Research Group, Department of Production Animal Clinical Science, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, N-0033 Oslo, Norway
| | - Janicke Nordgreen
- Animal Welfare Research Group, Department of Production Animal Clinical Science, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, N-0033 Oslo, Norway
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), 13418-900 Piracicaba, São Paulo, Brazil
| | - Andrew M Janczak
- Animal Welfare Research Group, Department of Production Animal Clinical Science, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, N-0033 Oslo, Norway
| | - Per Jensen
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, SE-58 183 Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, SE-58 183 Linköping, Sweden
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16
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Guerrero-Bosagna C. Evolution with No Reason: A Neutral View on Epigenetic Changes, Genomic Variability, and Evolutionary Novelty. Bioscience 2017. [DOI: 10.1093/biosci/bix021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Vargas AO, Krabichler Q, Guerrero-Bosagna C. An Epigenetic Perspective on the Midwife Toad Experiments of Paul Kammerer (1880-1926). J Exp Zool B Mol Dev Evol 2016; 328:179-192. [PMID: 27781385 DOI: 10.1002/jez.b.22708] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/29/2016] [Accepted: 09/24/2016] [Indexed: 12/14/2022]
Abstract
Paul Kammerer was the most outstanding neo-Lamarckian experimentalist of the early 20th century. He reported spectacular results in the midwife toad, including crosses of environmentally modified toads with normal toads, where acquired traits were inherited in Mendelian fashion. Accusations of fraud generated a great scandal, ending with Kammerer's suicide. Controversy reignited in the 1970s, when journalist Arthur Koestler argued against these accusations. Since then, others have argued that Kammerer's results, even if real, were not groundbreaking and could be explained by somatic plasticity, inadvertent selection, or conventional genetics. More recently, epigenetics has uncovered mechanisms by which inheritance can respond directly to environmental change, inviting a reanalysis of Kammerer's descriptions. Previous arguments for mere somatic plasticity have ignored the description of experiments showing heritable germ line modification. Alleged inadvertent selection associated with egg mortality can be discarded, since mortality decreased in a single generation, upon repeated exposures. The challenging implications did not escape the attention of Kammerer's noted contemporary, William Bateson, but he reacted with disbelief, thus encouraging fraud accusations. Nowadays, formerly puzzling phenomena can be explained by epigenetic mechanisms. Importantly, Kammerer described parent-of-origin effects, an effect of parental sex on dominance. Epigenetic mechanisms underlie these effects in genomic imprinting and experiments of transgenerational epigenetic inheritance. In the early 20th century, researchers had no reason to link them with the inheritance of acquired traits. Thus, the parent-of-origin effects in Kammerer's experiments specifically suggest authenticity. Ultimate proof should come from renewed experimentation. To encourage further research, we present a model of possible epigenetic mechanisms.
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Affiliation(s)
- Alexander O Vargas
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias Universidad de Chile, Las Palmeras, Ñuñoa, Santiago
| | - Quirin Krabichler
- Chair of Zoology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
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18
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Alonso-Magdalena P, Rivera FJ, Guerrero-Bosagna C. Bisphenol-A and metabolic diseases: epigenetic, developmental and transgenerational basis. Environ Epigenet 2016; 2:dvw022. [PMID: 29492299 PMCID: PMC5804535 DOI: 10.1093/eep/dvw022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 05/24/2023]
Abstract
Exposure to environmental toxicants is now accepted as a factor contributing to the increasing incidence of obesity and metabolic diseases around the world. Such environmental compounds are known as 'obesogens'. Among them, bisphenol-A (BPA) is the most widespread and ubiquitous compound affecting humans and animals. Laboratory animal work has provided conclusive evidence that early-life exposure to BPA is particularly effective in predisposing individuals to weight gain. Embryonic exposure to BPA is reported to generate metabolic disturbances later in life, such as obesity and diabetes. When BPA administration is combined with a high-fat diet, there is an exacerbation in the development of metabolic disorders. Remarkably, upon BPA exposure of gestating females, metabolic disturbances have been found both in the offspring and later in life in the mothers themselves. When considering the metabolic effects generated by an early developmental exposure to BPA, one of the questions that arises is the role of precursor cells in the etiology of metabolic disorders. Current evidence shows that BPA and other endocrine disruptors have the ability to alter fat tissue development and growth by affecting the capacity to generate functional adipocytes, as well as their rate of differentiation to specific cell types. Epigenetic mechanisms seem to be involved in the BPA-induced effects related to obesity, as they have been described in both in vitro and in vivo models. Moreover, recent reports also show that developmental exposure to BPA generates abnormalities that can be transmitted to future generations, in a process called as transgenerational epigenetic inheritance.
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Affiliation(s)
| | - Francisco J. Rivera
- Laboratory of Stem Cells and Neuroregeneration, Institute of Anatomy, Histology and Pathology, Faculty of Medicine and Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile
- Institute for Molecular Regenerative Medicine and Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus University, Salzburg, Austria
| | - Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
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Guerrero-Bosagna C. High type II error and interpretation inconsistencies when attempting to refute transgenerational epigenetic inheritance. Genome Biol 2016; 17:153. [PMID: 27405453 PMCID: PMC4943006 DOI: 10.1186/s13059-016-0982-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/10/2016] [Indexed: 12/03/2022] Open
Abstract
A recently published article in Genome Biology attempts to refute important aspects of the phenomenon of transgenerational epigenetic inheritance (TEI). An alternative explanation of the data is offered here, showing that TEI is indeed not contradicted. Please see related Correspondence article: www.dx.doi.org/10.1186/s13059-016-0981-5 and related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0619-z
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58 183, Sweden.
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20
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Pértille F, Guerrero-Bosagna C, Silva VHD, Boschiero C, Nunes JDRDS, Ledur MC, Jensen P, Coutinho LL. High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing. Sci Rep 2016; 6:26929. [PMID: 27220827 PMCID: PMC4879531 DOI: 10.1038/srep26929] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/10/2016] [Indexed: 12/23/2022] Open
Abstract
Chicken genotyping is becoming common practice in conventional animal breeding improvement. Despite the power of high-throughput methods for genotyping, their high cost limits large scale use in animal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and cost-effective genotyping by sequence approach developed in plants, for its application in chickens. Here we describe the successful genotyping of a large number of chickens (462) using CornellGBS approach. Genomic DNA was cleaved with the PstI enzyme, ligated to adapters with barcodes identifying individual animals, and then sequenced on Illumina platform. After filtering parameters were applied, 134,528 SNPs were identified in our experimental population of chickens. Of these SNPs, 67,096 had a minimum taxon call rate of 90% and were considered 'unique tags'. Interestingly, 20.7% of these unique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs were concordant with a previous Whole Chicken-genome re-sequencing dataset used for validation purposes. The application of CornellGBS in chickens showed high performance to infer SNPs, particularly in exonic regions and microchromosomes. This approach represents a cost-effective (~US$50/sample) and powerful alternative to current genotyping methods, which has the potential to improve whole-genome selection (WGS), and genome-wide association studies (GWAS) in chicken production.
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Affiliation(s)
- Fábio Pértille
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Carlos Guerrero-Bosagna
- IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Vinicius Henrique da Silva
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Clarissa Boschiero
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - José de Ribamar da Silva Nunes
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Mônica Corrêa Ledur
- Brazilian Agricultural Research Corporation (EMBRAPA) Swine &Poultry, Concórdia, Santa Catarina, Brazil
| | - Per Jensen
- IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
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Abstract
A variety of environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. This involves the germline transmission of epigenetic information between generations. Exposure specific transgenerational sperm epimutations have been previously observed. The current study was designed to investigate the potential role genetic mutations have in the process, using copy number variations (CNV). In the first (F1) generation following exposure, negligible CNV were identified; however, in the transgenerational F3 generation, a significant increase in CNV was observed in the sperm. The genome-wide locations of differential DNA methylation regions (epimutations) and genetic mutations (CNV) were investigated. Observations suggest the environmental induction of the epigenetic transgenerational inheritance of sperm epimutations promote genome instability, such that genetic CNV mutations are acquired in later generations. A combination of epigenetics and genetics is suggested to be involved in the transgenerational phenotypes. The ability of environmental factors to promote epigenetic inheritance that subsequently promotes genetic mutations is a significant advance in our understanding of how the environment impacts disease and evolution.
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Affiliation(s)
- Michael K Skinner
- a Center for Reproductive Biology; School of Biological Sciences; Washington State University ; Pullman , WA USA
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22
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Lind L, Lind PM, Lejonklou MH, Dunder L, Bergman Å, Guerrero-Bosagna C, Lampa E, Lee HK, Legler J, Nadal A, Pak YK, Phipps RP, Vandenberg LN, Zalko D, Ågerstrand M, Öberg M, Blumberg B, Heindel JJ, Birnbaum LS. Uppsala Consensus Statement on Environmental Contaminants and the Global Obesity Epidemic. Environ Health Perspect 2016; 124:A81-3. [PMID: 27135406 PMCID: PMC4858400 DOI: 10.1289/ehp.1511115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Summary: From the lectures presented at the 2nd International Workshop on Obesity and Environmental Contaminants, which was held in Uppsala, Sweden, on 8–9 October 2015, it became evident that the findings from numerous animal and epidemiological studies are consistent with the hypothesis that environmental contaminants could contribute to the global obesity epidemic. To increase awareness of this important issue among scientists, regulatory agencies, politicians, chemical industry management, and the general public, the authors summarize compelling scientific evidence that supports the hypothesis and discuss actions that could restrict the possible harmful effects of environmental contaminants on obesity.
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Affiliation(s)
- Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Address correspondence to L. Lind, Department of Medical Sciences, Akademiska sjukhuset, Entrance 40, Plan 5, Uppsala University, 75185, Uppsala, Sweden. Telephone: 46186114959. E-mail:
| | - P. Monica Lind
- Department of Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden
- Address correspondence to L. Lind, Department of Medical Sciences, Akademiska sjukhuset, Entrance 40, Plan 5, Uppsala University, 75185, Uppsala, Sweden. Telephone: 46186114959. E-mail:
| | - Margareta H. Lejonklou
- Department of Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden
| | - Linda Dunder
- Department of Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden
| | - Åke Bergman
- Swedish Toxicology Sciences Research Center (Swetox), Södertalje, Sweden
| | | | - Erik Lampa
- Uppsala Clinical Research (UCR) Center, Uppsala, Sweden
| | - Hong Kyu Lee
- Department of Internal Medicine, College of Medicine, Eulji University, Seoul, South Korea
| | - Juliette Legler
- Institute for Environmental Studies, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Angel Nadal
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, CIBERDEM Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Elche, Alicante, Spain
| | - Youngmi Kim Pak
- Department of Physiology, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Richard P. Phipps
- Department of Environmental Medicine, University of Rochester, Rochester, New York, USA
| | - Laura N. Vandenberg
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Daniel Zalko
- Institut National de la Recherche Agronomique (INRA) UMR1331 (Unité Mixe de Recherche 1331), Toxalim (Research Centre in Food Toxicology), Toulouse, France
- University of Toulouse, INPT (Institut National Polytechnique de Toulouse), UPS (Universite Paul Sabatier), Toulouse, France
| | - Marlene Ågerstrand
- Department of Environmental Science and Analytic Chemistry, Stockholm University, Stockholm, Sweden
| | - Mattias Öberg
- Swedish Toxicology Sciences Research Center (Swetox), Södertalje, Sweden
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
| | - Jerrold J. Heindel
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, USA
| | - Linda S. Birnbaum
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, USA
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Willems E, Guerrero-Bosagna C, Decuypere E, Janssens S, Buyse J, Buys N, Jensen P, Everaert N. Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model. Sci Rep 2016; 6:20837. [PMID: 26861190 PMCID: PMC4748411 DOI: 10.1038/srep20837] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/07/2016] [Indexed: 11/17/2022] Open
Abstract
Previously, long-term effects on body weight and reproductive performance have been demonstrated in the chicken model of prenatal protein undernutrition by albumen removal. Introduction of such persistent alterations in phenotype suggests stable changes in gene expression. Therefore, a genome-wide screening of the hepatic transcriptome by RNA-Seq was performed in adult hens. The albumen-deprived hens were created by partial removal of the albumen from eggs and replacement with saline early during embryonic development. Results were compared to sham-manipulated hens and non-manipulated hens. Grouping of the differentially expressed (DE) genes according to biological functions revealed the involvement of processes such as ‘embryonic and organismal development’ and ‘reproductive system development and function’. Molecular pathways that were altered were ‘amino acid metabolism’, ‘carbohydrate metabolism’ and ‘protein synthesis’. Three key central genes interacting with many DE genes were identified: UBC, NR3C1, and ELAVL1. The DNA methylation of 9 DE genes and 3 key central genes was examined by MeDIP-qPCR. The DNA methylation of a fragment (UBC_3) of the UBC gene was increased in the albumen-deprived hens compared to the non-manipulated hens. In conclusion, these results demonstrated that prenatal protein undernutrition by albumen removal leads to long-term alterations of the hepatic transcriptome in the chicken.
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Affiliation(s)
- Els Willems
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium.,Linköping University, IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping 581 83, Sweden
| | - Carlos Guerrero-Bosagna
- Linköping University, IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping 581 83, Sweden
| | - Eddy Decuypere
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Steven Janssens
- KU Leuven, Department of Biosystems, Research Group Livestock Genetics, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Johan Buyse
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Nadine Buys
- KU Leuven, Department of Biosystems, Research Group Livestock Genetics, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Per Jensen
- Linköping University, IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping 581 83, Sweden
| | - Nadia Everaert
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium.,University of Liège, Gembloux Agro-Bio Tech, Precision Livestock and Nutrition Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
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Abstract
Methylated DNA immunoprecipitation (MeDIP) is one of the most widely used methods to evaluate DNA methylation on a whole genome scale, and involves the capture of the methylated fraction of the DNA by an antibody specific to methyl-cytosine. MeDIP was initially coupled with microarray hybridization to detect local DNA methylation enrichments along the genome. More recently, MeDIP has been coupled with next generation sequencing, which highlights its current and future applicability. In previous studies in which MeDIP was applied, the protocol took around 3 days to be performed. Given the importance of MeDIP for studies involving DNA methylation, it was important to optimize the method in order to deliver faster turnouts. The present article describes optimization steps of the MeDIP method. The length of the procedure was reduced in half without compromising the quality of the results. This was achieved by:Reduction of the number of washes in different stages of the protocol, after a careful evaluation of the number of indispensable washes. Reduction of reaction times for detaching methylated DNA fragments from the complex agarose beads:antibody. Modification of the methods to purify methylated DNA, which incorporates new devices and procedures, and eliminates a lengthy phenol and chloroform:isoamyl alcohol extraction.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
| | - Per Jensen
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
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Guerrero-Bosagna C, Jensen P. Globalization, climate change, and transgenerational epigenetic inheritance: will our descendants be at risk? Clin Epigenetics 2015; 7:8. [PMID: 25628767 PMCID: PMC4307899 DOI: 10.1186/s13148-014-0043-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 12/26/2014] [Indexed: 12/14/2022] Open
Abstract
Transgenerational epigenetic inheritance has gained increased attention due to the possibility that exposure to environmental contaminants induce diseases that propagate across generations through epigenomic alterations in gametes. In laboratory animals, exposure to environmental toxicants such as fungicides, pesticides, or plastic compounds has been shown to produce abnormal reproductive or metabolic phenotypes that are transgenerationally transmitted. Human exposures to environmental toxicants have increased due to industrialization and globalization, as well as the incidence of diseases shown to be transgenerationally transmitted in animal models. This new knowledge poses an urgent call to study transgenerational consequences of current human exposures to environmental toxicants.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58 183 Sweden
| | - Per Jensen
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58 183 Sweden
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Skinner MK, Guerrero-Bosagna C. Role of CpG deserts in the epigenetic transgenerational inheritance of differential DNA methylation regions. BMC Genomics 2014; 15:692. [PMID: 25142051 PMCID: PMC4149044 DOI: 10.1186/1471-2164-15-692] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/15/2014] [Indexed: 12/31/2022] Open
Abstract
Background Previously a variety of environmental toxicants were found to promote the epigenetic transgenerational inheritance of disease through differential DNA methylation regions (DMRs), termed epimutations, present in sperm. The transgenerational epimutations in sperm and somatic cells identified in a number of previous studies were further investigated. Results The epimutations from six different environmental exposures were found to be predominantly exposure specific with negligible overlap. The current report describes a major genomic feature of all the unique epimutations identified (535) as a very low (<10 CpG/100 bp) CpG density in sperm and somatic cells associated with transgenerational disease. The genomic locations of these epimutations were found to contain DMRs with small clusters of CpG within a general region of very low density CpG. The potential role of these epimutations on gene expression is suggested to be important. Conclusions Observations suggest a potential regulatory role for lower density CpG regions termed “CpG deserts”. The potential evolutionary origins of these regions is also discussed.
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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.
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Manikkam M, Haque MM, Guerrero-Bosagna C, Nilsson EE, Skinner MK. Pesticide methoxychlor promotes the epigenetic transgenerational inheritance of adult-onset disease through the female germline. PLoS One 2014; 9:e102091. [PMID: 25057798 PMCID: PMC4109920 DOI: 10.1371/journal.pone.0102091] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/13/2014] [Indexed: 01/19/2023] Open
Abstract
Environmental compounds including fungicides, plastics, pesticides, dioxin and hydrocarbons can promote the epigenetic transgenerational inheritance of adult-onset disease in future generation progeny following ancestral exposure during the critical period of fetal gonadal sex determination. This study examined the actions of the pesticide methoxychlor to promote the epigenetic transgenerational inheritance of adult-onset disease and associated differential DNA methylation regions (i.e. epimutations) in sperm. Gestating F0 generation female rats were transiently exposed to methoxychlor during fetal gonadal development (gestation days 8 to 14) and then adult-onset disease was evaluated in adult F1 and F3 (great-grand offspring) generation progeny for control (vehicle exposed) and methoxychlor lineage offspring. There were increases in the incidence of kidney disease, ovary disease, and obesity in the methoxychlor lineage animals. In females and males the incidence of disease increased in both the F1 and the F3 generations and the incidence of multiple disease increased in the F3 generation. There was increased disease incidence in F4 generation reverse outcross (female) offspring indicating disease transmission was primarily transmitted through the female germline. Analysis of the F3 generation sperm epigenome of the methoxychlor lineage males identified differentially DNA methylated regions (DMR) termed epimutations in a genome-wide gene promoters analysis. These epimutations were found to be methoxychlor exposure specific in comparison with other exposure specific sperm epimutation signatures. Observations indicate that the pesticide methoxychlor has the potential to promote the epigenetic transgenerational inheritance of disease and the sperm epimutations appear to provide exposure specific epigenetic biomarkers for transgenerational disease and ancestral environmental exposures.
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Affiliation(s)
- Mohan Manikkam
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - M. Muksitul Haque
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Eric E. Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, 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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Guerrero-Bosagna C, Weeks S, Skinner MK. Identification of genomic features in environmentally induced epigenetic transgenerational inherited sperm epimutations. PLoS One 2014; 9:e100194. [PMID: 24937757 PMCID: PMC4061094 DOI: 10.1371/journal.pone.0100194] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 05/22/2014] [Indexed: 11/19/2022] Open
Abstract
A variety of environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. The process involves exposure of a gestating female and the developing fetus to environmental factors that promote permanent alterations in the epigenetic programming of the germline. The molecular aspects of the phenomenon involve epigenetic modifications (epimutations) in the germline (e.g. sperm) that are transmitted to subsequent generations. The current study integrates previously described experimental epigenomic transgenerational data and web-based bioinformatic analyses to identify genomic features associated with these transgenerationally transmitted epimutations. A previously identified genomic feature associated with these epimutations is a low CpG density (<12/100bp). The current observations suggest the transgenerational differential DNA methylation regions (DMR) in sperm contain unique consensus DNA sequence motifs, zinc finger motifs and G-quadruplex sequences. Interaction of molecular factors with these sequences could alter chromatin structure and accessibility of proteins with DNA methyltransferases to alter de novo DNA methylation patterns. G-quadruplex regions can promote the opening of the chromatin that may influence the action of DNA methyltransferases, or factors interacting with them, for the establishment of epigenetic marks. Zinc finger binding factors can also promote this chromatin remodeling and influence the expression of non-coding RNA. The current study identified genomic features associated with sperm epimutations that may explain in part how these sites become susceptible for transgenerational programming.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Physics, Biology and Chemistry, Linköping University, Linköping, Sweden
| | - Shelby Weeks
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Guerrero-Bosagna C, Skinner MK. Environmentally induced epigenetic transgenerational inheritance of male infertility. Curr Opin Genet Dev 2014; 26:79-88. [PMID: 25104619 PMCID: PMC4252707 DOI: 10.1016/j.gde.2014.06.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 06/05/2014] [Accepted: 06/17/2014] [Indexed: 11/26/2022]
Abstract
Decreasing male fertility has been observed for the past fifty years. Examples of affected reproductive parameters include decreases in sperm count and sperm quality and increases in testicular cancer, cryptorchidism and hypospadias. Exposures to environmental toxicants during fetal development and early postnatal life have been shown to promote infertility. Environmental exposures inducing epigenetic changes related to male infertility range from life style, occupational exposures, environmental toxicants and nutrition. Exposures during fetal gonadal sex determination have been shown to alter the epigenetic programming of the germline that then can transmit this altered epigenetic information to subsequent generations in the absence of any exposures. This environmentally induced epigenetic transgenerational inheritance of disease will be a component of the etiology of male infertility.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behaviourial Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, United States.
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Abstract
Environmental exposures to factors such as toxicants or nutrition can have impacts on testis biology and male fertility. The ability of these factors to influence epigenetic mechanisms in early life exposures or from ancestral exposures will be reviewed. A growing number of examples suggest environmental epigenetics will be a critical factor to consider in male reproduction.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
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Skinner MK, Manikkam M, Tracey R, Guerrero-Bosagna C, Haque M, Nilsson EE. Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity. BMC Med 2013; 11:228. [PMID: 24228800 PMCID: PMC3853586 DOI: 10.1186/1741-7015-11-228] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/27/2013] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Ancestral environmental exposures to a variety of environmental factors and toxicants have been shown to promote the epigenetic transgenerational inheritance of adult onset disease. The present work examined the potential transgenerational actions of the insecticide dichlorodiphenyltrichloroethane (DDT) on obesity and associated disease. METHODS Outbred gestating female rats were transiently exposed to a vehicle control or DDT and the F1 generation offspring bred to generate the F2 generation and F2 generation bred to generate the F3 generation. The F1 and F3 generation control and DDT lineage rats were aged and various pathologies investigated. The F3 generation male sperm were collected to investigate methylation between the control and DDT lineage male sperm. RESULTS The F1 generation offspring (directly exposed as a fetus) derived from the F0 generation exposed gestating female rats were not found to develop obesity. The F1 generation DDT lineage animals did develop kidney disease, prostate disease, ovary disease and tumor development as adults. Interestingly, the F3 generation (great grand-offspring) had over 50% of males and females develop obesity. Several transgenerational diseases previously shown to be associated with metabolic syndrome and obesity were observed in the testis, ovary and kidney. The transgenerational transmission of disease was through both female (egg) and male (sperm) germlines. F3 generation sperm epimutations, differential DNA methylation regions (DMR), induced by DDT were identified. A number of the genes associated with the DMR have previously been shown to be associated with obesity. CONCLUSIONS Observations indicate ancestral exposure to DDT can promote obesity and associated disease transgenerationally. The etiology of disease such as obesity may be in part due to environmentally induced epigenetic transgenerational inheritance.
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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.
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Skinner MK, Guerrero-Bosagna C, Haque M, Nilsson E, Bhandari R, McCarrey JR. Environmentally induced transgenerational epigenetic reprogramming of primordial germ cells and the subsequent germ line. PLoS One 2013; 8:e66318. [PMID: 23869203 PMCID: PMC3712023 DOI: 10.1371/journal.pone.0066318] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/03/2013] [Indexed: 12/15/2022] Open
Abstract
A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germ line are those associated with primordial germ cell development and subsequent fetal germline development. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation germline transcriptome and epigenome (DNA methylation) were altered transgenerationally. Interestingly, disruptions in DNA methylation patterns and altered transcriptomes were distinct between germ cells at the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DNA methylation abnormalities (epimutations) and transcriptional alterations were observed in the E13 germ cells than in the E16 germ cells. These observations indicate that altered transgenerational epigenetic reprogramming and function of the male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, USA.
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Tracey R, Manikkam M, Guerrero-Bosagna C, Skinner MK. Hydrocarbons (jet fuel JP-8) induce epigenetic transgenerational inheritance of obesity, reproductive disease and sperm epimutations. Reprod Toxicol 2013; 36:104-16. [PMID: 23453003 PMCID: PMC3587983 DOI: 10.1016/j.reprotox.2012.11.011] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 10/16/2012] [Accepted: 11/23/2012] [Indexed: 02/08/2023]
Abstract
Environmental compounds have been shown to promote epigenetic transgenerational inheritance of disease. The current study was designed to determine if a hydrocarbon mixture involving jet fuel (JP-8) promotes epigenetic transgenerational inheritance of disease. Gestating F0 generation female rats were transiently exposed during the fetal gonadal development period. The direct exposure F1 generation had an increased incidence of kidney abnormalities in both females and males, prostate and pubertal abnormalities in males, and primordial follicle loss and polycystic ovarian disease in females. The first transgenerational generation is the F3 generation, and the jet fuel lineage had an increased incidence of primordial follicle loss and polycystic ovarian disease in females, and obesity in both females and males. Analysis of the jet fuel lineage F3 generation sperm epigenome identified 33 differential DNA methylation regions, termed epimutations. Observations demonstrate hydrocarbons can promote epigenetic transgenerational inheritance of disease and sperm epimutations, potential biomarkers for ancestral exposures.
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MESH Headings
- Abnormalities, Drug-Induced/metabolism
- Abnormalities, Drug-Induced/pathology
- Abnormalities, Multiple/chemically induced
- Abnormalities, Multiple/metabolism
- Abnormalities, Multiple/pathology
- Animals
- DNA Methylation/drug effects
- Epigenesis, Genetic/drug effects
- Female
- Genitalia, Male/abnormalities
- Genitalia, Male/drug effects
- Genitalia, Male/metabolism
- Genitalia, Male/pathology
- Hydrocarbons/toxicity
- Infertility, Female/chemically induced
- Infertility, Female/genetics
- Infertility, Female/metabolism
- Infertility, Female/pathology
- Infertility, Male/chemically induced
- Infertility, Male/genetics
- Infertility, Male/metabolism
- Infertility, Male/pathology
- Male
- Maternal Exposure/adverse effects
- Mutagens/toxicity
- Mutation/drug effects
- Obesity/chemically induced
- Obesity/genetics
- Obesity/metabolism
- Obesity/pathology
- Ovary/abnormalities
- Ovary/drug effects
- Ovary/metabolism
- Ovary/pathology
- Paternal Exposure/adverse effects
- Pregnancy
- Random Allocation
- Rats
- Rats, Sprague-Dawley
- Spermatozoa/drug effects
- Spermatozoa/metabolism
- Spermatozoa/pathology
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Affiliation(s)
- Rebecca Tracey
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. Plastics derived endocrine disruptors (BPA, DEHP and DBP) induce epigenetic transgenerational inheritance of obesity, reproductive disease and sperm epimutations. PLoS One 2013. [PMID: 23359474 DOI: 10.1371/journal.pone.0055387\rpone-d-12-15587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Environmental compounds are known to promote epigenetic transgenerational inheritance of adult onset disease in subsequent generations (F1-F3) following ancestral exposure during fetal gonadal sex determination. The current study was designed to determine if a mixture of plastic derived endocrine disruptor compounds bisphenol-A (BPA), bis(2-ethylhexyl)phthalate (DEHP) and dibutyl phthalate (DBP) at two different doses promoted epigenetic transgenerational inheritance of adult onset disease and associated DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to either the "plastics" or "lower dose plastics" mixture during embryonic days 8 to 14 of gonadal sex determination and the incidence of adult onset disease was evaluated in F1 and F3 generation rats. There were significant increases in the incidence of total disease/abnormalities in F1 and F3 generation male and female animals from plastics lineages. Pubertal abnormalities, testis disease, obesity, and ovarian disease (primary ovarian insufficiency and polycystic ovaries) were increased in the F3 generation animals. Kidney and prostate disease were only observed in the direct fetally exposed F1 generation plastic lineage animals. Analysis of the plastics lineage F3 generation sperm epigenome previously identified 197 differential DNA methylation regions (DMR) in gene promoters, termed epimutations. A number of these transgenerational DMR form a unique direct connection gene network and have previously been shown to correlate with the pathologies identified. Observations demonstrate that a mixture of plastic derived compounds, BPA and phthalates, can promote epigenetic transgenerational inheritance of adult onset disease. The sperm DMR provide potential epigenetic biomarkers for transgenerational disease and/or ancestral environmental exposures.
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Affiliation(s)
- Mohan Manikkam
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, USA
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Guerrero-Bosagna C, Covert TR, Haque MM, Settles M, Nilsson EE, Anway MD, Skinner MK. Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers. Reprod Toxicol 2012; 34:694-707. [PMID: 23041264 PMCID: PMC3513496 DOI: 10.1016/j.reprotox.2012.09.005] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 01/20/2023]
Abstract
The endocrine disruptor vinclozolin has previously been shown to promote epigenetic transgenerational inheritance of adult onset disease in the rat. The current study was designed to investigate the transgenerational actions of vinclozolin on the mouse. Transient exposure of the F0 generation gestating female during gonadal sex determination promoted transgenerational adult onset disease in F3 generation male and female mice, including spermatogenic cell defects, testicular abnormalities, prostate abnormalities, kidney abnormalities and polycystic ovarian disease. Pathology analysis demonstrated 75% of the vinclozolin lineage animals developed disease with 34% having two or more different disease states. Interestingly, the vinclozolin induced transgenerational disease was observed in the outbred CD-1 strain, but not the inbred 129 mouse strain. Analysis of the F3 generation sperm epigenome identified differential DNA methylation regions that can potentially be utilized as epigenetic biomarkers for transgenerational exposure and disease.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. Dioxin (TCDD) induces epigenetic transgenerational inheritance of adult onset disease and sperm epimutations. PLoS One 2012; 7:e46249. [PMID: 23049995 PMCID: PMC3458876 DOI: 10.1371/journal.pone.0046249] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/30/2012] [Indexed: 01/05/2023] Open
Abstract
Environmental compounds can promote epigenetic transgenerational inheritance of adult-onset disease in subsequent generations following ancestral exposure during fetal gonadal sex determination. The current study examined the ability of dioxin (2,3,7,8-tetrachlorodibenzo[p]dioxin, TCDD) to promote epigenetic transgenerational inheritance of disease and DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to dioxin during fetal day 8 to 14 and adult-onset disease was evaluated in F1 and F3 generation rats. The incidences of total disease and multiple disease increased in F1 and F3 generations. Prostate disease, ovarian primordial follicle loss and polycystic ovary disease were increased in F1 generation dioxin lineage. Kidney disease in males, pubertal abnormalities in females, ovarian primordial follicle loss and polycystic ovary disease were increased in F3 generation dioxin lineage animals. Analysis of the F3 generation sperm epigenome identified 50 differentially DNA methylated regions (DMR) in gene promoters. These DMR provide potential epigenetic biomarkers for transgenerational disease and ancestral environmental exposures. Observations demonstrate dioxin exposure of a gestating female promotes epigenetic transgenerational inheritance of adult onset disease and sperm epimutations.
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Affiliation(s)
- Mohan Manikkam
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Rebecca Tracey
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. Pesticide and insect repellent mixture (permethrin and DEET) induces epigenetic transgenerational inheritance of disease and sperm epimutations. Reprod Toxicol 2012; 34:708-19. [PMID: 22975477 DOI: 10.1016/j.reprotox.2012.08.010] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 08/02/2012] [Accepted: 08/03/2012] [Indexed: 11/16/2022]
Abstract
Environmental compounds are known to promote epigenetic transgenerational inheritance of disease. The current study was designed to determine if a "pesticide mixture" (pesticide permethrin and insect repellent N,N-diethyl-meta-toluamide, DEET) promotes epigenetic transgenerational inheritance of disease and associated DNA methylation epimutations in sperm. Gestating F0 generation female rats were exposed during fetal gonadal sex determination and the incidence of disease evaluated in F1 and F3 generations. There were significant increases in the incidence of total diseases in animals from pesticide lineage F1 and F3 generation animals. Pubertal abnormalities, testis disease, and ovarian disease (primordial follicle loss and polycystic ovarian disease) were increased in F3 generation animals. Analysis of the pesticide lineage F3 generation sperm epigenome identified 363 differential DNA methylation regions (DMR) termed epimutations. Observations demonstrate that a pesticide mixture (permethrin and DEET) can promote epigenetic transgenerational inheritance of adult onset disease and potential sperm epigenetic biomarkers for ancestral environmental exposures.
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Affiliation(s)
- Mohan Manikkam
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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Guerrero-Bosagna C, Skinner MK. Environmentally induced epigenetic transgenerational inheritance of phenotype and disease. Mol Cell Endocrinol 2012; 354:3-8. [PMID: 22020198 PMCID: PMC3312615 DOI: 10.1016/j.mce.2011.10.004] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/03/2011] [Accepted: 10/05/2011] [Indexed: 12/15/2022]
Abstract
Environmental epigenetics has an important role in regulating phenotype formation or disease etiology. The ability of environmental factors and exposures early in life to alter somatic cell epigenomes and subsequent development is a critical factor in how environment affects biology. Environmental epigenetics provides a molecular mechanism to explain long term effects of environment on the development of altered phenotypes and "emergent" properties, which the "genetic determinism" paradigm cannot. When environmental factors permanently alter the germ line epigenome, then epigenetic transgenerational inheritance of these environmentally altered phenotypes and diseases can occur. This environmental epigenetic transgenerational inheritance of phenotype and disease is reviewed with a systems biology perspective.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Nilsson E, Larsen G, Manikkam M, Guerrero-Bosagna C, Savenkova MI, Skinner MK. Environmentally induced epigenetic transgenerational inheritance of ovarian disease. PLoS One 2012; 7:e36129. [PMID: 22570695 PMCID: PMC3343040 DOI: 10.1371/journal.pone.0036129] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/30/2012] [Indexed: 01/21/2023] Open
Abstract
The actions of environmental toxicants and relevant mixtures in promoting the epigenetic transgenerational inheritance of ovarian disease was investigated with the use of a fungicide, a pesticide mixture, a plastic mixture, dioxin and a hydrocarbon mixture. After transient exposure of an F0 gestating female rat during embryonic gonadal sex determination, the F1 and F3 generation progeny adult onset ovarian disease was assessed. Transgenerational disease phenotypes observed included an increase in cysts resembling human polycystic ovarian disease (PCO) and a decrease in the ovarian primordial follicle pool size resembling primary ovarian insufficiency (POI). The F3 generation granulosa cells were isolated and found to have a transgenerational effect on the transcriptome and epigenome (differential DNA methylation). Epigenetic biomarkers for environmental exposure and associated gene networks were identified. Epigenetic transgenerational inheritance of ovarian disease states was induced by all the different classes of environmental compounds, suggesting a role of environmental epigenetics in ovarian disease etiology.
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Affiliation(s)
| | | | | | | | | | - Michael K. Skinner
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
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Manikkam M, Guerrero-Bosagna C, Tracey R, Haque MM, Skinner MK. Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures. PLoS One 2012; 7:e31901. [PMID: 22389676 PMCID: PMC3289630 DOI: 10.1371/journal.pone.0031901] [Citation(s) in RCA: 302] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/15/2012] [Indexed: 11/23/2022] Open
Abstract
Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm) that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET), a plastic mixture (bisphenol A and phthalates), dioxin (TCDD) and a hydrocarbon mixture (jet fuel, JP8). After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation). Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR) were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.
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Affiliation(s)
| | | | | | | | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
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Skinner MK, Manikkam M, Guerrero-Bosagna C. Epigenetic transgenerational actions of endocrine disruptors. Reprod Toxicol 2010; 31:337-43. [PMID: 21055462 DOI: 10.1016/j.reprotox.2010.10.012] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 10/21/2010] [Accepted: 10/26/2010] [Indexed: 12/22/2022]
Abstract
Environmental factors have a significant impact on biology. Therefore, environmental toxicants through similar mechanisms can modulate biological systems to influence physiology and promote disease states. The majority of environmental toxicants do not have the capacity to modulate DNA sequence, but can alter the epigenome. In the event an environmental toxicant such as an endocrine disruptor modifies the epigenome of a somatic cell, this may promote disease in the individual exposed, but not be transmitted to the next generation. In the event a toxicant modifies the epigenome of the germ line permanently, then the disease promoted can become transgenerationaly transmitted to subsequent progeny. The current review focuses on the ability of environmental factors such as endocrine disruptors to promote transgenerational phenotypes.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States.
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Guerrero-Bosagna C, Settles M, Lucker B, Skinner MK. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome. PLoS One 2010; 5. [PMID: 20927350 PMCID: PMC2948035 DOI: 10.1371/journal.pone.0013100] [Citation(s) in RCA: 289] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 08/31/2010] [Indexed: 12/16/2022] Open
Abstract
Previous observations have demonstrated that embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes transgenerational adult onset disease such as male infertility, kidney disease, prostate disease, immune abnormalities and tumor development. The current study investigates genome-wide promoter DNA methylation alterations in the sperm of F3 generation rats whose F0 generation mother was exposed to vinclozolin. A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip) procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. Mass spectrometry bisulfite analysis was used to map the CpG DNA methylation and 16 differential DNA methylation regions were confirmed, while the remainder could not be analyzed due to bisulfite technical limitations. Analysis of these validated regions identified a consensus DNA sequence (motif) that associated with 75% of the promoters. Interestingly, only 16.8% of a random set of 125 promoters contained this motif. One candidate promoter (Fam111a) was found to be due to a copy number variation (CNV) and not a methylation change, suggesting initial alterations in the germline epigenome may promote genetic abnormalities such as induced CNV in later generations. This study identifies differential DNA methylation sites in promoter regions three generations after the initial exposure and identifies common genome features present in these regions. In addition to primary epimutations, a potential indirect genetic abnormality was identified, and both are postulated to be involved in the epigenetic transgenerational inheritance observed. This study confirms that an environmental agent has the ability to induce epigenetic transgenerational changes in the sperm epigenome.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Matthew Settles
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Ben Lucker
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Skinner MK, Manikkam M, Guerrero-Bosagna C. Epigenetic transgenerational actions of environmental factors in disease etiology. Trends Endocrinol Metab 2010; 21:214-22. [PMID: 20074974 PMCID: PMC2848884 DOI: 10.1016/j.tem.2009.12.007] [Citation(s) in RCA: 458] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 12/09/2009] [Accepted: 12/14/2009] [Indexed: 12/26/2022]
Abstract
The ability of environmental factors to promote a phenotype or disease state not only in the individual exposed but also in subsequent progeny for successive generations is termed transgenerational inheritance. The majority of environmental factors such as nutrition or toxicants such as endocrine disruptors do not promote genetic mutations or alterations in DNA sequence. However, these factors do have the capacity to alter the epigenome. Epimutations in the germline that become permanently programmed can allow transmission of epigenetic transgenerational phenotypes. This review provides an overview of the epigenetics and biology of how environmental factors can promote transgenerational phenotypes and disease.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4236, USA.
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Abstract
The ability of an environmental factor or toxicant to promote a phenotype or disease state not only in the individual exposed, but also in subsequent progeny for multiple generations, is termed transgenerational inheritance. The majority of environmental agents do not promote genetic mutations or alterations in DNA sequence, but do have the capacity to alter the epigenome. Although most environmental exposures will influence somatic cells and not allow the transgenerational transmission of a phenotype, the ability of an environmental factor to reprogram the germline epigenome can promote a transgenerational inheritance of phenotypes and disease states. A limited number of critical developmental periods exist when environmental signals can produce a significant epigenetic reprogramming of the germline. In this review, the ability of environmental factors or toxicants to promote epigenetic transgenerational phenotypes is reviewed.
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Hirsch S, Ronco AM, Guerrero-Bosagna C, de la Maza MP, Leiva L, Barrera G, Llanos M, Alliende MA, Silva F, Bunout D. Methylation status in healthy subjects with normal and high serum folate concentration. Nutrition 2008; 24:1103-9. [PMID: 18653314 DOI: 10.1016/j.nut.2008.05.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/05/2008] [Accepted: 05/18/2008] [Indexed: 11/24/2022]
Abstract
OBJECTIVE We assessed the impact of high serum folate concentration on erythrocyte S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH) concentrations, SAM/SAH ratio, CpG methylation levels across the promoter region of the extracellular superoxide dismutase (ec-SOD) gene, and ec-SOD activity in healthy men. METHODS Serum folate levels were measured in 111 subjects who were categorized in quintiles according to their folate status. Subjects located at the lowest, middle, and upper quintiles were selected for assessment of SAM and SAH by high-performance liquid chromatography, C677T genotype of the 5,10-methylenetetrahydrofolate reductase (MTHFR) gene, ec-SOD methylation of CpG sites in lymphocytes genomic DNA by bisulfate treatment, and ec-SOD activity by a chemical assay. RESULTS Sixteen subjects were in the lowest serum folate quintile (<23.6 nmol/L), 17 in the middle (>34-<42 nmol/L), and 14 in the highest (>45nmol/L). SAM concentration was higher in the upper than in the middle and lowest quintiles (5.57 +/- 1.58, 2.52 +/- 0.97, 2.29 +/- 1.2 micromol/L; P < 0.0001). SAH concentration was higher in the upper compared with the lowest quintile (0.76 +/- 0.24 versus 0.52 +/- 0.23 micromol/L, P < 0.001). There were no differences in the SAM/SAH ratio, ec-SOD activity, methylation status of CpG sites of the ec-SOD gene, and TMTHFR C677T genotype between groups. CONCLUSION Serum folate concentrations in the highest quintile among healthy humans are associated with increased erythrocyte SAM and SAH concentrations, but not with SAM/SAH ratio or with methylation levels of CpG sites across the promoter region of the ec-SOD gene. Further research is required to determine if these findings are beneficial or harmful.
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Affiliation(s)
- Sandra Hirsch
- Aging and Chronic Diseases Laboratory, INTA, University of Chile, Santiago, Chile.
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Guerrero-Bosagna C, Sabat P, Valladares L. Environmental signaling and evolutionary change: can exposure of pregnant mammals to environmental estrogens lead to epigenetically induced evolutionary changes in embryos? Evol Dev 2005; 7:341-50. [PMID: 15982371 DOI: 10.1111/j.1525-142x.2005.05033.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA methylation is one of the epigenetic and hereditary mechanisms regulating genetic expression in mammalian cells. In this review, we propose how certain natural agents, through their dietary consumption, could induce changes in physiological aspects in mammalian mothers, leading to alterations in DNA methylation patterns of the developing fetus and to the emergence of new phenotypes and evolutionary change. Nevertheless, we hypothesize that this process would require (i) certain key periods in the ontogeny of the organism where the environmental stimuli could produce effects, (ii) particular environmental agents as such stimuli, and (iii) that a genomic persistent change be consequently produced in a population. Depending on the persistence of the environmental stimuli and on whether the affected genes are imprinted genes, induced changes in DNA methylation patterns could become persistent. Moreover, some fragments could be more frequently methylated than others over several generations, leading to biased base change and evolutionary consequences.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Laboratorio de Hormonas y Receptores, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.
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Ronco AM, Garrido A, Llanos MN, Guerrero-Bosagna C, Tamayo D, Hirsch S. Effect of homocysteine, folates, and cobalamin on endothelial cell- and copper-induced LDL oxidation. Lipids 2005; 40:259-64. [PMID: 15957251 DOI: 10.1007/s11745-005-1380-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxidation of LDL contributes to endothelial dysfunction and atherosclerosis. This process could be associated with hyperhomocysteinemia, a condition that can be reduced after folic acid treatment. Because a reduction in LDL oxidation may improve endothelial function, we studied the effect of some vitamins (folic acid, 5-methyltetrahydrofolic acid, and vitamin B-12) on LDL oxidation, either in the presence or absence of homocysteine. For this purpose, two in vitro systems were used: an endothelial cell-catalyzed LDL oxidation system and a cell-free copper-initiated LDL oxidation system. The kinetics of copper-catalyzed LDL oxidation was determined by continuous monitoring of the production of conjugated dienes in the reaction medium. TBARS production, a parameter of lipid peroxidation, was also evaluated. In both in vitro systems, only 5-methyltetrahydrofolic acid was able to decrease TBARS production in a concentration-dependent manner, independently of the presence or absence of homocysteine. In the copper-induced LDL oxidation system, vitamin B-12 and 5-methyltetrahydrofolic acid increased the lag time of conjugated diene production by 25 and 47%, respectively, suggesting that both vitamins in this system had antioxidant properties. Folic acid was unable to show antioxidant properties when included in either in vitro system. The results demonstrate that 5-methyltetrahydrofolic acid and vitamin B-12 are important protective agents against LDL oxidative modifications.
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Affiliation(s)
- Ana María Ronco
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Casilla 138-11, Santiago, Chile.
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