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AlSabah AA, Alsalmi M, Massie R, Bilodeau MC, Campeau PM, McGraw S, D'Agostino MD. An adult patient with Tatton-Brown-Rahman syndrome caused by a novel DNMT3A variant and axonal polyneuropathy. Am J Med Genet A 2024; 194:e63484. [PMID: 38041495 DOI: 10.1002/ajmg.a.63484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
Tatton-Brown-Rahman syndrome (TBRS) is a rare autosomal dominant overgrowth syndrome first reported in 2014 and caused by pathogenic variants in the DNA methyltransferase 3A (DNMT3A) gene. All individuals reported to date share a phenotype of somatic overgrowth, dysmorphic features, and intellectual disability. Peripheral neuropathy was not described in these cases. We report an adult patient with TBRS caused by a novel pathogenic DNMT3A variant (NM_175629.2: c.2036G>A, p.(Arg688His)) harboring an axonal length-dependent sensory-motor polyneuropathy. Extensive laboratory and molecular genetic work-up failed to identify alternative causes for this patient's neuropathy. We propose that axonal neuropathy may be a novel, age-dependent phenotypic feature in adults with TBRS and suggest that this syndrome should be considered in the differential diagnosis of patients with overgrowth, cognitive and psychiatric difficulties, and peripheral neuropathy.
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Affiliation(s)
- Al-Alya AlSabah
- Department of Neurology and Neurosurgery, McGill University, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | - Mohammed Alsalmi
- Department of Neurology and Neurosurgery, McGill University, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | - Rami Massie
- Department of Neurology and Neurosurgery, McGill University, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | - Marie-Claude Bilodeau
- Clinique de Psychiatrie, Santé Mentale et Dépendances, CIUSSS MCQ, Hôpital Sainte-Croix, Drummondville, Quebec, Canada
| | - Philippe M Campeau
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Serge McGraw
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
- Department of Obstetrics and Gynecology, Université de Montreal, Montreal, Quebec, Canada
| | - Maria Daniela D'Agostino
- Division of Medical Genetics, Departments of Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
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2
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Choudhury S, Anne A, Singh M, Chaillet JR, Mohan KN. DNMT1 Y495C mutation interferes with maintenance methylation of imprinting control regions. Int J Biochem Cell Biol 2024; 169:106535. [PMID: 38281697 DOI: 10.1016/j.biocel.2024.106535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Hereditary Sensory and Autonomic Neuropathy Type 1E (HSAN1E) is a rare autosomal dominant neurological disorder due to missense mutations in DNA methyltransferase 1 (DNMT1). To investigate the nature of the dominant effect, we compared methylomes of transgenic R1wtDnmt1 and R1Dnmt1Y495C mouse embryonic stem cells (mESCs) overexpressing WT and the mutant mouse proteins respectively, with the R1 (wild-type) cells. In case of R1Dnmt1Y495C, 15 out of the 20 imprinting control regions were hypomethylated with transcript level dysregulation of multiple imprinted genes in ESCs and neurons. Non-imprinted regions, minor satellites, major satellites, LINE1 and IAP repeats were unaffected. These data mirror the specific imprinting defects associated with transient removal of DNMT1 in mESCs, deletion of the maternal-effect DNMT1o variant in preimplantation mouse embryos, and in part, reprogramming to naïve human iPSCs. This is the first DNMT1 mutation demonstrated to specifically affect Imprinting Control Regions (ICRs), and reinforces the differences in maintenance methylation of ICRs over non-imprinted regions. Consistent with nervous system abnormalities in the HSAN1E disorder and involvement of imprinted genes in normal development and neurogenesis, R1Dnmt1Y495C cells showed dysregulated pluripotency and neuron marker genes, and yielded more slender, shorter, and extensively branched neurons. We speculate that R1Dnmt1Y495C cells produce predominantly dimers containing mutant proteins, leading to a gradual and specific loss of ICR methylation during early human development.
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Affiliation(s)
- Sumana Choudhury
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - John Richard Chaillet
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India.
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3
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Karahan G, Martel J, Rahimi S, Farag M, Matias F, MacFarlane AJ, Chan D, Trasler J. Higher incidence of embryonic defects in mouse offspring conceived with assisted reproduction from fathers with sperm epimutations. Hum Mol Genet 2023; 33:48-63. [PMID: 37740387 PMCID: PMC10729866 DOI: 10.1093/hmg/ddad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/30/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023] Open
Abstract
Assisted reproductive technologies (ART) account for 1-6% of births in developed countries. While most children conceived are healthy, increases in birth and genomic imprinting defects have been reported; such abnormal outcomes have been attributed to underlying parental infertility and/or the ART used. Here, we assessed whether paternal genetic and lifestyle factors, that are associated with male infertility and affect the sperm epigenome, can influence ART outcomes. We examined how paternal factors, haploinsufficiency for Dnmt3L, an important co-factor for DNA methylation reactions, and/or diet-induced obesity, in combination with ART (superovulation, in vitro fertilization, embryo culture and embryo transfer), could adversely influence embryo development and DNA methylation patterning in mice. While male mice fed high-fat diets (HFD) gained weight and showed perturbed metabolic health, their sperm DNA methylation was minimally affected by the diet. In contrast, Dnmt3L haploinsufficiency induced a marked loss of DNA methylation in sperm; notably, regions affected were associated with neurodevelopmental pathways and enriched in young retrotransposons, sequences that can have functional consequences in the next generation. Following ART, placental imprinted gene methylation and growth parameters were impacted by one or both paternal factors. For embryos conceived by natural conception, abnormality rates were similar for WT and Dnmt3L+/- fathers. In contrast, paternal Dnmt3L+/- genotype, as compared to WT fathers, resulted in a 3-fold increase in the incidence of morphological abnormalities in embryos generated by ART. Together, the results indicate that embryonic morphological and epigenetic defects associated with ART may be exacerbated in offspring conceived by fathers with sperm epimutations.
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Affiliation(s)
- Gurbet Karahan
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Sophia Rahimi
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Mena Farag
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
| | - Fernando Matias
- Nutrition Research Division, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | | | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
- Department of Pediatrics, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
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4
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Breton-Larrivée M, Elder E, Legault LM, Langford-Avelar A, MacFarlane AJ, McGraw S. Mitigating the detrimental developmental impact of early fetal alcohol exposure using a maternal methyl donor-enriched diet. FASEB J 2023; 37:e22829. [PMID: 36856720 DOI: 10.1096/fj.202201564r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/23/2023] [Accepted: 02/03/2023] [Indexed: 03/02/2023]
Abstract
Fetal alcohol exposure at any stage of pregnancy can lead to fetal alcohol spectrum disorder (FASD), a group of life-long conditions characterized by congenital malformations, as well as cognitive, behavioral, and emotional impairments. The teratogenic effects of alcohol have long been publicized; yet fetal alcohol exposure is one of the most common preventable causes of birth defects. Currently, alcohol abstinence during pregnancy is the best and only way to prevent FASD. However, alcohol consumption remains astoundingly prevalent among pregnant women; therefore, additional measures need to be made available to help protect the developing embryo before irreparable damage is done. Maternal nutritional interventions using methyl donors have been investigated as potential preventative measures to mitigate the adverse effects of fetal alcohol exposure. Here, we show that a single acute preimplantation (E2.5; 8-cell stage) fetal alcohol exposure (2 × 2.5 g/kg ethanol with a 2h interval) in mice leads to long-term FASD-like morphological phenotypes (e.g. growth restriction, brain malformations, skeletal delays) in late-gestation embryos (E18.5) and demonstrate that supplementing the maternal diet with a combination of four methyl donor nutrients, folic acid, choline, betaine, and vitamin B12, prior to conception and throughout gestation effectively reduces the incidence and severity of alcohol-induced morphological defects without altering DNA methylation status of imprinting control regions and regulation of associated imprinted genes. This study clearly supports that preimplantation embryos are vulnerable to the teratogenic effects of alcohol, emphasizes the dangers of maternal alcohol consumption during early gestation, and provides a potential proactive maternal nutritional intervention to minimize FASD progression, reinforcing the importance of adequate preconception and prenatal nutrition.
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Affiliation(s)
- Mélanie Breton-Larrivée
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Elizabeth Elder
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Lisa-Marie Legault
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Alexandra Langford-Avelar
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Amanda J MacFarlane
- Agriculture, Food, and Nutrition Evidence Center, Texas A&M University, Texas, Fort Worth, USA.,Department of Nutrition, Texas A&M University, College Station, Texas, USA
| | - Serge McGraw
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada.,Department of Obstetrics and Gynecology, Université de Montréal, Montreal, Canada
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5
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Li S. Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns. Cancer Treat Res 2023; 190:375-393. [PMID: 38113008 DOI: 10.1007/978-3-031-45654-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Tumor cells evolve through space and time, generating genetically and phenotypically diverse cancer cell populations that are continually subjected to the selection pressures of their microenvironment and cancer treatment.
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Affiliation(s)
- Sheng Li
- The Jackson Laboratory for Genomic Medicine and Cancer Center, Farmington, USA.
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6
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Ihirwe RG, Martel J, Rahimi S, Trasler J. Protective and sex-specific effects of moderate dose folic acid supplementation on the placenta following assisted reproduction in mice. FASEB J 2023; 37:e22677. [PMID: 36515682 PMCID: PMC10108070 DOI: 10.1096/fj.202201428r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
Epigenetic defects induced by assisted reproductive technologies (ART) have been suggested as a potential mechanism contributing to suboptimal placentation. Here, we hypothesize that ART perturbs DNA methylation (DNAme) and gene expression during early placenta development, leading to abnormal placental phenotypes observed at term. Since folic acid (FA) plays a crucial role in epigenetic regulation, we propose that FA supplementation can rescue ART-induced placental defects. Female mice were placed on a control diet (CD), a moderate 4-fold (FAS4) or high dose 10-fold (FAS10) FA-supplemented diet prior to ART and compared to a natural mating group. ART resulted in 41 and 28 differentially expressed genes (DEGs) in E10.5 female and male placentas, respectively. Many DEGs were implicated in early placenta development and associated with DNAme changes; a number clustered at known imprinting control regions (ICR). In females, FAS4 partially corrected alterations in gene expression while FAS10 showed evidence of male-biased adverse effects. DNAme and gene expression for five genes involved in early placentation (Phlda2, EphB2, Igf2, Peg3, L3mbtl1) were followed up in placentas from normal as well as delayed and abnormal embryos. Phlda2 and Igf2 expression levels were lowest after ART in placentas of female delayed embryos. Moreover, ART concomitantly reduced DNAme at the Kcnq1ot1 ICR which regulates Phlda2 expression; FAS4 partially improved DNAme in a sex-specific manner. In conclusion, ART-associated placental DNAme and transcriptome alterations observed at mid-gestation are sex-specific; they may help explain adverse placental phenotypes detected at term and are partially corrected by maternal moderate dose FA supplementation.
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Affiliation(s)
- Rita Gloria Ihirwe
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Sophia Rahimi
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jacquetta Trasler
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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7
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Legault LM, Doiron K, Breton-Larrivée M, Langford-Avelar A, Lemieux A, Caron M, Jerome-Majewska LA, Sinnett D, McGraw S. Pre-implantation alcohol exposure induces lasting sex-specific DNA methylation programming errors in the developing forebrain. Clin Epigenetics 2021; 13:164. [PMID: 34425890 PMCID: PMC8381495 DOI: 10.1186/s13148-021-01151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/11/2021] [Indexed: 12/26/2022] Open
Abstract
Background Prenatal alcohol exposure is recognized for altering DNA methylation profiles of brain cells during development, and to be part of the molecular basis underpinning Fetal Alcohol Spectrum Disorder (FASD) etiology. However, we have negligible information on the effects of alcohol exposure during pre-implantation, the early embryonic window marked with dynamic DNA methylation reprogramming, and on how this may rewire the brain developmental program. Results Using a pre-clinical in vivo mouse model, we show that a binge-like alcohol exposure during pre-implantation at the 8-cell stage leads to surge in morphological brain defects and adverse developmental outcomes during fetal life. Genome-wide DNA methylation analyses of fetal forebrains uncovered sex-specific alterations, including partial loss of DNA methylation maintenance at imprinting control regions, and abnormal de novo DNA methylation profiles in various biological pathways (e.g., neural/brain development). Conclusion These findings support that alcohol-induced DNA methylation programming deviations during pre-implantation could contribute to the manifestation of neurodevelopmental phenotypes associated with FASD. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01151-0.
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Affiliation(s)
- L M Legault
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - K Doiron
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - M Breton-Larrivée
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - A Langford-Avelar
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - A Lemieux
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - M Caron
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - L A Jerome-Majewska
- McGill University Health Centre Glen Site, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada.,Department of Pediatrics, McGill University, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada
| | - D Sinnett
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Pediatrics, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - S McGraw
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada. .,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada. .,Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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8
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Karahan G, Chan D, Shirane K, McClatchie T, Janssen S, Baltz JM, Lorincz M, Trasler J. Paternal MTHFR deficiency leads to hypomethylation of young retrotransposons and reproductive decline across two successive generations. Development 2021; 148:dev199492. [PMID: 34128976 PMCID: PMC8276981 DOI: 10.1242/dev.199492] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/01/2021] [Indexed: 12/17/2022]
Abstract
5,10-Methylenetetrahydrofolate reductase (MTHFR) is a crucial enzyme in the folate metabolic pathway with a key role in generating methyl groups. As MTHFR deficiency impacts male fertility and sperm DNA methylation, there is the potential for epimutations to be passed to the next generation. Here, we assessed whether the impact of MTHFR deficiency on testis morphology and sperm DNA methylation is exacerbated across generations in mouse. Although MTHFR deficiency in F1 fathers has only minor effects on sperm counts and testis weights and histology, F2 generation sons show further deterioration in reproductive parameters. Extensive loss of DNA methylation is observed in both F1 and F2 sperm, with >80% of sites shared between generations, suggestive of regions consistently susceptible to MTHFR deficiency. These regions are generally methylated during late embryonic germ cell development and are enriched in young retrotransposons. As retrotransposons are resistant to reprogramming of DNA methylation in embryonic germ cells, their hypomethylated state in the sperm of F1 males could contribute to the worsening reproductive phenotype observed in F2 MTHFR-deficient males, compatible with the intergenerational passage of epimutations.
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Affiliation(s)
- Gurbet Karahan
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Kenjiro Shirane
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Taylor McClatchie
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Departments of Obstetrics and Gynecology and Cellular and Molecular Medicine, University of Ottawa Faculty of Medicine, Ottawa, ON K1H 8M5, Canada
| | - Sanne Janssen
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jay M. Baltz
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Departments of Obstetrics and Gynecology and Cellular and Molecular Medicine, University of Ottawa Faculty of Medicine, Ottawa, ON K1H 8M5, Canada
| | - Matthew Lorincz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
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9
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Legault LM, Doiron K, Lemieux A, Caron M, Chan D, Lopes FL, Bourque G, Sinnett D, McGraw S. Developmental genome-wide DNA methylation asymmetry between mouse placenta and embryo. Epigenetics 2020; 15:800-815. [PMID: 32056496 PMCID: PMC7518706 DOI: 10.1080/15592294.2020.1722922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/03/2020] [Accepted: 01/15/2020] [Indexed: 12/27/2022] Open
Abstract
In early embryos, DNA methylation is remodelled to initiate the developmental program but for mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution DNA methylation maps of mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryonic and placental DNA methylation patterns. We show that the asymmetry occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, the de novo methyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially compensate in the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principal de novo methyltransferase, the compensatory DNA methylation mechanism of DNMT3B on DMRs becomes less effective.
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Affiliation(s)
- LM Legault
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
| | - K Doiron
- Research Center of the CHU Sainte-Justine, Montreal, Canada
| | - A Lemieux
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
| | - M Caron
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - D Chan
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - FL Lopes
- School of Veterinary Medicine, São Paulo State University (Unesp), Aracatuba, Brazil
| | - G Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
- Canadian Center for Computational Genomics, Montreal, Quebec, Canada
| | - D Sinnett
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Pediatrics, Université De Montréal, Montreal, Canada
| | - S McGraw
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
- Department of Obstetrics and Gynecology, Université De Montréal, Montreal, Canada
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10
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Rahimi S, Martel J, Karahan G, Angle C, Behan NA, Chan D, MacFarlane AJ, Trasler JM. Moderate maternal folic acid supplementation ameliorates adverse embryonic and epigenetic outcomes associated with assisted reproduction in a mouse model. Hum Reprod 2020; 34:851-862. [PMID: 30989206 DOI: 10.1093/humrep/dez036] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/14/2019] [Indexed: 01/08/2023] Open
Abstract
STUDY QUESTION Could clinically-relevant moderate and/or high dose maternal folic acid supplementation prevent aberrant developmental and epigenetic outcomes associated with assisted reproductive technologies (ART)? SUMMARY ANSWER Our results demonstrate dose-dependent and sex-specific effects of folic acid supplementation in ART and provide evidence that moderate dose supplements may be optimal for both sexes. WHAT IS KNOWN ALREADY Children conceived using ART are at an increased risk for growth and genomic imprinting disorders, often associated with DNA methylation defects. Folic acid supplementation is recommended during pregnancy to prevent adverse offspring outcomes; however, the effects of folic acid supplementation in ART remain unclear. STUDY DESIGN, SIZE, DURATION Outbred female mice were fed three folic acid-supplemented diets, control (rodent daily recommended intake or DRI; CD), moderate (4-fold DRI; 4FASD) or high (10-fold DRI; 10FASD) dose, for six weeks prior to ART and throughout gestation. Mouse ART involved a combination of superovulation, in vitro fertilisation, embryo culture and embryo transfer. PARTICIPANTS/MATERIALS, SETTING, METHODS Midgestation embryos and placentas (n = 74-99/group) were collected; embryos were assessed for developmental delay and gross morphological abnormalities and embryos and placentas were examined for epigenetic defects. We assessed methylation at four imprinted genes (Snrpn, Kcnq1ot1, Peg1 and H19) in matched midgestation embryos and placentas (n = 31-32/group) using bisulfite pyrosequencing. In addition, we examined genome-wide DNA methylation patterns in placentas (n = 6 normal placentas per sex/group) and embryos (n = 6 normal female embryos/group; n = 3 delayed female embryos/group) using reduced representation bisulfite sequencing (RRBS). MAIN RESULTS AND THE ROLE OF CHANCE Moderate, but not high dose supplementation, was associated with a decrease in the proportion of developmentally delayed embryos. Although moderate dose folic acid supplementation reduced DNA methylation variance at certain imprinted genes in embryonic and placental tissues, high dose supplementation exacerbated the negative effects of ART at imprinted loci. Furthermore, folic acid supplements resolved female-biased aberrant imprinted gene methylation. Supplementation was more effective at correcting ART-induced genome-wide methylation defects in male versus female placentas; however, folic acid supplementation also led to additional methylation perturbations which were more pronounced in males. LARGE-SCALE DATA The RRBS data from this study have been submitted to the NCBI Gene Expression Omnibus under the accession number GSE123143. LIMITATIONS REASONS FOR CAUTION Although the combination of mouse ART utilised in this study consisted of techniques commonly used in human fertility clinics, there may be species differences. Therefore, human studies, designed to determine the optimal levels of folic acid supplementation for ART pregnancies, and taking into account foetal sex, are warranted. WIDER IMPLICATIONS OF THE FINDINGS Taken together, our findings support moderation in the dose of folic acid supplements taken during ART. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by the Canadian Institutes of Health Research (FDN-148425). The authors declare no conflict of interest.
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Affiliation(s)
- Sophia Rahimi
- Child Health and Human Development Program (CHHD), Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal QC, Canada.,Department of Human Genetics, McGill University, 3640 rue University, Montréal QC, Canada
| | - Josée Martel
- Child Health and Human Development Program (CHHD), Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal QC, Canada
| | - Gurbet Karahan
- Child Health and Human Development Program (CHHD), Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal QC, Canada.,Department of Human Genetics, McGill University, 3640 rue University, Montréal QC, Canada
| | - Camille Angle
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montréal QC, Canada
| | - Nathalie A Behan
- Nutrition Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa ON, Canada
| | - Donovan Chan
- Child Health and Human Development Program (CHHD), Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal QC, Canada
| | - Amanda J MacFarlane
- Nutrition Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa ON, Canada
| | - Jacquetta M Trasler
- Child Health and Human Development Program (CHHD), Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal QC, Canada.,Department of Human Genetics, McGill University, 3640 rue University, Montréal QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montréal QC, Canada.,Department of Pediatrics, McGill University, 1001 Décarie Boulevard, Montréal QC, Canada
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11
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Ly L, Chan D, Landry M, Angle C, Martel J, Trasler J. Impact of mothers' early life exposure to low or high folate on progeny outcome and DNA methylation patterns. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa018. [PMID: 33240529 PMCID: PMC7673481 DOI: 10.1093/eep/dvaa018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/03/2020] [Accepted: 09/19/2020] [Indexed: 05/14/2023]
Abstract
The dynamic patterning of DNA and histone methylation during oocyte development presents a potentially susceptible time for epigenetic disruption due to early life environmental exposure of future mothers. We investigated whether maternal exposure to folic acid deficient and supplemented diets starting in utero could affect oocytes and cause adverse developmental and epigenetic effects in next generation progeny. Female BALB/c mice (F0) were placed on one of four amino acid defined diets for 4 weeks before pregnancy and throughout gestation and lactation: folic acid control (rodent recommended daily intake; Ctrl), 7-fold folic acid deficient, 10-fold folic acid supplemented or 20-fold folic acid supplemented diets. F1 female pups were weaned onto Ctrl diets, mated to produce the F2 generation and the F2 offspring were examined at E18.5 for developmental and epigenetic abnormalities. Resorption rates were increased and litter sizes decreased amongst F2 E18.5-day litters in the 20-fold folic acid supplemented group. Increases in abnormal embryo outcomes were observed in all three folic acid deficient and supplemented groups. Subtle genome-wide DNA methylation alterations were found in the placentas and brains of F2 offspring in the 7-fold folic acid deficient , 10-fold folic acid supplemented and 20-fold folic acid supplemented groups; in contrast, global and imprinted gene methylation were not affected. The findings show that early life female environmental exposures to both low and high folate prior to oocyte maturation can compromise oocyte quality, adversely affecting offspring of the next generation, in part by altering DNA methylation patterns.
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Affiliation(s)
- Lundi Ly
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mylène Landry
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Camille Angle
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Correspondence address. Research Institute of the McGill University Health Centre, 1001 Boulevard Décarie, Block E.M.0.3211, Montreal, QC, Canada H4A 3J1. Tel: +1-514-934-1934 (ext. 25235); Fax: +1-514-933-9673; E-mail:
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12
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Pierre WC, Legault L, Londono I, McGraw S, Lodygensky GA. Alteration of the brain methylation landscape following postnatal inflammatory injury in rat pups. FASEB J 2020; 34:432-445. [PMID: 31914673 PMCID: PMC6972494 DOI: 10.1096/fj.201901461r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/26/2019] [Accepted: 10/08/2019] [Indexed: 12/18/2022]
Abstract
Preterm infants are vulnerable to inflammation-induced white matter injury (WMI), which is associated with neurocognitive impairment and increased risk of neuropsychiatric diseases in adulthood. Epigenetic mechanisms, particularly DNA methylation, play a role in normal development and modulate the response to pathological challenges. Our aims were to determine how WMI triggered DNA methylation alterations in brains of neonatal rats and if such changes persisted over time. We used a robust model of WMI by injecting lipopolysaccharide (LPS) or sterile saline in the corpus callosum of 3-day-old (P3) rat pups. Brains were collected 24 hours (P4) and 21 days post-injection (P24). We extracted genomic DNA from the brain to establish genome-wide quantitative DNA methylation profiles using reduced representation bisulfite sequencing. Neonatal LPS exposure induced a persistent increased methylation of genes related to nervous system development and a reduced methylation of genes associated with inflammatory pathways. These findings suggest that early-life neuroinflammatory exposure impacts the cerebral methylation landscape with determining widespread epigenetic modifications especially in genes related to neurodevelopment.
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Affiliation(s)
- Wyston C. Pierre
- Department of PediatricsUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Lisa‐Marie Legault
- Department of Biochemistry and Molecular MedicineUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Irene Londono
- Department of PediatricsUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Serge McGraw
- Department of Biochemistry and Molecular MedicineUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
- Department of Obstetrics & GynecologyUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Gregory A. Lodygensky
- Department of PediatricsUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
- Department of Pharmacology and PhysiologyUniversité de MontréalMontréalQCCanada
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13
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Abstract
The first crucial step in the developmental program occurs during pre-implantation, the time after the oocyte has been fertilized and before the embryo implants in the uterus. This period represents a vulnerable window as the epigenome undergoes dynamic changes in DNA methylation profiles. Alterations in the early embryonic reprogramming wave can impair DNA methylation patterns and induce permanent changes to the developmental program, leading to the onset of adverse health outcomes in offspring. Although there is an increasing body of evidence indicating that harmful exposures during pre-implantation embryo development can trigger lasting epigenetic alterations in offspring, the mechanisms are still not fully understood. Since physiological or pathological changes in DNA methylation can occur as a response to environmental cues, proper environmental milieu plays a critical role in the success of embryonic development. In this review, we depict the mechanisms behind the embryonic epigenetic reprogramming of DNA methylation and highlight how maternal environmental stressors (e.g., alcohol, heat stress, nutrient availability) during pre-implantation and assisted reproductive technology procedures affect development and DNA methylation marks.
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Affiliation(s)
- Mélanie Breton-Larrivée
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada
| | - Elizabeth Elder
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada
| | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada.,Department of Obstetrics & Gynecology, Université de Montréal, Research Center of the CHU Sainte-Justine, Montréal, Canada
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14
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Legault LM, Chan D, McGraw S. Rapid Multiplexed Reduced Representation Bisulfite Sequencing Library Prep (rRRBS). Bio Protoc 2019; 9:e3171. [PMID: 33654977 DOI: 10.21769/bioprotoc.3171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/21/2019] [Accepted: 02/23/2019] [Indexed: 12/09/2022] Open
Abstract
DNA methylation is a common mechanism of epigenetic regulation involved in transcriptional modulation and genome stability. With the evolution of next-generation sequencing technologies, establishing quantitative genome-wide DNA methylation profiles is becoming routine in many laboratories. However, many of these approaches take several days to accomplish and use subjective PCR methods to amplify sequencing libraries, which can induce amplification bias. Here we propose a rapid Reduced Representation Bisulfite Sequencing (rRRBS) protocol to minimize PCR amplification bias and reduce total time of multiplexed library construction. In this modified approach, the precise quantification of the final library amplification step is accomplished and monitored by qPCR, instead of using standard PCR and gel electrophoresis, to determine the appropriate number of cycles to perform. The main advantages of this rRRBS method are: i) Reduced amount of amplification enzyme used for library prep, ii) Reduced number of PCR cycles resulting in less PCR amplification bias, and iii) Preparation of quality multiplexed rRRBS libraries in only ~2 days.
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Affiliation(s)
- Lisa-Marie Legault
- CHU Sainte-Justine Research Center, Montréal, Quebec, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Serge McGraw
- CHU Sainte-Justine Research Center, Montréal, Quebec, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada.,Department of Obstetrics & Gynecology, Université de Montréal, Montréal, Quebec, Canada
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15
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Chu A, Casero D, Thamotharan S, Wadehra M, Cosi A, Devaskar SU. The Placental Transcriptome in Late Gestational Hypoxia Resulting in Murine Intrauterine Growth Restriction Parallels Increased Risk of Adult Cardiometabolic Disease. Sci Rep 2019; 9:1243. [PMID: 30718791 PMCID: PMC6361888 DOI: 10.1038/s41598-018-37627-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/11/2018] [Indexed: 12/19/2022] Open
Abstract
Intrauterine growth restriction (IUGR) enhances risk for adult onset cardiovascular disease (CVD). The mechanisms underlying IUGR are poorly understood, though inadequate blood flow and oxygen/nutrient provision are considered common endpoints. Based on evidence in humans linking IUGR to adult CVD, we hypothesized that in murine pregnancy, maternal late gestational hypoxia (LG-H) exposure resulting in IUGR would result in (1) placental transcriptome changes linked to risk for later CVD, and 2) adult phenotypes of CVD in the IUGR offspring. After subjecting pregnant mice to hypoxia (10.5% oxygen) from gestational day (GD) 14.5 to 18.5, we undertook RNA sequencing from GD19 placentas. Functional analysis suggested multiple changes in structural and functional genes important for placental health and function, with maximal dysregulation involving vascular and nutrient transport pathways. Concordantly, a ~10% decrease in birthweights and ~30% decrease in litter size was observed, supportive of placental insufficiency. We also found that the LG-H IUGR offspring exhibit increased risk for CVD at 4 months of age, manifesting as hypertension, increased abdominal fat, elevated leptin and total cholesterol concentrations. In summary, this animal model of IUGR links the placental transcriptional response to the stressor of gestational hypoxia to increased risk of developing cardiometabolic disease.
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Affiliation(s)
- Alison Chu
- David Geffen School of Medicine at UCLA, Department of Pediatrics, Division of Neonatology & Developmental Biology, Neonatal Research Center of the UCLA Children's Discovery and Innovation Institute, 10833 Le Conte Avenue, MDCC B2-375, Los Angeles, CA, 90095, USA.
| | - David Casero
- David Geffen School of Medicine at UCLA, Department of Pathology and Laboratory Medicine, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East, Los Angeles, CA, 90095, USA.
| | - Shanthie Thamotharan
- David Geffen School of Medicine at UCLA, Department of Pediatrics, Division of Neonatology & Developmental Biology, Neonatal Research Center of the UCLA Children's Discovery and Innovation Institute, 10833 Le Conte Avenue, MDCC B2-375, Los Angeles, CA, 90095, USA
| | - Madhuri Wadehra
- David Geffen School of Medicine at UCLA, Department of Pathology and Laboratory Medicine, 4525 MacDonald Research Laboratories, Los Angeles, CA, 90095, USA
| | - Amy Cosi
- David Geffen School of Medicine at UCLA, Department of Pediatrics, Division of Neonatology & Developmental Biology, Neonatal Research Center of the UCLA Children's Discovery and Innovation Institute, 10833 Le Conte Avenue, MDCC B2-375, Los Angeles, CA, 90095, USA
| | - Sherin U Devaskar
- David Geffen School of Medicine at UCLA, Department of Pediatrics, Division of Neonatology & Developmental Biology, Neonatal Research Center of the UCLA Children's Discovery and Innovation Institute, 10833 Le Conte Avenue, MDCC B2-375, Los Angeles, CA, 90095, USA
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16
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Aarabi M, Christensen KE, Chan D, Leclerc D, Landry M, Ly L, Rozen R, Trasler J. Testicular MTHFR deficiency may explain sperm DNA hypomethylation associated with high dose folic acid supplementation. Hum Mol Genet 2019; 27:1123-1135. [PMID: 29360980 DOI: 10.1093/hmg/ddy021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/09/2018] [Indexed: 12/24/2022] Open
Abstract
Supplementation with high doses of folic acid, an important mediator of one-carbon transfers for DNA methylation, is used clinically to improve sperm parameters in infertile men. We recently detected an unexpected loss of DNA methylation in the sperm of idiopathic infertile men after 6 months of daily supplementation with 5 mg folic acid (>10× the daily recommended intake-DRI), exacerbated in men homozygous for a common variant in the gene encoding an important enzyme in folate metabolism, methylenetetrahydrofolate reductase (MTHFR 677C>T). To investigate the epigenomic impact and mechanism underlying effects of folic acid on male germ cells, wild-type and heterozygote mice for a targeted inactivation of the Mthfr gene were fed high-dose folic acid (10× the DRI) or control diets (CDs) for 6 months. No changes were detected in general health, sperm counts or methylation of imprinted genes. Reduced representation bisulfite sequencing revealed sperm DNA hypomethylation in Mthfr+/- mice on the 10× diets. Wild-type mice demonstrated sperm hypomethylation only with a very high dose (20×) of folic acid for 12 months. Testicular MTHFR protein levels decreased significantly in wild-type mice on the 20× diet but not in those on the 10× diet, suggesting a possible role for MTHFR deficiency in sperm DNA hypomethylation. In-depth analysis of the folic acid-exposed sperm DNA methylome suggested mouse/human susceptibility of sequences with potential importance to germ cell and embryo development. Our data provide evidence for a similar cross-species response to high dose folic acid supplementation, of sperm DNA hypomethylation, and implicate MTHFR downregulation as a possible mechanism.
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Affiliation(s)
- Mahmoud Aarabi
- Department of Human Genetics, McGill University, Montreal, QC H4A 3J1, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Karen E Christensen
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Daniel Leclerc
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Mylène Landry
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Lundi Ly
- Department of Human Genetics, McGill University, Montreal, QC H4A 3J1, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Rima Rozen
- Department of Human Genetics, McGill University, Montreal, QC H4A 3J1, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada.,Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC H4A 3J1, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada.,Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada.,Department of Pharmacology & Therapeutics, McGill University, Montreal, QC H4A 3J1, Canada
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17
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Abstract
Epigenetic information refers to heritable changes in gene expression that occur without modifications at the DNA sequence level. These changes are orchestrated by different epigenetic mechanisms such as DNA methylation, posttranslational modifications of histones, and the presence of noncoding RNAs. Epigenetic information regulates chromatin structure to confer cell-specific gene expression.The sperm epigenome is the result of three periods of global resetting during men's life. Germ cell epigenome reprogramming is designed to allow cell totipotency and to prevent the transmission of epimutations via spermatozoa. At the end of these reprogramming events, the sperm epigenome has a very specific epigenetic pattern that is a footprint of past reprogramming events and has an influence on embryo development.Several data demonstrate that not all regions of the epigenome are erased during the reprogramming periods, suggesting the transmission of epigenetic information from fathers to offspring via spermatozoa. Moreover, it is becoming increasingly clear that the sperm epigenome is sensitive to environmental factors during the process of gamete differentiation, suggesting the plasticity of the sperm epigenetic signature according to the circumstances of the individual's life.In this chapter, we provided strong evidences about the association between variations of the sperm epigenome and the exposure to environmental factors. Moreover, we will present data about how epigenetic mechanisms are candidates for transferring paternal environmental information to offspring.
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18
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Yarychkivska O, Shahabuddin Z, Comfort N, Boulard M, Bestor TH. BAH domains and a histone-like motif in DNA methyltransferase 1 (DNMT1) regulate de novo and maintenance methylation in vivo. J Biol Chem 2018; 293:19466-19475. [PMID: 30341171 DOI: 10.1074/jbc.ra118.004612] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/12/2018] [Indexed: 12/31/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is a multidomain protein believed to be involved only in the passive transmission of genomic methylation patterns via maintenance methylation. The mechanisms that regulate DNMT1 activity and targeting are complex and poorly understood. We used embryonic stem (ES) cells to investigate the function of the uncharacterized bromo-adjacent homology (BAH) domains and the glycine-lysine (GK) repeats that join the regulatory and catalytic domains of DNMT1. We removed the BAH domains by means of a CRISPR/Cas9-mediated deletion within the endogenous Dnmt1 locus. The internally deleted protein failed to associate with replication foci during S phase in vivo and lost the ability to mediate maintenance methylation. The data indicate that ablation of the BAH domains causes DNMT1 to be excluded from replication foci even in the presence of the replication focus-targeting sequence (RFTS). The GK repeats resemble the N-terminal tails of histones H2A and H4 and are normally acetylated. Substitution of lysines within the GK repeats with arginines to prevent acetylation did not alter the maintenance activity of DNMT1 but unexpectedly activated de novo methylation of paternal imprinting control regions (ICRs) in mouse ES cells; maternal ICRs remained unmethylated. We propose a model under which DNMT1 deposits paternal imprints in male germ cells in an acetylation-dependent manner. These data reveal that DNMT1 responds to multiple regulatory inputs that control its localization as well as its activity and is not purely a maintenance methyltransferase but can participate in the de novo methylation of a small but essential compartment of the genome.
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Affiliation(s)
| | | | - Nicole Comfort
- Environmental Health Science, College of Physicians and Surgeons of Columbia University, New York, New York 10032, and
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19
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Legault LM, Bertrand-Lehouillier V, McGraw S. Pre-implantation alcohol exposure and developmental programming of FASD: an epigenetic perspective. Biochem Cell Biol 2018; 96:117-130. [DOI: 10.1139/bcb-2017-0141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Exposure to alcohol during in-utero development can permanently change the developmental programming of physiological responses, thereby increasing the risk of neurological illnesses during childhood and later adverse health outcomes associated with fetal alcohol spectrum disorder (FASD). There is an increasing body of evidence indicating that exposure to alcohol during gestation triggers lasting epigenetic alterations in offspring, long after the initial insult; together, these studies support the role of epigenetics in FASD etiology. However, we still have little information about how ethanol interferes with the fundamental epigenetic reprogramming wave (e.g., erasure and re-establishment of DNA methylation marks) that characterizes pre-implantation embryo development. This review examines key epigenetic processes that occur during pre-implantation development and especially focus on the current knowledge regarding how prenatal exposure to alcohol during this period could affect the developmental programming of the early stage pre-implantation embryo. We will also outline the current limitations of studies examining the in-vivo and in-vitro effects of alcohol exposure on embryos and underline the next critical steps to be taken if we want to better understand the implicated mechanisms to strengthen the translational potential for epigenetic markers for non-invasive early detection, and the treatment of newborns that have higher risk of developing FASD.
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Affiliation(s)
- Lisa-Marie Legault
- Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, QC H3T 1C5, Canada
| | - Virginie Bertrand-Lehouillier
- Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, QC H3T 1C5, Canada
| | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, QC H3T 1C5, Canada
- Obstetrics and Gynecology, Université de Montreal, Research Center of the CHU Sainte-Justine, Montreal, Canada
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20
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Whidden L, Martel J, Rahimi S, Chaillet JR, Chan D, Trasler JM. Compromised oocyte quality and assisted reproduction contribute to sex-specific effects on offspring outcomes and epigenetic patterning. Hum Mol Genet 2018; 25:4649-4660. [PMID: 28173052 DOI: 10.1093/hmg/ddw293] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/04/2016] [Accepted: 08/25/2016] [Indexed: 11/13/2022] Open
Abstract
Clinical studies have revealed an increased incidence of growth and genomic imprinting disorders in children conceived using assisted reproductive technologies (ARTs), and aberrant DNA methylation has been implicated. We propose that compromised oocyte quality associated with female infertility may make embryos more susceptible to the induction of epigenetic defects by ART. DNA methylation patterns in the preimplantation embryo are dependent on the oocyte-specific DNA methyltransferase 1o (DNMT1o), levels of which are decreased in mature oocytes of aging females. Here, we assessed the effects of maternal deficiency in DNMT1o (Dnmt1Δ1o/+) in combination with superovulation and embryo transfer on offspring DNA methylation and development. We demonstrated a significant increase in the rates of morphological abnormalities in offspring collected from Dnmt1Δ1o/+ females only when combined with ART. Together, maternal oocyte DNMT1o deficiency and ART resulted in an accentuation of placental imprinting defects and the induction of genome-wide DNA methylation alterations, which were exacerbated in the placenta compared to the embryo. Significant sex-specific trends were also apparent, with a preponderance of DNA hypomethylation in females. Among genic regions affected, a significant enrichment for neurodevelopmental pathways was observed. Taken together, our results demonstrate that oocyte DNMT1o-deficiency exacerbates genome-wide DNA methylation abnormalities induced by ART in a sex-specific manner and plays a role in mediating poor embryonic outcome.
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Affiliation(s)
- Laura Whidden
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Josée Martel
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Sophia Rahimi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - J Richard Chaillet
- Department of OB/GYN and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donovan Chan
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jacquetta M Trasler
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada,Department of Human Genetics, McGill University, Montreal, QC, Canada,Department of Pediatrics, McGill University, Montreal, QC, Canada
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Canovas S, Ross PJ, Kelsey G, Coy P. DNA Methylation in Embryo Development: Epigenetic Impact of ART (Assisted Reproductive Technologies). Bioessays 2017; 39. [DOI: 10.1002/bies.201700106] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/14/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Sebastian Canovas
- Physiology of Reproduction Group; University of Murcia; Murcia Spain
- IMIB-Arrixaca Spain; Murcia Spain
| | - Pablo J. Ross
- Department of Animal Science; UC Davis; Davis CA USA
| | - Gavin Kelsey
- Epigenetics Programme; The Babraham Institute; Cambridge UK
| | - Pilar Coy
- Physiology of Reproduction Group; University of Murcia; Murcia Spain
- IMIB-Arrixaca Spain; Murcia Spain
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22
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Zheng F, Wu J, Tang Q, Xiao Q, Wu W, Hann SS. The enhancement of combination of berberine and metformin in inhibition of DNMT1 gene expression through interplay of SP1 and PDPK1. J Cell Mol Med 2017; 22:600-612. [PMID: 28840963 PMCID: PMC5742731 DOI: 10.1111/jcmm.13347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
Abstract
Berberine (BBR), one of active alkaloid found in the rhizome, exhibited anti‐cancer properties. We have showed that BBR inhibited growth of non‐small cell lung cancer (NSCLC) cells through mitogen‐activated protein kinase (MAPK)‐mediated increase in forkhead box O3a (FOXO3a). However, the in‐depth mechanism underlying the anti‐tumor effects still remained to be elucidated. Herein, we further confirmed that BBR not only induced cell cycle arrest, but also reduced migration and invasion of NSCLC cells. Mechanistically, we observed that BBR reduced 3‐phosphoinositide‐dependent protein kinase‐1 (PDPK1) and transcription factor SP1 protein expressions. Exogenously expressed SP1 overcame BBR‐inhibited PDPK1 expression. Moreover, BBR inhibited DNA methyltransferase 1 (DNMT1) gene expression and overexpressed DNMT1 resisted BBR‐inhibited cell growth. Intriguingly, overexpressed PDPK1 antagonized BBR‐inhibited SP1 and DNMT1 expressions. Finally, metformin enhanced the effects of BBR both in vitro and in vivo. Collectively, we observe that BBR inhibits proliferation of NSCLC cells through inhibition of SP1 and PDPK1; this results in a reduction of DNMT1 expression. The interplay of PDPK1 and SP1 contributes to the inhibition of DNMT1 in response to BBR. In addition, there is a synergy of BBR and metformin. This study uncovers a new mechanism of BBR in combination with metformin for NSCLC‐associated therapy.
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Affiliation(s)
- Fang Zheng
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - JingJing Wu
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Qing Tang
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Qian Xiao
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - WanYin Wu
- Department of Medical Oncology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Swei Sunny Hann
- Department of Medical Oncology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
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23
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Wu J, Tang Q, Yang L, Chen Y, Zheng F, Hann SS. Interplay of DNA methyltransferase 1 and EZH2 through inactivation of Stat3 contributes to β-elemene-inhibited growth of nasopharyngeal carcinoma cells. Sci Rep 2017; 7:509. [PMID: 28360411 PMCID: PMC5428779 DOI: 10.1038/s41598-017-00626-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 03/07/2017] [Indexed: 12/22/2022] Open
Abstract
β-elemene, a compound extracted from Curcuma wenyujin plant, exhibits anticancer activity in many cancer types. However, the detailed mechanism by which β-elemene inhibits growth of nasopharyngeal carcinoma (NPC) cells remains unknown. We showed that β-elemene reduced phosphorylation of signal transducer and activator of transcription 3 (Stat3), and protein expressions of DNA methyltransferase 1 (DNMT1) and enhancer of zeste homolog 2 (EZH2). Exogenously expressed Stat3 antagonized the effect of β-elemene on DNMT1 and EZH2 expressions. Furthermore, overexpressions of DNMT1 and EZH2 reversed the effect of β-elemene on phosphorylation of Stat3 and cell growth inhibition. Intriguingly, exogenously expressed DNMT1 overcame β-elemene-inhibited EZH2 protein expression and promoter activity. On the contrary, silencing of EZH2 and DNMT1 genes feedback strengthened the effect of β-elemene on phosphorylation of Stat3. Consistent with this, β-elemene inhibited tumor growth, phosphorylation of Stat3, expressions of DNMT1 and EZH2 in a mouse xenograft model. Collectively, this study shows that β-elemene inhibits NPC cell growth via inactivation of Stat3, and reduces DNMT1 and EZH2 expressions. The interplay of DNMT1 and EZH2, and the mutual regulations among Stat3, EZH2 and DNMT1 contribute to the overall responses of β-elemene. This study uncovers a novel mechanism by which β-elemene inhibits growth of NPC cells.
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Affiliation(s)
- JingJing Wu
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China
| | - Qing Tang
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China
| | - LiJuan Yang
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China
| | - YuQing Chen
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China
| | - Fang Zheng
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical Collage, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
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24
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Chan D, McGraw S, Klein K, Wallock LM, Konermann C, Plass C, Chan P, Robaire B, Jacob RA, Greenwood CMT, Trasler JM. Stability of the human sperm DNA methylome to folic acid fortification and short-term supplementation. Hum Reprod 2016; 32:272-283. [PMID: 27994001 DOI: 10.1093/humrep/dew308] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/26/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
STUDY QUESTION Do short-term and long-term exposures to low-dose folic acid supplementation alter DNA methylation in sperm? SUMMARY ANSWER No alterations in sperm DNA methylation patterns were found following the administration of low-dose folic acid supplements of 400 μg/day for 90 days (short-term exposure) or when pre-fortification of food with folic acid and post-fortification sperm samples (long-term exposure) were compared. WHAT IS KNOWN ALREADY Excess dietary folate may be detrimental to health and DNA methylation profiles due to folate's role in one-carbon metabolism and the formation of S-adenosyl methionine, the universal methyl donor. DNA methylation patterns are established in developing male germ cells and have been suggested to be affected by high-dose (5 mg/day) folic acid supplementation. STUDY DESIGN, SIZE, DURATION This is a control versus treatment study where genome-wide sperm DNA methylation patterns were examined prior to fortification of food (1996-1997) in men with no history of infertility at baseline and following 90-day exposure to placebo (n = 9) or supplement containing 400 μg folic acid/day (n = 10). Additionally, pre-fortification sperm DNA methylation profiles (n = 19) were compared with those of a group of post-fortification (post-2004) men (n = 8) who had been exposed for several years to dietary folic acid fortification. PARTICIPANTS/MATERIALS, SETTING, METHODS Blood and seminal plasma folate levels were measured in participants before and following the 90-day treatment with placebo or supplement. Sperm DNA methylation was assessed using the whole-genome and genome-wide techniques, MassArray epityper, restriction landmark genomic scanning, methyl-CpG immunoprecipitation and Illumina HumanMethylation450 Bead Array. MAIN RESULTS AND THE ROLE OF CHANCE Following treatment, supplemented individuals had significantly higher levels of blood and seminal plasma folates compared to placebo. Initial first-generation genome-wide analyses of sperm DNA methylation showed little evidence of changes when comparing pre- and post-treatment samples. With Illumina HumanMethylation450 BeadChip arrays, no significant changes were observed in individual probes following low-level supplementation; when compared with those of the post-fortification cohort, there were also few differences in methylation despite exposure to years of fortified foods. LARGE SCALE DATA Illumina HumanMethylation450 BeadChip data from this study have been submitted to the NCBI Gene Expression Omnibus under the accession number GSE89781. LIMITATIONS, REASONS FOR CAUTION This study was limited to the number of participants available in each cohort, in particular those who were not exposed to early (pre-1998) fortification of food with folic acid. While genome-wide DNA methylation was assessed with several techniques that targeted genic and CpG-rich regions, intergenic regions were less well interrogated. WIDER IMPLICATIONS OF THE FINDINGS Overall, our findings provide evidence that short-term exposure to low-dose folic acid supplements of 400 μg/day, over a period of 3 months, a duration of time that might occur during infertility treatments, has no major impact on the sperm DNA methylome. STUDY FUNDING/COMPETING INTERESTS This work was supported by a grant to J.M.T. from the Canadian Institutes of Health Research (CIHR: MOP-89944). The authors have no conflicts of interest to declare.
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Affiliation(s)
- D Chan
- Departments of Pediatrics and of Human Genetics of McGill University, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Glen Site, 1001 Décarie Boulevard Block E- Room EM0.2236 Montreal, QC H4A 3J1, Canada
| | - S McGraw
- Department of Obstetrics and Gynaecology, Biochemistry and Molecular Medicine of Université de Montréal, Research Center of the Sainte-Justine University Hospital, Montreal, QC H3T 1C5, Canada
| | - K Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - L M Wallock
- Department of Biological Sciences, Diablo Valley College, Pleasant Hill, CA 94523, USA
| | - C Konermann
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - C Plass
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - P Chan
- Royal Victoria Hospital of the McGill University Health Centre and Department of Surgery, McGill University, Montréal, QC H4A 3J1, Canada
| | - B Robaire
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3A 0G4, Canada
| | - R A Jacob
- USDA, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA 95616, USA
| | - C M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.,Departments of Oncology, Epidemiology, Biostatistics and Occupational Health, and Human Genetics, McGill University, Montréal, QC H4A 3J1, Canada
| | - J M Trasler
- Departments of Pediatrics and of Human Genetics of McGill University, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Glen Site, 1001 Décarie Boulevard Block E- Room EM0.2236 Montreal, QC H4A 3J1, Canada .,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3A 0G4, Canada
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25
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Bunkar N, Pathak N, Lohiya NK, Mishra PK. Epigenetics: A key paradigm in reproductive health. Clin Exp Reprod Med 2016; 43:59-81. [PMID: 27358824 PMCID: PMC4925870 DOI: 10.5653/cerm.2016.43.2.59] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/06/2016] [Accepted: 03/16/2016] [Indexed: 12/17/2022] Open
Abstract
It is well established that there is a heritable element of susceptibility to chronic human ailments, yet there is compelling evidence that some components of such heritability are transmitted through non-genetic factors. Due to the complexity of reproductive processes, identifying the inheritance patterns of these factors is not easy. But little doubt exists that besides the genomic backbone, a range of epigenetic cues affect our genetic programme. The inter-generational transmission of epigenetic marks is believed to operate via four principal means that dramatically differ in their information content: DNA methylation, histone modifications, microRNAs and nucleosome positioning. These epigenetic signatures influence the cellular machinery through positive and negative feedback mechanisms either alone or interactively. Understanding how these mechanisms work to activate or deactivate parts of our genetic programme not only on a day-to-day basis but also over generations is an important area of reproductive health research.
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Affiliation(s)
- Neha Bunkar
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India
| | - Neelam Pathak
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Nirmal Kumar Lohiya
- Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Pradyumna Kumar Mishra
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Department of Molecular Biology, National Institute for Research in Environmental Health (ICMR), Bhopal, India
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26
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He H, Ye A, Kim J. Transcriptional Truncation of the Long Coding Imprinted Gene Usp29. PLoS One 2016; 11:e0158004. [PMID: 27327533 PMCID: PMC4915674 DOI: 10.1371/journal.pone.0158004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/08/2016] [Indexed: 11/18/2022] Open
Abstract
Usp29 (Ubiquitin-specific protease 29) is a paternally expressed gene located upstream of another imprinted gene Peg3. In the current study, the transcription of this long coding gene spanning a 250-kb genomic distance was truncated using a knockin allele. According to the results, paternal transmission of the mutant allele resulted in reduced body and litter sizes whereas the maternal transmission caused no obvious effects. In the paternal mutant, the expression levels of Usp29 were reduced to 14-18% level of the wild-type littermates due to the Poly-A signal included in the knockin cassette. Expression analyses further revealed an unusual female-specific up-regulation of the adjacent imprinted gene Zfp264 in the mutant. Consistent with this, the promoter of Zfp264 was hypomethylated only in the female mutant. Interestingly, this female-specific hypomethylation by the knockin allele was not detected in the offspring of an interspecific crossing, indicating its sensitivity to genetic background. Overall, the results suggest that the transcription of Usp29 may be involved in DNA methylation setting of Zfp264 promoter in a sex-specific manner.
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Affiliation(s)
- Hongzhi He
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - An Ye
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States of America
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27
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Hogg K, Western PS. Refurbishing the germline epigenome: Out with the old, in with the new. Semin Cell Dev Biol 2015; 45:104-13. [PMID: 26597001 DOI: 10.1016/j.semcdb.2015.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 09/21/2015] [Indexed: 12/25/2022]
Abstract
Mammalian germline reprogramming involves the erasure and re-establishment of epigenetic information critical for germ cell function and inheritance in offspring. The bi-faceted nature of such reprogramming ensures germline repression of somatic programmes and the establishment of a carefully constructed epigenome essential for fertilisation and embryonic development in the next generation. While the majority of the germline epigenome is erased in preparation for embryonic development, certain genomic sequences remain resistant to this and may represent routes for transmission of epigenetic changes through the germline. Epigenetic reprogramming is regulated by highly conserved epigenetic modifiers, which function to establish, maintain and remove DNA methylation and chromatin modifications. In this review, we discuss recent findings from a considerable body of work illustrating the critical requirement of epigenetic modifiers that influence the epigenetic signature present in mature gametes, and have the potential to affect developmental outcomes in the offspring. We also briefly discuss the similarities of these mechanisms in the human germline and consider the potential for inheritance of epigenetically induced germline genetic errors that could impact on offspring phenotypes.
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Affiliation(s)
- Kirsten Hogg
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC 3168, Australia; Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Patrick S Western
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC 3168, Australia; Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3168, Australia.
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28
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Siklenka K, Erkek S, Godmann M, Lambrot R, McGraw S, Lafleur C, Cohen T, Xia J, Suderman M, Hallett M, Trasler J, Peters AHFM, Kimmins S. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science 2015; 350:aab2006. [PMID: 26449473 DOI: 10.1126/science.aab2006] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/18/2015] [Indexed: 12/28/2022]
Abstract
A father's lifetime experiences can be transmitted to his offspring to affect health and development. However, the mechanisms underlying paternal epigenetic transmission are unclear. Unlike in somatic cells, there are few nucleosomes in sperm, and their function in epigenetic inheritance is unknown. We generated transgenic mice in which overexpression of the histone H3 lysine 4 (H3K4) demethylase KDM1A (also known as LSD1) during spermatogenesis reduced H3K4 dimethylation in sperm. KDM1A overexpression in one generation severely impaired development and survivability of offspring. These defects persisted transgenerationally in the absence of KDM1A germline expression and were associated with altered RNA profiles in sperm and offspring. We show that epigenetic inheritance of aberrant development can be initiated by histone demethylase activity in developing sperm, without changes to DNA methylation at CpG-rich regions.
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Affiliation(s)
- Keith Siklenka
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Serap Erkek
- Friedrich Miescher Institute for Biomedical Research (FMI), CH-4058 Basel, Switzerland. Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Maren Godmann
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Romain Lambrot
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Serge McGraw
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Tamara Cohen
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada. Institute of Parasitology, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Matthew Suderman
- MRC Integrative Epidemiology Unity, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Michael Hallett
- McGill Centre for Bioinformatics, School of Computer Science, Faculty of Science, McGill University, Montreal, Quebec, Canada
| | - Jacquetta Trasler
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada. Department of Human Genetics and Department of Pharmacology and Therapeutics, Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research (FMI), CH-4058 Basel, Switzerland. Faculty of Sciences, University of Basel, Basel, Switzerland.
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada. Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada.
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29
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Aarabi M, San Gabriel MC, Chan D, Behan NA, Caron M, Pastinen T, Bourque G, MacFarlane AJ, Zini A, Trasler J. High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism. Hum Mol Genet 2015; 24:6301-13. [PMID: 26307085 DOI: 10.1093/hmg/ddv338] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Dietary folate is a major source of methyl groups required for DNA methylation, an epigenetic modification that is actively maintained and remodeled during spermatogenesis. While high-dose folic acid supplementation (up to 10 times the daily recommended dose) has been shown to improve sperm parameters in infertile men, the effects of supplementation on the sperm epigenome are unknown. To assess the impact of 6 months of high-dose folic acid supplementation on the sperm epigenome, we studied 30 men with idiopathic infertility. Blood folate concentrations increased significantly after supplementation with no significant improvements in sperm parameters. Methylation levels of the differentially methylated regions of several imprinted loci (H19, DLK1/GTL2, MEST, SNRPN, PLAGL1, KCNQ1OT1) were normal both before and after supplementation. Reduced representation bisulfite sequencing (RRBS) revealed a significant global loss of methylation across different regions of the sperm genome. The most marked loss of DNA methylation was found in sperm from patients homozygous for the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism, a common polymorphism in a key enzyme required for folate metabolism. RRBS analysis also showed that most of the differentially methylated tiles were located in DNA repeats, low CpG-density and intergenic regions. Ingenuity Pathway Analysis revealed that methylation of promoter regions was altered in several genes involved in cancer and neurobehavioral disorders including CBFA2T3, PTPN6, COL18A1, ALDH2, UBE4B, ERBB2, GABRB3, CNTNAP4 and NIPA1. Our data reveal alterations of the human sperm epigenome associated with high-dose folic acid supplementation, effects that were exacerbated by a common polymorphism in MTHFR.
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Affiliation(s)
- Mahmoud Aarabi
- Department of Human Genetics, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Maria C San Gabriel
- Division of Urology, Department of Surgery and, Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Donovan Chan
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Nathalie A Behan
- Nutrition Research Division, Health Canada, Ottawa, ON, Canada K1A 0K9 and
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada H3A 1A4
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada H3A 1A4
| | - Guillaume Bourque
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada H3A 1A4
| | | | - Armand Zini
- Division of Urology, Department of Surgery and, Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Jacquetta Trasler
- Department of Human Genetics, Departments of Pediatrics and Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H4A 3J1, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1,
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