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Hao C, Chu S, Quan X, Zhou T, Shi J, Huang X, Wu G, Tortorella MD, Pei D. Establishing extended pluripotent stem cells from human urine cells. Cell Biosci 2023; 13:88. [PMID: 37194020 DOI: 10.1186/s13578-023-01051-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Extended pluripotent stem cells (EPSCs) can contribute to both embryonic and trophectoderm-derived extraembryonic tissues. Therefore, EPSCs have great application significance for both research and industry. However, generating EPSCs from human somatic cells remains inefficient and cumbersome. RESULTS In this study, we established a novel and robust EPSCs culture medium OCM175 with defined and optimized ingredients. Our OCM175 medium contains optimized concentration of L-selenium-methylcysteine as a source of selenium and ROCK inhibitors to maintain the single cell passaging ability of pluripotent stem cells. We also used Matrigel or the combination of laminin 511 and laminin 521(1:1) to bypass the requirement of feeder cells. With OCM175 medium, we successfully converted integration-free iPSCs from easily available human Urine-Derived Cells (hUC-iPSCs) into EPSCs (O-IPSCs). We showed that our O-IPSCs have the ability to form both intra- and extra- embryonic chimerism, and could contribute to the trophoblast ectoderm lineage and three germ layer cell lineages. CONCLUSIONS In conclusion, our novel OCM175 culture medium has defined, optimized ingredients, which enables efficient generation of EPSCs in a feeder free manner. With the robust chimeric and differentiation potential, we believe that this system provides a solid basis to improve the application of EPSCs in regenerative medicine.
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Affiliation(s)
- Chunfang Hao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shilong Chu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Xiongzhi Quan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Junjie Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Xiaofen Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Guangming Wu
- Division of Basic Research, Guangzhou Laboratory, Guangzhou, 510005, China
| | - Micky Daniel Tortorella
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 31003, China.
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Bina M. Defining Candidate Imprinted loci in Bos taurus. Genes (Basel) 2023; 14:1036. [PMID: 37239396 PMCID: PMC10217866 DOI: 10.3390/genes14051036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: CNNM1 and CNR1. I also give examples of candidate ICRs in loci that influence muscle development: SIX1 and BCL6. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the SIX1 promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of BCL6 locus to regulatory proteins in mouse ESCs and examined tissues.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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3
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Vargas LN, Silveira MM, Franco MM. Epigenetic Reprogramming and Somatic Cell Nuclear Transfer. Methods Mol Biol 2023; 2647:37-58. [PMID: 37041328 DOI: 10.1007/978-1-0716-3064-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Epigenetics is an area of genetics that studies the heritable modifications in gene expression and phenotype that are not controlled by the primary sequence of DNA. The main epigenetic mechanisms are DNA methylation, post-translational covalent modifications in histone tails, and non-coding RNAs. During mammalian development, there are two global waves of epigenetic reprogramming. The first one occurs during gametogenesis and the second one begins immediately after fertilization. Environmental factors such as exposure to pollutants, unbalanced nutrition, behavioral factors, stress, in vitro culture conditions can negatively affect epigenetic reprogramming events. In this review, we describe the main epigenetic mechanisms found during mammalian preimplantation development (e.g., genomic imprinting, X chromosome inactivation). Moreover, we discuss the detrimental effects of cloning by somatic cell nuclear transfer on the reprogramming of epigenetic patterns and some molecular alternatives to minimize these negative impacts.
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Affiliation(s)
- Luna N Vargas
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Márcia M Silveira
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Maurício M Franco
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil.
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
- School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
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4
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Yu T, Meng R, Song W, Sun H, An Q, Zhang C, Zhang Y, Su J. ZFP57 regulates DNA methylation of imprinted genes to facilitate embryonic development of somatic cell nuclear transfer embryos in Holstein cows. J Dairy Sci 2022; 106:769-782. [DOI: 10.3168/jds.2022-22427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
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5
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Shao P, Peng Y, Wu Y, Wang J, Pan Z, Yang Y, Aini N, Guo C, Shui G, Chao L, Tian X, An Q, Yang Q, You C, Lu L, Zhang X, Wang M, Nie X. Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:988647. [PMID: 36212380 PMCID: PMC9532966 DOI: 10.3389/fpls.2022.988647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
Fruit branch angle (FBA), a pivotal component of cotton plant architecture, is vital for field and mechanical harvesting. However, the molecular mechanism of FBA formation is poorly understood in cotton. To uncover the genetic basis for FBA formation in cotton, we performed a genome-wide association study (GWAS) of 163 cotton accessions with re-sequencing data. A total of 55 SNPs and 18 candidate genes were significantly associated with FBA trait. By combining GWAS and transcriptome analysis, four genes underlying FBA were identified. An FBA-associated candidate gene Ghi_A09G08736, which is homologous to SAUR46 in Arabidopsis thaliana, was detected in our study. In addition, transcriptomic evidence was provided to show that gravity and light were implicated in the FBA formation. This study provides new insights into the genetic architecture of FBA that informs architecture breeding in cotton.
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Affiliation(s)
- Panxia Shao
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Yabin Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanlong Wu
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Jing Wang
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhenyuan Pan
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Yang
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Nurimanguli Aini
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Chunping Guo
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Guangling Shui
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Lei Chao
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaomin Tian
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Qiushuang An
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Qingyong Yang
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunyuan You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- Cotton Research Institute of the Shihezi Academy of Agriculture Science, Shihezi, Xinjiang, China
| | - Lu Lu
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
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6
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Murthy GG, Prideaux MA, Armstrong M, Kenney HM, Latchney SE, Susiarjo M, Murphy SP. Characterization of the temporal, cell-specific and interferon-inducible patterns of indoleamine 2,3 dioxygenase 1 (IDO1) expression in the human placenta across gestation. Placenta 2021; 115:129-138. [PMID: 34619429 DOI: 10.1016/j.placenta.2021.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/09/2021] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The human placenta performs multiple functions necessary for successful pregnancy, but the metabolic pathways and molecular mechanisms responsible for regulating placental development and functions remain incompletely understood. Catabolism of the essential amino acid tryptophan has numerous critical roles in normal physiology, including inflammation. The kynurenine pathway, which accounts for ∼90% of tryptophan breakdown, is mediated by indoleamine 2,3 dioxygenase 1 (IDO1) in the placenta. In pregnant mice, alterations of IDO1 activity or expression result in fetal resorption and a preeclampsia-like phenotype. Decreased IDO1 expression at the maternal-fetal interface has also been linked to preeclampsia, in utero growth restriction and recurrent miscarriage in humans. These collective observations suggest essential role(s) for IDO1 in maintaining healthy pregnancy. Despite these important roles, the precise temporal, cell-specific and inflammatory cytokine-mediated patterns of IDO1 expression in the human placenta have not been thoroughly characterized across gestation. METHODS Western blot and whole mount immunofluorescence (WMIF) were utilized to characterize and quantify basal and interferon (IFN)-inducible IDO1 expression in 1st trimester (7-13 weeks), 2nd trimester (14-22 weeks) and term (39-41 weeks) placental villi. RESULTS IDO1 expression is activated in the human placenta between the 13th and 14th weeks of pregnancy, increases through the 2nd trimester and remains elevated at term. Constitutive IDO1 expression is restricted to placental endothelial cells. Interestingly, different types of IFNs have distinct effects on IDO1 expression in the human placenta. DISCUSSION Our collective results are consistent with potential role(s) for IDO1 in the regulation of vascular functions in placental villi.
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Affiliation(s)
- Gayathri Guru Murthy
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Mallory A Prideaux
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Madison Armstrong
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - H Mark Kenney
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sarah E Latchney
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Martha Susiarjo
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Shawn P Murphy
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA; Department of Obstetrics and Gynecology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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7
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Brabazon DC, Callanan JJ, Nolan CM. Imprinting of canine IGF2 and H19. Anim Genet 2021; 53:108-118. [PMID: 34676575 DOI: 10.1111/age.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 11/29/2022]
Abstract
Genomic imprinting occurs in therian mammals and is a phenomenon whereby the two alleles of a gene are differentially expressed, based on the sex of the parent from whom the alleles were inherited. The allelic differences in expression are the consequence of different epigenetic modifications that are established in the sperm or oocyte during gametogenesis and transmitted at fertilization to offspring. A small minority of genes is regulated in this way but they have important biological functions, and aberrant regulation of imprinted genes contributes to disease aetiology in humans and other animals. The factors driving the evolution of imprinted genes are also of considerable interest, as these genes appear to forego the benefits of diploidy. To broaden the phylogenetic analysis of genomic imprinting, we began a study of imprinted genes in the domestic dog, Canis familiaris. In this report, we show that canine IGF2 and H19 are imprinted, with parent-of origin-dependent monoallelic expression patterns in neonatal umbilical cord. We identify a putative imprint control region associated with the genes, and provide evidence for differential methylation of this region in a somatic tissue (umbilical cord) and for its hypermethylation in the male germline. Canis familiaris is fast becoming a highly informative system for elucidating disease processes and evolution, and the study of imprinted genes in this species may help in understanding how these genes contribute to the generation of morphological and behavioral diversity.
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Affiliation(s)
- D C Brabazon
- University College Dublin School of Biology and Environmental Science, Belfield, Dublin 4, Ireland
| | - J J Callanan
- University College Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - C M Nolan
- University College Dublin School of Biology and Environmental Science, Belfield, Dublin 4, Ireland
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8
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Park KS, Rahat B, Lee HC, Yu ZX, Noeker J, Mitra A, Kean CM, Knutsen RH, Springer D, Gebert CM, Kozel BA, Pfeifer K. Cardiac pathologies in mouse loss of imprinting models are due to misexpression of H19 long noncoding RNA. eLife 2021; 10:67250. [PMID: 34402430 PMCID: PMC8425947 DOI: 10.7554/elife.67250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022] Open
Abstract
Maternal loss of imprinting (LOI) at the H19/IGF2 locus results in biallelic IGF2 and reduced H19 expression and is associated with Beckwith–-Wiedemann syndrome (BWS). We use mouse models for LOI to understand the relative importance of Igf2 and H19 mis-expression in BWS phenotypes. Here we focus on cardiovascular phenotypes and show that neonatal cardiomegaly is exclusively dependent on increased Igf2. Circulating IGF2 binds cardiomyocyte receptors to hyperactivate mTOR signaling, resulting in cellular hyperplasia and hypertrophy. These Igf2-dependent phenotypes are transient: cardiac size returns to normal once Igf2 expression is suppressed postnatally. However, reduced H19 expression is sufficient to cause progressive heart pathologies including fibrosis and reduced ventricular function. In the heart, H19 expression is primarily in endothelial cells (ECs) and regulates EC differentiation both in vivo and in vitro. Finally, we establish novel mouse models to show that cardiac phenotypes depend on H19 lncRNA interactions with Mirlet7 microRNAs.
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Affiliation(s)
- Ki-Sun Park
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Beenish Rahat
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Hyung Chul Lee
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Zu-Xi Yu
- Pathology Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jacob Noeker
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Apratim Mitra
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Connor M Kean
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Russell H Knutsen
- Laboratory of Vascular and Matrix Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Danielle Springer
- Murine Phenotyping Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Claudia M Gebert
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Beth A Kozel
- Laboratory of Vascular and Matrix Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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Prickett AR, Montibus B, Barkas N, Amante SM, Franco MM, Cowley M, Puszyk W, Shannon MF, Irving MD, Madon-Simon M, Ward A, Schulz R, Baldwin HS, Oakey RJ. Imprinted Gene Expression and Function of the Dopa Decarboxylase Gene in the Developing Heart. Front Cell Dev Biol 2021; 9:676543. [PMID: 34239874 PMCID: PMC8258389 DOI: 10.3389/fcell.2021.676543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Dopa decarboxylase (DDC) synthesizes serotonin in the developing mouse heart where it is encoded by Ddc_exon1a, a tissue-specific paternally expressed imprinted gene. Ddc_exon1a shares an imprinting control region (ICR) with the imprinted, maternally expressed (outside of the central nervous system) Grb10 gene on mouse chromosome 11, but little else is known about the tissue-specific imprinted expression of Ddc_exon1a. Fluorescent immunostaining localizes DDC to the developing myocardium in the pre-natal mouse heart, in a region susceptible to abnormal development and implicated in congenital heart defects in human. Ddc_exon1a and Grb10 are not co-expressed in heart nor in brain where Grb10 is also paternally expressed, despite sharing an ICR, indicating they are mechanistically linked by their shared ICR but not by Grb10 gene expression. Evidence from a Ddc_exon1a gene knockout mouse model suggests that it mediates the growth of the developing myocardium and a thinning of the myocardium is observed in a small number of mutant mice examined, with changes in gene expression detected by microarray analysis. Comparative studies in the human developing heart reveal a paternal expression bias with polymorphic imprinting patterns between individual human hearts at DDC_EXON1a, a finding consistent with other imprinted genes in human.
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Affiliation(s)
- Adam R. Prickett
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Bertille Montibus
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Nikolaos Barkas
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Samuele M. Amante
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Maurício M. Franco
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Michael Cowley
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - William Puszyk
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Matthew F. Shannon
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Melita D. Irving
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- Department of Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Marta Madon-Simon
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Andrew Ward
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - H. Scott Baldwin
- Department of Pediatrics (Cardiology), Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rebecca J. Oakey
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
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Pal A, Oakes J, Elnagheeb M, Ideraabdullah FY. Maternal Microdeletion at the H19/Igf2 ICR in Mice Increases Offspring Susceptibility to In Utero Environmental Perturbation. Epigenet Insights 2020; 13:2516865720970575. [PMID: 33313480 PMCID: PMC7716063 DOI: 10.1177/2516865720970575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/09/2020] [Indexed: 12/01/2022] Open
Abstract
Deficiency of methyl donor nutrients folate, choline, and methionine (methyl deficiency) during gestation can impair fetal development and perturb DNA methylation. Here, we assessed genetic susceptibility to methyl deficiency by comparing effects in wildtype C57BL/6J (B6) mice to mutant mice carrying a 1.3 kb deletion at the H19/Igf2 Imprinting Control Region (ICR) (H19 ICRΔ2,3). The H19 ICRΔ2,3 mutation mimics microdeletions observed in Beckwith-Wiedemann syndrome (BWS) patients, who exhibit epimutations in cis that cause loss of imprinting and fetal overgrowth. Dams were treated during pregnancy with 1 of 4 methyl sufficient (MS) or methyl deficient (MD) diets, with or without the antibiotic commonly used to deplete folate producing gut microbes. As expected, after ~9 weeks of treatment, dams in MD and MD + antibiotic groups exhibited substantially reduced plasma folate concentrations. H19 ICRΔ2,3 mutant lines were more susceptible to adverse pregnancy outcomes caused by methyl deficiency (reduced birth rate and increased pup lethality) and antibiotic (decreased litter size and litter survival). Surprisingly, pup growth/development was only minimally affected by methyl deficiency, while antibiotic treatment caused inverse effects on B6 and H19 ICRΔ2,3 lines. B6 pups treated with antibiotic exhibited increased neonatal and weanling bodyweight, while both wildtype and mutant pups of heterozygous H19 ICRΔ2,3/+ dams exhibited decreased neonatal bodyweight that persisted into adulthood. Interestingly, only antibiotic-treated pups carrying the H19 ICRΔ2,3 mutation exhibited altered DNA methylation at the H19/Igf2 ICR, suggesting ICR epimutation was not sufficient to explain the altered phenotypes. These findings demonstrate that genetic mutation of the H19/Igf2 ICR increases offspring susceptibility to developmental perturbation in the methyl deficiency model, maternal and pup genotype play an essential role, and antibiotic treatment in the model also plays a key independent role.
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Affiliation(s)
- Anandita Pal
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Judy Oakes
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Marwa Elnagheeb
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Folami Y Ideraabdullah
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Hammerle CM, Sandovici I, Brierley GV, Smith NM, Zimmer WE, Zvetkova I, Prosser HM, Sekita Y, Lam BYH, Ma M, Cooper WN, Vidal-Puig A, Ozanne SE, Medina-Gómez G, Constância M. Mesenchyme-derived IGF2 is a major paracrine regulator of pancreatic growth and function. PLoS Genet 2020; 16:e1009069. [PMID: 33057429 PMCID: PMC7678979 DOI: 10.1371/journal.pgen.1009069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 11/20/2020] [Accepted: 08/20/2020] [Indexed: 01/09/2023] Open
Abstract
The genetic mechanisms that determine the size of the adult pancreas are poorly understood. Imprinted genes, which are expressed in a parent-of-origin-specific manner, are known to have important roles in development, growth and metabolism. However, our knowledge regarding their roles in the control of pancreatic growth and function remains limited. Here we show that many imprinted genes are highly expressed in pancreatic mesenchyme-derived cells and explore the role of the paternally-expressed insulin-like growth factor 2 (Igf2) gene in mesenchymal and epithelial pancreatic lineages using a newly developed conditional Igf2 mouse model. Mesenchyme-specific Igf2 deletion results in acinar and beta-cell hypoplasia, postnatal whole-body growth restriction and maternal glucose intolerance during pregnancy, suggesting that the mesenchyme is a developmental reservoir of IGF2 used for paracrine signalling. The unique actions of mesenchymal IGF2 are demonstrated by the absence of any discernible growth or functional phenotypes upon Igf2 deletion in the developing pancreatic epithelium. Additionally, increased IGF2 levels specifically in the mesenchyme, through conditional Igf2 loss-of-imprinting or Igf2r deletion, leads to pancreatic acinar overgrowth. Furthermore, ex-vivo exposure of primary acinar cells to exogenous IGF2 activates AKT, a key signalling node, and increases their number and amylase production. Based on these findings, we propose that mesenchymal Igf2, and perhaps other imprinted genes, are key developmental regulators of adult pancreas size and function.
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Affiliation(s)
- Constanze M. Hammerle
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Ionel Sandovici
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Gemma V. Brierley
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Nicola M. Smith
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Warren E. Zimmer
- Department of Medical Physiology, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Ilona Zvetkova
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Haydn M. Prosser
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, United Kingdom
| | - Yoichi Sekita
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Brian Y. H. Lam
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Marcella Ma
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Wendy N. Cooper
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Susan E. Ozanne
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Gema Medina-Gómez
- Área de Bioquímica y Biología Molecular, Departamento de Ciencias Básicas de la Salud, Universidad Rey Juan Carlos, 28922-Alcorcón, Madrid, Spain
| | - Miguel Constância
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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12
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Rivera RM. Consequences of assisted reproductive techniques on the embryonic epigenome in cattle. Reprod Fertil Dev 2020; 32:65-81. [PMID: 32188559 DOI: 10.1071/rd19276] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Procedures used in assisted reproduction have been under constant scrutiny since their inception with the goal of improving the number and quality of embryos produced. However, invitro production of embryos is not without complications because many fertilised oocytes fail to become blastocysts, and even those that do often differ in the genetic output compared with their invivo counterparts. Thus only a portion of those transferred complete normal fetal development. An unwanted consequence of bovine assisted reproductive technology (ART) is the induction of a syndrome characterised by fetal overgrowth and placental abnormalities, namely large offspring syndrome; a condition associated with inappropriate control of the epigenome. Epigenetics is the study of chromatin and its effects on genetic output. Establishment and maintenance of epigenetic marks during gametogenesis and embryogenesis is imperative for the maintenance of cell identity and function. ARTs are implemented during times of vast epigenetic reprogramming; as a result, many studies have identified ART-induced deviations in epigenetic regulation in mammalian gametes and embryos. This review describes the various layers of epigenetic regulation and discusses findings pertaining to the effects of ART on the epigenome of bovine gametes and the preimplantation embryo.
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Affiliation(s)
- Rocío Melissa Rivera
- Division of Animal Science University of Missouri, Columbia, Missouri 65211, USA.
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13
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Wang Y, Liu Q, Kang J, Zhang Y, Quan F. Overexpression of PGC7 in donor cells maintains the DNA methylation status of imprinted genes in goat embryos derived from somatic cell nuclear transfer technology. Theriogenology 2020; 151:86-94. [PMID: 32344274 DOI: 10.1016/j.theriogenology.2020.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/26/2020] [Accepted: 04/11/2020] [Indexed: 11/27/2022]
Abstract
Abnormal methylation of imprinted genes is commonly observed in the embryos cloned by somatic cell nuclear transfer (SCNT) procedure and is one of the primary reasons for their abnormal development and high mortality. Primordial germ cell 7 (PGC7), a developmentally regulated gene highly expressed in primordial germ cells, maintains the methylation level of imprinted genes by reducing the levels of 5-hydroxy-methylcytosine(5hmC) and increasing the levels of 5-methylcytosine(5 mC) during embryonic development. In this study, we explored the methylation status of H19 differentially methylated regions (DMRs) in the organs of SCNT-cloned goat fetuses. Our results showed abnormal methylation patterns of the imprinted genes in the lungs and placenta of dead cloned goat fetuses than those in normal goat fetuses. The Igf2r DMRs were hypomethylated in the heart, liver, spleen, lungs, kidneys, and placenta of dead cloned goat fetuses compared with normal goat fetuses (P < 0.05). In addition, imprinted gene Igf2r DMRs were hypomethylated in the early-stage SCNT embryos than the IVF embryos. In contrast, imprinted gene Xist DMRs were hypermethylated in SCNT embryos than the IVF embryos. Significantly, the use of PGC7 overexpressing donor cells corrected the abnormal methylation of imprinted genes Igf2r and Xist in SCNT embryos (P < 0.05). Our results suggested that PGC7 plays a vital role in maintaining the methylation of imprinted genes during goat early embryonic development. Moreover, PGC7 overexpression in donor cells may reduce the developmental abnormalities associated with the SCNT embryos, while significantly enhancing both the pregnancy and kids born rates (P < 0.05) thereby increasing SCNT efficiency in livestock.
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Affiliation(s)
- Yufei Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jian Kang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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14
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Abstract
Epigenetic effects can be mediated by changes in chromatin state that are transmitted from parent to child via gametes, but support is gathering for maternal yolk, which is deposited into ooctyes, as an extranuclear epigenetic factor that can contribute to phenotypic plasticity across generations in Caenorhabditis elegans.
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Affiliation(s)
- Robert H Dowen
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Shawn Ahmed
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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15
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16
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Thamban T, Agarwaal V, Khosla S. Role of genomic imprinting in mammalian development. J Biosci 2020; 45:20. [PMID: 31965998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-mendelian inheritance refers to the group of phenomena and observations related to the inheritance of genetic information that cannot be merely explained by Mendel's laws of inheritance. Phenomenon including Genomic imprinting, X-chromosome Inactivation, Paramutations are some of the best studied examples of non-mendelian inheritance. Genomic imprinting is a process that reversibly marks one of the two homologous loci, chromosome or chromosomal sets during development, resulting in functional non-equivalence of gene expression. Genomic imprinting is known to occur in a few insect species, plants, and placental mammals. Over the years, studies on imprinted genes have contributed immensely to highlighting the role of epigenetic modifications and the epigenetic circuitry during gene expression and development. In this review, we discuss the phenomenon of genomic imprinting in mammals and the role it plays especially during fetoplacental growth and early development.
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Affiliation(s)
- Thushara Thamban
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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17
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Ben Maamar M, King SE, Nilsson E, Beck D, Skinner MK. Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations. Dev Biol 2019; 458:106-119. [PMID: 31682807 PMCID: PMC6987017 DOI: 10.1016/j.ydbio.2019.10.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Epigenetic transgenerational inheritance potentially impacts disease etiology, phenotypic variation, and evolution. An increasing number of environmental factors from nutrition to toxicants have been shown to promote the epigenetic transgenerational inheritance of disease. Previous observations have demonstrated that the agricultural fungicide vinclozolin and pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation, ncRNA, and histone modifications or retention. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. This model allows the parental allelic transmission of disease and epimutations to be investigated. There was increased pathology incidence in the MOC F4 generation male prostate, kidney, obesity, and multiple diseases through a maternal allelic transmission. The POC F4 generation female offspring had increased pathology incidence for kidney, obesity and multiple types of diseases through the paternal allelic transmission. Some disease such as testis or ovarian pathology appear to be transmitted through the combined actions of both male and female alleles. Analysis of the F4 generation sperm epigenomes identified differential DNA methylated regions (DMRs) in a genome-wide analysis. Observations demonstrate that DDT and vinclozolin have the potential to promote the epigenetic transgenerational inheritance of disease and sperm epimutations to the outcross F4 generation in a sex specific and exposure specific manner. The parent-of-origin allelic transmission observed appears similar to the process involved with imprinted-like genes.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Stephanie E King
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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18
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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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19
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Rhon-Calderon EA, Vrooman LA, Riesche L, Bartolomei MS. The effects of Assisted Reproductive Technologies on genomic imprinting in the placenta. Placenta 2019; 84:37-43. [PMID: 30871810 DOI: 10.1016/j.placenta.2019.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 12/29/2022]
Abstract
The placenta is a complex and poorly understood organ, which serves as the connection between the mother and the developing fetus. Genomic imprinting, defined as a regulatory process resulting in the expression of a gene in a parent-of-origin-specific manner, plays an important role in fetal development and placental function. Disturbances that occur during the establishment and maintenance of imprinting could compromise the placenta and fetus, and ultimately, offspring health. Assisted Reproductive Technologies (ART) have been widely used to overcome infertility, however experimental studies have shown that ART procedures affect placentation and the expression of imprinted genes. Here we briefly review the role of imprinted genes in placental development and the evidence from mouse and human studies suggesting ART disrupts imprinted gene regulation in the placenta.
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Affiliation(s)
- Eric A Rhon-Calderon
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA
| | - Lisa A Vrooman
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA
| | - Laren Riesche
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA; Department of Family and Community Health, Claire M. Fagin School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA.
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20
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Zhang W, Yang J, Lv Y, Li S, Qiang M. Paternal benzo[a]pyrene exposure alters the sperm DNA methylation levels of imprinting genes in F0 generation mice and their unexposed F1-2 male offspring. CHEMOSPHERE 2019; 228:586-594. [PMID: 31059956 DOI: 10.1016/j.chemosphere.2019.04.092] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Benzo[a]pyrene (BaP) is an environmental pollutant known to cause teratogenesis. However, the mechanism underlying this teratogenic effect is not fully understood. Recently, the alteration of DNA methylation of imprinting genes has emerged as a specific epigenetic mechanism linking the impact of environmental pollutants on embryonic development to paternal exposures. The aim of this study was to investigate the transgenerational effects of paternal BaP exposure on the imprinting genes in mouse sperm DNA. METHODS Male C57BL/6J mice received BaP (1.0 or 2.5 mg/kg) or olive oil twice a week for 12 weeks. The methylation status of 6 imprinting genes (H19, Meg3, Peg1, Peg3, Igf2 and Snrpn) was examined by bisulfite pyrosequencing of the sperm DNA of BaP-exposed F0 generation and their offspring. RESULTS BaP exposure reduced the methylation levels in the imprinting genes H19 and Meg3 and increased the methylation levels of Peg1 and Peg3; however, no significant differences was observed for the methylation levels of Igf2 or Snrpn in the sperm DNA. Furthermore, BaP-exposed male mice were mated with unexposed female mice to generate F1-2 generations. The methylation levels of the 6 genes in the sperm DNA from F1-2 offspring showed a similar pattern as that of the F0 male. The effects were attenuated in F1-2 generations. CONCLUSIONS Paternal BaP exposure altered the methylation levels of imprinting genes, implicating that imprinting genes are susceptible to environmental toxicants. Furthermore, a similar alteration was observed in the F1-2 generations although the attenuated in methylation in F2 generation, revealing a potential transgenerational effect.
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Affiliation(s)
- Wenping Zhang
- Department of Toxicology, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan 030001, China
| | - Jia Yang
- Department of Children and Adolescences Health, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan 030001, China
| | - Yi Lv
- Department of Toxicology, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan 030001, China
| | - Senlin Li
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Mei Qiang
- Department of Children and Adolescences Health, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan 030001, China.
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21
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Spinelli P, Latchney SE, Reed JM, Fields A, Baier BS, Lu X, McCall MN, Murphy SP, Mak W, Susiarjo M. Identification of the novel Ido1 imprinted locus and its potential epigenetic role in pregnancy loss. Hum Mol Genet 2019; 28:662-674. [PMID: 30403776 DOI: 10.1093/hmg/ddy383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/29/2018] [Indexed: 11/14/2022] Open
Abstract
Previous studies show that aberrant tryptophan catabolism reduces maternal immune tolerance and adversely impacts pregnancy outcomes. Tryptophan depletion in pregnancy is facilitated by increased activity of tryptophan-depleting enzymes [i.e. the indolamine-2,3 dioxygenase (IDO)1 and IDO2) in the placenta. In mice, inhibition of IDO1 activity during pregnancy results in fetal loss; however, despite its important role, regulation of Ido1 gene transcription is unknown. The current study shows that the Ido1 and Ido2 genes are imprinted and maternally expressed in mouse placentas. DNA methylation analysis demonstrates that nine CpG sites at the Ido1 promoter constitute a differentially methylated region that is highly methylated in sperm but unmethylated in oocytes. Bisulfite cloning sequencing analysis shows that the paternal allele is hypermethylated while the maternal allele shows low levels of methylation in E9.5 placenta. Further study in E9.5 placentas from the CBA/J X DBA/2 spontaneous abortion mouse model reveals that aberrant methylation of Ido1 is linked to pregnancy loss. DNA methylation analysis in humans shows that IDO1 is hypermethylated in human sperm but partially methylated in placentas, suggesting similar methylation patterns to mouse. Importantly, analysis in euploid placentas from first trimester pregnancy loss reveals that IDO1 methylation significantly differs between the two placenta cohorts, with most CpG sites showing increased percent of methylation in miscarriage placentas. Our study suggests that DNA methylation is linked to regulation of Ido1/IDO1 expression and altered Ido1/IDO1 DNA methylation can adversely influence pregnancy outcomes.
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Affiliation(s)
- Philip Spinelli
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sarah E Latchney
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jasmine M Reed
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ashley Fields
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Brian S Baier
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Xiang Lu
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Shawn P Murphy
- Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, NY, USA
| | - Winifred Mak
- Department of Obstetric Gynecology, Dell Medical School, University of Texas, Austin, TX, USA
| | - Martha Susiarjo
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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22
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Kim JY, Youn HY, Pfeifer K, Eun B. Paternal bias expression of Igf2as is enhancer-dependent on the imprinting cluster of Igf2, H19 and Nctc1 in muscle cells. Anim Cells Syst (Seoul) 2019; 23:288-293. [PMID: 31489250 PMCID: PMC6711144 DOI: 10.1080/19768354.2019.1612780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 11/22/2022] Open
Abstract
Igf2, H19, and Nctc1 are linked co-regulated genes on distal mouse chromosome 7. This locus is an important model both for studying mechanisms of monoallelic expression and for elucidating the role of cis-regulatory elements – enhancers and insulators – in organizing chromatin and gene expression across a large domain. In this study we characterize regulated expression of the Igf2 antisense transcript (Igf2as) in primary muscle cells. We demonstrate that Igf2as is imprinted (expressed only from the paternal chromosome). We also show that Igf2as expression during differentiation follows the same patterns as Igf2 and H19. Moreover, this expression is dependent upon the same shared enhancer element. Thus, our work shows that the imprinted cluster includes Igf2as in addition to H19, Igf2, and Nctc1.
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Affiliation(s)
- Jae-Young Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Hwa Young Youn
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Karl Pfeifer
- National Institute of Child Health and Development, National Institutes of Health, Bethesda, USA
| | - Bokkee Eun
- Core-Laboratory for Convergent Translational Research, Korea University College of Medicine, Seoul, South Korea
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23
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Ni W, Pan C, Pan Q, Fei Q, Huang X, Zhang C. Methylation levels of
IGF2
and
KCNQ1
in spermatozoa from infertile men are associated with sperm DNA damage. Andrologia 2019; 51:e13239. [PMID: 30680773 DOI: 10.1111/and.13239] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/21/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wuhua Ni
- Department of Clinical Laboratory, Jinling Hospital, Nanjing School of Clinical Medicine Southern Medical University (Nanjing General Hospital of Nanjing Military Region) Nanjing China
- Reproductive Medicine CenterThe First Affiliated Hospital of Wenzhou Medical University Wenzhou China
| | - Chengshuang Pan
- Reproductive Medicine CenterThe First Affiliated Hospital of Wenzhou Medical University Wenzhou China
| | - Qiongqiong Pan
- Reproductive Medicine CenterThe First Affiliated Hospital of Wenzhou Medical University Wenzhou China
| | - Qianjin Fei
- Reproductive Medicine CenterThe First Affiliated Hospital of Wenzhou Medical University Wenzhou China
| | - Xuefeng Huang
- Reproductive Medicine CenterThe First Affiliated Hospital of Wenzhou Medical University Wenzhou China
| | - Chunni Zhang
- Department of Clinical Laboratory, Jinling Hospital, Nanjing School of Clinical Medicine Southern Medical University (Nanjing General Hospital of Nanjing Military Region) Nanjing China
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24
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Tunster SJ, Van de Pette M, Creeth HDJ, Lefebvre L, John RM. Fetal growth restriction in a genetic model of sporadic Beckwith-Wiedemann syndrome. Dis Model Mech 2018; 11:dmm.035832. [PMID: 30158284 PMCID: PMC6262809 DOI: 10.1242/dmm.035832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/17/2018] [Indexed: 12/19/2022] Open
Abstract
Beckwith–Wiedemann syndrome (BWS) is a complex imprinting disorder involving fetal overgrowth and placentomegaly, and is associated with a variety of genetic and epigenetic mutations affecting the expression of imprinted genes on human chromosome 11p15.5. Most BWS cases are linked to loss of methylation at the imprint control region 2 (ICR2) within this domain, which in mice regulates the silencing of several maternally expressed imprinted genes. Modelling this disorder in mice is confounded by the unique embryonic requirement for Ascl2, which is imprinted in mice but not in humans. To overcome this issue, we generated a novel model combining a truncation of distal chromosome 7 allele (DelTel7) with transgenic rescue of Ascl2 expression. This novel model recapitulated placentomegaly associated with BWS, but did not lead to fetal overgrowth. Summary: A novel genetic mouse model of sporadic Beckwith–Wiedemann syndrome (BWS) recapitulates placentomegaly, but placental defects lead to late gestation fetal growth restriction, which contrasts with the fetal overgrowth characteristic of BWS in humans.
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Affiliation(s)
- Simon J Tunster
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Hugo D J Creeth
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Louis Lefebvre
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
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Chen R, Xia L, Tu K, Duan M, Kukurba K, Li-Pook-Than J, Xie D, Snyder M. Longitudinal personal DNA methylome dynamics in a human with a chronic condition. Nat Med 2018; 24:1930-1939. [PMID: 30397358 DOI: 10.1038/s41591-018-0237-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/27/2018] [Indexed: 02/05/2023]
Abstract
Epigenomics regulates gene expression and is as important as genomics in precision personal health, as it is heavily influenced by environment and lifestyle. We profiled whole-genome DNA methylation and the corresponding transcriptome of peripheral blood mononuclear cells collected from a human volunteer over a period of 36 months, generating 28 methylome and 57 transcriptome datasets. We found that DNA methylomic changes are associated with infrequent glucose level alteration, whereas the transcriptome underwent dynamic changes during events such as viral infections. Most DNA meta-methylome changes occurred 80-90 days before clinically detectable glucose elevation. Analysis of the deep personal methylome dataset revealed an unprecedented number of allelic differentially methylated regions that remain stable longitudinally and are preferentially associated with allele-specific gene regulation. Our results revealed that changes in different types of 'omics' data associate with different physiological aspects of this individual: DNA methylation with chronic conditions and transcriptome with acute events.
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Affiliation(s)
- Rui Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Roche Sequencing Solutions, Pleasanton, CA, USA
| | - Lin Xia
- Center of Precision Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and National Collaborative Innovation Center, Sichuan, China
| | - Kailing Tu
- Center of Precision Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and National Collaborative Innovation Center, Sichuan, China
| | - Meixue Duan
- Center of Precision Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and National Collaborative Innovation Center, Sichuan, China
| | - Kimberly Kukurba
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Dan Xie
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Center of Precision Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and National Collaborative Innovation Center, Sichuan, China.
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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Mattern F, Heinzmann J, Herrmann D, Lucas-Hahn A, Haaf T, Niemann H. Gene-specific profiling of DNA methylation and mRNA expression in bovine oocytes derived from follicles of different size categories. Reprod Fertil Dev 2018; 29:2040-2051. [PMID: 28152377 DOI: 10.1071/rd16327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/14/2016] [Indexed: 12/20/2022] Open
Abstract
Epigenetic changes, such as DNA methylation, play an essential role in the acquisition of full developmental competence by mammalian oocytes during the late follicular growth phase. Here we used the bovine model to investigate the DNA methylation profiles of seven candidate genes (imprinted: bH19, bSNRPN; non-imprinted: bZAR1, bDNMT3A, bOCT4, bDNMT3 Lo and bDNMT3 Ls) and the mRNA expression of nine candidate genes (imprinted: bSNRPN, bPEG3, bIGF2R; non-imprinted: bPRDX1, bDNMT1B, bDNMT3A, bZAR1, bHSF1 and bNLRP9) in oocytes from antral follicles of three different size classes (≤2mm, 3-5mm, ≥6mm) to unravel the epigenetic contribution to this process. We observed an increased number of aberrantly methylated alleles in bH19, bSNRPN and bDNMT3 Lo of oocytes from small antral follicles (≤2mm), correlating with lower developmental competence. Furthermore, we detected an increased frequency of CpG sites with an unclear methylation status for DNMT3 Ls, specifically in oocytes from follicles ≥6mm, predominantly at three CpG positions (CpG2, CpG7 and CpG8), of which CpG7 is a potential regulatory site. No major differences in mRNA expression were observed, indicating that the transcriptional machinery may not yet be active during the follicular growth phase. Our results support the notion that a follicle diameter of ~2mm is a critical stage for establishing DNA methylation profiles and indicate a link between DNA methylation and the acquisition of oocyte developmental competence.
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Affiliation(s)
- F Mattern
- Institute of Human Genetics, Julius Maximilians University, 97070 Würzburg, Germany
| | - J Heinzmann
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
| | - D Herrmann
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
| | - A Lucas-Hahn
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
| | - T Haaf
- Institute of Human Genetics, Julius Maximilians University, 97070 Würzburg, Germany
| | - H Niemann
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
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Wan Y, Deng M, Zhang G, Ren C, Liu Z, Wang F. Analysis of H19/Igf2 Methylation Status in the Sperm of Cloned Goats and Their Offspring. Cell Reprogram 2018; 20:66-75. [DOI: 10.1089/cell.2017.0029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingtian Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Guomin Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Caifang Ren
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zifei Liu
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Park KS, Mitra A, Rahat B, Kim K, Pfeifer K. Loss of imprinting mutations define both distinct and overlapping roles for misexpression of IGF2 and of H19 lncRNA. Nucleic Acids Res 2018; 45:12766-12779. [PMID: 29244185 PMCID: PMC5727439 DOI: 10.1093/nar/gkx896] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/26/2017] [Indexed: 12/26/2022] Open
Abstract
Imprinted genes occur in discrete clusters that are coordinately regulated by shared DNA elements called Imprinting Control Regions. H19 and Igf2 are linked imprinted genes that play critical roles in development. Loss of imprinting (LOI) at the IGF2/H19 locus on the maternal chromosome is associated with the developmental disorder Beckwith Wiedemann Syndrome (BWS) and with several cancers. Here we use comprehensive genetic and genomic analyses to follow muscle development in a mouse model of BWS to dissect the separate and shared roles for misexpression of Igf2 and H19 in the disease phenotype. We show that LOI results in defects in muscle differentiation and hypertrophy and identify primary downstream targets: Igf2 overexpression results in over-activation of MAPK signaling while loss of H19 lncRNA prevents normal down regulation of p53 activity and therefore results in reduced AKT/mTOR signaling. Moreover, we demonstrate instances where H19 and Igf2 misexpression work separately, cooperatively, and antagonistically to establish the developmental phenotype. This study thus identifies new biochemical roles for the H19 lncRNA and underscores that LOI phenotypes are multigenic so that complex interactions will contribute to disease outcomes.
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Affiliation(s)
- Ki-Sun Park
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20814, USA
| | - Apratim Mitra
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20814, USA
| | - Beenish Rahat
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20814, USA
| | - Keekwang Kim
- Department of Biochemistry, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20814, USA
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Camprubí C, Cigliano RA, Salas-Huetos A, Garrido N, Blanco J. What the human sperm methylome tells us. Epigenomics 2017; 9:1299-1315. [DOI: 10.2217/epi-2017-0049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: To characterize the sperm methylome in semen samples from 19 donors with proven fertility. Materials & methods: Bisulfite-converted sperm DNA was hybridized on the HumanMethylation450 Infinium BeadChip platform. CpG fluorescence intensities were extracted and converted to β-values. Results: The sperm methylome is highly homogeneous and hypomethylated. Genes with hypomethylated promoters are ontologically associated to biological functions related to spermatogenesis and embryogenesis. Sex chromosomes are the most hypomethylated chromosomes, supporting data that indicated their essential role in spermatogenesis. A total of 94 genes are resistant to demethylation, being strong candidates for transgenerational inheritance. Conclusion: Spermatozoa carry a homogeneous methylation profile that is a footprint of past events (spermatogenesis), is designed to facilitate future events (embryogenesis) and has a possible influence in the adult life (transgenerational effects).
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Affiliation(s)
- Cristina Camprubí
- Genetics of Male Fertility Group, Unitat de Biologia Cellular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193-Bellaterra (Cerdanyola del Vallès), Spain
- GenIntegral, Barcelona, Spain
- Reference Laboratory Genetics, Pablo Iglesias 57-59, 08908-L'Hospitalet de Llobregat, Barcelona, Spain
| | - Riccardo Aiese Cigliano
- Sequentia Biotech, Edifici Eureka, Campus UAB, 08193-Bellaterra (Cerdanyola del Vallès), Spain
| | - Albert Salas-Huetos
- Genetics of Male Fertility Group, Unitat de Biologia Cellular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193-Bellaterra (Cerdanyola del Vallès), Spain
| | - Nicolas Garrido
- IVI Foundation, Parc Científic Universitat de València, 46980-Paterna, Spain
| | - Joan Blanco
- Genetics of Male Fertility Group, Unitat de Biologia Cellular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193-Bellaterra (Cerdanyola del Vallès), Spain
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Provenzi L, Guida E, Montirosso R. Preterm behavioral epigenetics: A systematic review. Neurosci Biobehav Rev 2017; 84:262-271. [PMID: 28867654 DOI: 10.1016/j.neubiorev.2017.08.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/28/2017] [Accepted: 08/30/2017] [Indexed: 12/24/2022]
Abstract
Behavioral epigenetics is revealing new pathways that lead individuals from early adversity exposures to later-in-life detrimental outcomes. Preterm birth constitutes one of the major adverse events in human development. Preterm infants are hospitalized in the Neonatal Intensive Care Unit (NICU) where they are exposed to life-saving yet pain-inducing procedures and to protective care. The application of behavioral epigenetics to the field of preterm studies (i.e., Preterm Behavioral Epigenetics, PBE) is rapidly growing and holds promises to provide valid insights for research and clinical activity. Here, the evidence of the epigenetic correlates of prenatal adversities, NICU-related environment and development of preterm infants is systematically reviewed. The findings suggest that a number of prenatal adverse (e.g., maternal depression and stress) and post-natal (e.g., NICU-related pain-related stress) events affect the developmental trajectories of preterm infants and children via epigenetic alterations of imprinted and stress-related genes. Nonetheless, the potential epigenetic vestiges of early care and protective interventions in NICU have not been investigated yet and this represents a fascinating challenge for future PBE research.
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Affiliation(s)
- Livio Provenzi
- 0-3 Centre for the at-Risk Infant, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, LC, Italy.
| | - Elena Guida
- 0-3 Centre for the at-Risk Infant, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, LC, Italy
| | - Rosario Montirosso
- 0-3 Centre for the at-Risk Infant, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, LC, Italy
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31
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Wang D, Liu Z, Yao H, Hao Y, Zhou L, Du J, Zhu Y, Xu Y, Wang G, Song Y, Li Z. Disruption of NNAT, NAP1L5 and MKRN3 DNA methylation and transcription in rabbit parthenogenetic fetuses. Gene 2017; 626:158-162. [PMID: 28526651 DOI: 10.1016/j.gene.2017.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/06/2017] [Accepted: 05/15/2017] [Indexed: 10/19/2022]
Abstract
Parthenogenetically activated oocytes cannot develop to term in mammals due to lack of paternal gene expression. Disruption of imprinted gene expression and DNA methylation status in parthenogenetic fetuses has been reported in mice and pigs, but not in rabbits. In this study, the genomic imprinting status of the paternally expressed genes Neuronatin (NNAT), Nucleosome assembly protein 1-like 5 (NAP1L5), and Makorin ring finger protein 3 (MKRN3) was compared between rabbit parthenogenetic (PA) and normally fertilized fetuses (Con) using quantitative real-time PCR (qRT-PCR) and bisulfite sequencing PCR (BSP). The results revealed a significantly reduced expression of NNAT, NAP1L5, and MKRN3 in rabbit PA fetuses compared with Con fetuses (p<0.05). In addition, the BSP results demonstrated hypermethylation in the differentially methylated regions (DMRs) of NNAT, NAP1L5, and MKRN3 in rabbit PA fetuses. Taken together, these results suggest that hypermethylation of DMRs is associated with decreased NNAT, NAP1L5, and MKRN3 expression, which may be responsible for developmental failure of rabbit PA fetuses.
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Affiliation(s)
- Dongxu Wang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Zhiquan Liu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Haobin Yao
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Yang Hao
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Lina Zhou
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Jian Du
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Yixin Zhu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Yuxin Xu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Guodong Wang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Yuning Song
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Zhanjun Li
- College of Animal Science, Jilin University, Changchun 130062, China.
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Gebert C, Correia L, Li Z, Petrie HT, Love PE, Pfeifer K. Chromosome choice for initiation of V-(D)-J recombination is not governed by genomic imprinting. Immunol Cell Biol 2017; 95:473-477. [PMID: 28244489 PMCID: PMC5788196 DOI: 10.1038/icb.2017.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/16/2016] [Accepted: 12/18/2016] [Indexed: 01/04/2023]
Abstract
V-(D)-J recombination generates the antigen receptor diversity necessary for immune cell function, while allelic exclusion ensures that each cell expresses a single antigen receptor. V-(D)-J recombination of the Ig, Tcrb, Tcrg and Tcrd antigen receptor genes is ordered and sequential so that only one allele generates a productive rearrangement. The mechanism controlling sequential rearrangement of antigen receptor genes, in particular how only one allele is selected to initiate recombination while at least temporarily leaving the other intact, remains unresolved. Genomic imprinting, a widespread phenomenon wherein maternal or paternal allele inheritance determines allele activity, could represent a regulatory mechanism for controlling sequential V-(D)-J rearrangement. We used strain-specific single-nucleotide polymorphisms within antigen receptor genes to determine if maternal vs paternal inheritance could underlie chromosomal choice for the initiation of recombination. We found no parental chromosomal bias in the initiation of V-(D)-J recombination in T or B cells, eliminating genomic imprinting as a potential regulator for this tightly regulated process.
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Affiliation(s)
- Claudia Gebert
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Lauren Correia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Zhenhu Li
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | | | - Paul E Love
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
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Disparities in Cervical Cancer Incidence and Mortality: Can Epigenetics Contribute to Eliminating Disparities? Adv Cancer Res 2017; 133:129-156. [PMID: 28052819 DOI: 10.1016/bs.acr.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Screening for uterine cervical intraepithelial neoplasia (CIN) followed by aggressive treatment has reduced invasive cervical cancer (ICC) incidence and mortality. However, ICC cases and carcinoma in situ (CIS) continue to be diagnosed annually in the United States, with minorities bearing the brunt of this burden. Because ICC peak incidence and mortality are 10-15 years earlier than other solid cancers, the number of potential years of life lost to this cancer is substantial. Screening for early signs of CIN is still the mainstay of many cervical cancer control programs. However, the accuracy of existing screening tests remains suboptimal. Changes in epigenetic patterns that occur as a result of human papillomavirus infection contribute to CIN progression to cancer, and can be harnessed to improve existing screening tests. However, this requires a concerted effort to identify the epigenomic landscape that is reliably altered by HPV infection specific to ICC, distinct from transient changes.
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Brekke TD, Henry LA, Good JM. Genomic imprinting, disrupted placental expression, and speciation. Evolution 2016; 70:2690-2703. [PMID: 27714796 PMCID: PMC5123974 DOI: 10.1111/evo.13085] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022]
Abstract
The importance of regulatory incompatibilities to the early stages of speciation remains unclear. Hybrid mammals often show extreme parent-of-origin growth effects that are thought to be a consequence of disrupted genetic imprinting (parent-specific epigenetic gene silencing) during early development. Here, we test the long-standing hypothesis that abnormal hybrid growth reflects disrupted gene expression due to loss of imprinting (LOI) in hybrid placentas, resulting in dosage imbalances between paternal growth factors and maternal growth repressors. We analyzed placental gene expression in reciprocal dwarf hamster hybrids that show extreme parent-of-origin growth effects relative to their parental species. In massively enlarged hybrid placentas, we observed both extensive transgressive expression of growth-related genes and biallelic expression of many genes that were paternally silenced in normal sized hybrids. However, the apparent widespread disruption of paternal silencing was coupled with reduced gene expression levels overall. These patterns are contrary to the predictions of the LOI model and indicate that hybrid misexpression of dosage-sensitive genes is caused by other regulatory mechanisms in this system. Collectively, our results support a central role for disrupted gene expression and imprinting in the evolution of mammalian hybrid inviability, but call into question the generality of the widely invoked LOI model.
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Affiliation(s)
- Thomas D. Brekke
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Lindy A. Henry
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
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Plona K, Kim T, Halloran K, Wynshaw-Boris A. Chromosome therapy: Potential strategies for the correction of severe chromosome aberrations. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:422-430. [PMID: 27813255 DOI: 10.1002/ajmg.c.31530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Large chromosomal aberrations occur commonly during development, resulting in complex and multisystem diseases. In spite of this high frequency, there are currently no means for correcting these disorders due to their complexity and involvement of multiple genes. Recently, several new approaches have been devised that target whole chromosomes in vitro, which are collectively referred to as "Chromosome Therapies." These include silencing and selection for loss of the extra chromosome in trisomies, promotion of euploidy in an aneuploid culture, and forced loss and replacement of a chromosome. Here, we provide a review of Chromosome Therapy, and discuss potential directions for these methods clinically, as well as research applications and cellular models that can be made using these technologies. © 2016 Wiley Periodicals, Inc.
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Xue J, Schoenrock SA, Valdar W, Tarantino LM, Ideraabdullah FY. Maternal vitamin D depletion alters DNA methylation at imprinted loci in multiple generations. Clin Epigenetics 2016; 8:107. [PMID: 27777636 PMCID: PMC5062906 DOI: 10.1186/s13148-016-0276-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/07/2016] [Indexed: 01/07/2023] Open
Abstract
Background Environmental perturbation of epigenetic mechanisms is linked to a growing number of diseases. Characterizing the role environmental factors play in modifying the epigenome is important for disease etiology. Vitamin D is an essential nutrient affecting brain, bone, heart, immune and reproductive health. Vitamin D insufficiency is a global issue, and the role in maternal and child health remains under investigation. Methods We used Collaborative Cross (CC) inbred mice to characterize the effect of maternal vitamin D depletion on offspring phenotypic and epigenetic outcomes at imprinted domains (H19/Igf2, Snrpn, Dlk1/Gtl2, and Grb10) in the soma (liver) and germline (sperm). We assessed outcomes in two generations of offspring to determine heritability. We used reciprocal crosses between lines CC001/Unc and CC011/Unc to investigate parent of origin effects. Results Maternal vitamin D deficiency led to altered body weight and DNA methylation in two generations of offspring. Loci assayed in adult liver and sperm were mostly hypomethylated, but changes were few and small in effect size (<7 % difference on average). There was no change in total expression of genes adjacent to methylation changes in neonatal liver. Methylation changes were cell type specific such that changes at IG-DMR were present in sperm but not in liver. Some methylation changes were distinct between generations such that methylation changes at the H19ICR in second-generation liver were not present in first-generation sperm or liver. Interestingly, some diet-dependent changes in body weight and methylation were seemingly influenced by parent of origin such that reciprocal crosses exhibited inverse effects. Conclusions These findings demonstrate that maternal vitamin D status plays a role in determining DNA methylation state in the germline and soma. Detection of methylation changes in the unexposed second-generation demonstrates that maternal vitamin D depletion can have long-term effects on the epigenome of subsequent generations. Differences in vitamin D-dependent epigenetic state between cell types and generations indicate perturbation of the epigenetic landscape rather than a targeted, locus-specific effect. While the biological importance of these subtle changes remains unclear, they warrant an investigation of epigenome-wide effects of maternal vitamin D depletion. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0276-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Xue
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081 USA
| | - Sarah A Schoenrock
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599 USA ; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC 27599 USA
| | - William Valdar
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599 USA ; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Lisa M Tarantino
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599 USA ; Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Folami Y Ideraabdullah
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081 USA ; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599 USA ; Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599 USA
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Hur SK, Freschi A, Ideraabdullah F, Thorvaldsen JL, Luense LJ, Weller AH, Berger SL, Cerrato F, Riccio A, Bartolomei MS. Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver-Russell syndrome phenotypes. Proc Natl Acad Sci U S A 2016; 113:10938-43. [PMID: 27621468 PMCID: PMC5047210 DOI: 10.1073/pnas.1603066113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic imprinting affects a subset of genes in mammals, such that they are expressed in a monoallelic, parent-of-origin-specific manner. These genes are regulated by imprinting control regions (ICRs), cis-regulatory elements that exhibit allele-specific differential DNA methylation. Although genomic imprinting is conserved in mammals, ICRs are genetically divergent across species. This raises the fundamental question of whether the ICR plays a species-specific role in regulating imprinting at a given locus. We addressed this question at the H19/insulin-like growth factor 2 (Igf2) imprinted locus, the misregulation of which is associated with the human imprinting disorders Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). We generated a knock-in mouse in which the endogenous H19/Igf2 ICR (mIC1) is replaced by the orthologous human ICR (hIC1) sequence, designated H19(hIC1) We show that hIC1 can functionally replace mIC1 on the maternal allele. In contrast, paternally transmitted hIC1 leads to growth restriction, abnormal hIC1 methylation, and loss of H19 and Igf2 imprinted expression. Imprint establishment at hIC1 is impaired in the male germ line, which is associated with an abnormal composition of histone posttranslational modifications compared with mIC1. Overall, this study reveals evolutionarily divergent paternal imprinting at IC1 between mice and humans. The conserved maternal imprinting mechanism and function at IC1 demonstrates the possibility of modeling maternal transmission of hIC1 mutations associated with BWS in mice. In addition, we propose that further analyses in the paternal knock-in H19(+/hIC1) mice will elucidate the molecular mechanisms that may underlie SRS.
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Affiliation(s)
- Stella K Hur
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Andrea Freschi
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Folami Ideraabdullah
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Joanne L Thorvaldsen
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Lacey J Luense
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Angela H Weller
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Flavia Cerrato
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy;
| | - Andrea Riccio
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy; Institute of Genetics and Biophysics A. Buzzati-Traverso, 80131 Naples, Italy
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104;
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Ren YY, Koch LG, Britton SL, Qi NR, Treutelaar MK, Burant CF, Li JZ. Selection-, age-, and exercise-dependence of skeletal muscle gene expression patterns in a rat model of metabolic fitness. Physiol Genomics 2016; 48:816-825. [PMID: 27637250 DOI: 10.1152/physiolgenomics.00118.2015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 09/09/2016] [Indexed: 11/22/2022] Open
Abstract
Intrinsic aerobic exercise capacity can influence many complex traits including obesity and aging. To study this connection we established two rat lines by divergent selection of untrained aerobic capacity. After 32 generations the high capacity runners (HCR) and low capacity runners (LCR) differed in endurance running distance and body fat, blood glucose, other health indicators, and natural life span. To understand the interplay among genetic differences, chronological age, and acute exercise we performed microarray-based gene expression analyses in skeletal muscle with a 2×2×2 design to simultaneously compare HCR and LCR, old and young animals, and rest and exhaustion. Transcripts for mitochondrial function are expressed higher in HCRs than LCRs at both rest and exhaustion and for both age groups. Expression of cell adhesion and extracellular matrix genes tend to decrease with age. This and other age effects are more prominent in LCRs than HCRs, suggesting that HCRs have a slower aging process and this may be partly due to their better metabolic health. Strenuous exercise mainly affects transcription regulation and cellular response. The effects of any one factor often depend on the other two. For example, there are ∼140 and ∼110 line-exercise "interacting" genes for old and young animals, respectively. Many genes highlighted in our study are consistent with prior reports, but many others are novel. The gene- and pathway-level statistics for the main effects, either overall or stratified, and for all possible interactions, represent a rich reference dataset for understanding the interdependence among lines, aging, and exercise.
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Affiliation(s)
- Yu-Yu Ren
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Lauren G Koch
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan; and
| | - Steven L Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan; and
| | - Nathan R Qi
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Mary K Treutelaar
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan;
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Rienecker KDA, Hill MJ, Isles AR. Methods of epigenome editing for probing the function of genomic imprinting. Epigenomics 2016; 8:1389-1398. [PMID: 27625199 DOI: 10.2217/epi-2016-0073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The curious patterns of imprinted gene expression draw interest from several scientific disciplines to the functional consequences of genomic imprinting. Methods of probing the function of imprinting itself have largely been indirect and correlational, relying heavily on conventional transgenics. Recently, the burgeoning field of epigenome editing has provided new tools and suggested strategies for asking causal questions with site specificity. This perspective article aims to outline how these new methods may be applied to questions of functional imprinting and, with this aim in mind, to suggest new dimensions for the expansion of these epigenome-editing tools.
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Affiliation(s)
- Kira DA Rienecker
- MRC Centre for Neuropsychiatric Genetics & Genomics, Department of Psychological Medicine & Clinical Neuroscience, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Matthew J Hill
- MRC Centre for Neuropsychiatric Genetics & Genomics, Department of Psychological Medicine & Clinical Neuroscience, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Anthony R Isles
- MRC Centre for Neuropsychiatric Genetics & Genomics, Department of Psychological Medicine & Clinical Neuroscience, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
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Linglart A, Maupetit-Méhouas S, Silve C. GNAS -Related Loss-of-Function Disorders and the Role of Imprinting. Horm Res Paediatr 2016; 79:119-29. [PMID: 23548772 DOI: 10.1159/000348516] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 01/27/2013] [Indexed: 11/19/2022] Open
Abstract
GNAS (guanine nucleotide-binding protein, α stimulating) is a complex imprinted locus coding, besides the α-stimulatory subunit of the G protein, the paternally (extra-large, antisense and A/B) and maternally (neuroendocrine secretory protein) transcripts. Heterozygous mutations in the coding sequence of GNAS produce dominant phenotypes (combination of resistances to hormones signaling through G-protein-coupled receptors, osteodystrophy and obesity) that depend on the parental origin of the mutated allele. Likewise, alterations in the methylation at promoters of GNAS transcripts, associated or not with deletions of imprinting control regions in the nearby STX16 gene or within GNAS, prompt resistance to parathormone when affecting the maternal allele. Therefore, imprinting of GNAS is the determining factor for the variability of the phenotype. Knowledge of the various phenotypes is necessary for genetic counseling as well as an appropriate therapeutic balance between regular follow-up, prevention of disease complications and iatrogeny.
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Affiliation(s)
- Agnès Linglart
- Endocrinology and Diabetology for Children and French Center of Reference for Rare Disorders of Calcium and Phosphorus Metabolism, Bicêtre-Paris-Sud Hospital, Le Kremlin Bicêtre, France
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Pervjakova N, Kasela S, Morris AP, Kals M, Metspalu A, Lindgren CM, Salumets A, Mägi R. Imprinted genes and imprinting control regions show predominant intermediate methylation in adult somatic tissues. Epigenomics 2016; 8:789-99. [PMID: 27004446 PMCID: PMC5066126 DOI: 10.2217/epi.16.8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/03/2016] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting is an epigenetic feature characterized by parent-specific monoallelic gene expression. The aim of this study was to compare the DNA methylation status of imprinted genes and imprinting control regions (ICRs), harboring differentially methylated regions (DMRs) in a comprehensive panel of 18 somatic tissues. The germline DMRs analyzed were divided into ubiquitously imprinted and placenta-specific DMRs, which show identical and different methylation imprints in adult somatic and placental tissues, respectively. We showed that imprinted genes and ICR DMRs maintain methylation patterns characterized by intermediate methylation levels in somatic tissues, which are pronounced in a specific region of the promoter area, located 200-1500 bp from the transcription start site. This intermediate methylation is concordant with gene expression from a single unmethylated allele and silencing of a reciprocal parental allele through DNA methylation. The only exceptions were seen for ICR DMRs of placenta-specific imprinted genes, which showed low levels of methylation, suggesting that these genes escape parent-specific epigenetic regulation in somatic tissues.
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Affiliation(s)
- Natalia Pervjakova
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- National Institute for Health & Welfare, University of Helsinki, Helsinki FI-00271, Finland
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Silva Kasela
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu 50409, Estonia
| | - Andres Metspalu
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Big Data Institute, University of Oxford, Oxford, OX3 7BN, UK
- Broad Institute of the Massachusetts Institute of Technology & Harvard University, Cambridge, MA 02142, USA
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu 50410, Estonia
- Department of Obstetrics & Gynecology, University of Tartu, Tartu 51014, Estonia
- Institute of Bio- & Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
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Gonzalez-Rodriguez P, Cantu J, O’Neil D, Seferovic MD, Goodspeed DM, Suter MA, Aagaard KM. Alterations in expression of imprinted genes from the H19/IGF2 loci in a multigenerational model of intrauterine growth restriction (IUGR). Am J Obstet Gynecol 2016; 214:625.e1-625.e11. [PMID: 26880735 DOI: 10.1016/j.ajog.2016.01.194] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 01/16/2016] [Accepted: 01/20/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND The H19/IGF2 imprinted loci have attracted recent attention because of their role in cellular differentiation and proliferation, heritable gene regulation, and in utero or early postnatal growth and development. Expression from the imprinted H19/IGF2 locus involves a complex interplay of 3 means of epigenetic regulation: proper establishment of DNA methylation, promoter occupancy of CTCF, and expression of microRNA-675. We have demonstrated previously in a multigenerational rat model of intrauterine growth restriction the epigenetic heritability of adult metabolic syndrome in a F2 generation. We have further demonstrated abrogation of the F2 adult metabolic syndrome phenotype with essential nutrient supplementation of intermediates along the 1-carbon pathway and shown that alterations in the metabolome precede the adult onset of metabolic syndrome. The upstream molecular and epigenomic mediators underlying these observations, however, have yet to be elucidated fully. OBJECTIVE In the current study, we sought to characterize the impact of the intrauterine growth-restricted lineage and essential nutrient supplementation on both levels and molecular mediators of H19 and IGF2 gene expression in the F2 generation. STUDY DESIGN F2 intrauterine growth-restricted and sham lineages were obtained by exposing P1 (grandmaternal) pregnant dams to bilateral uterine artery ligation or sham surgery at gestational day 19.5. F1 pups were allocated to the essential nutrient supplemented or control diet at postnatal day 21, and bred at 6-7 weeks of age. Hepatic tissues from the resultant F2 offspring at birth and at weaning (day 21) were obtained. Bisulfite modification and sequencing was employed for methylation analysis. H19 and IGF2 expression was measured by quantitative polymerase chain reaction. Promoter occupancy was quantified by the use of chromatin immunoprecipitation, or ChIP, against CTCF insulator proteins. RESULTS Growth-restricted F2 on control diet demonstrated significant down-regulation in H19 expression compared with sham lineage (0.7831 vs 1.287; P < .05); however, essential nutrient supplementation diet abrogates this difference (4.995 vs 5.100; P > .05). Conversely, Igf2 was up-regulated by essential nutrient supplemented diet on the sham lineage (2.0 fold, P = .01), an effect that was not observed in the growth restricted offspring. A significant differential methylation was observed in the promoter region of region H19 among the intrauterine growth-restricted lineage (18% vs 25%; P < .05) on a control diet, whereas the essential nutrient supplemented diet was alternately associated with hypermethylation in both lineages (sham: 50%; intrauterine growth restriction: 84%, P < .05). Consistent with essential nutrient supplementation impacting the epigenome, a decrease of CTCF promoter occupancy was observed in CTCF4 of the growth restricted lineage (2.45% vs 0.56%; P < .05) on the control diet, an effect that was repressed with essential nutrient supplementation. CONCLUSION Heritable growth restriction is associated with changes in H19 gene expression; these changes are reversible with diet supplementation to favorably impact adult metabolic syndrome.
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Elhamamsy AR. DNA methylation dynamics in plants and mammals: overview of regulation and dysregulation. Cell Biochem Funct 2016; 34:289-98. [PMID: 27003927 DOI: 10.1002/cbf.3183] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 12/22/2022]
Abstract
DNA methylation is a major epigenetic marking mechanism regulating various biological functions in mammals and plant. The crucial role of DNA methylation has been observed in cellular differentiation, embryogenesis, genomic imprinting and X-chromosome inactivation. Furthermore, DNA methylation takes part in disease susceptibility, responses to environmental stimuli and the biodiversity of natural populations. In plant, different types of environmental stress have demonstrated the ability to alter the archetype of DNA methylation through the genome, change gene expression and confer a mechanism of adaptation. DNA methylation dynamics are regulated by three processes de novo DNA methylation, methylation maintenance and DNA demethylation. These processes have their similarities and differences between mammals and plants. Furthermore, the dysregulation of DNA methylation dynamics represents one of the primary molecular mechanisms of developing diseases in mammals. This review discusses the regulation and dysregulation of DNA methylation in plants and mammals. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Clinical Pharmacy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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Huang W, Qi CB, Lv SW, Xie M, Feng YQ, Huang WH, Yuan BF. Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry. Anal Chem 2016; 88:1378-84. [PMID: 26707930 DOI: 10.1021/acs.analchem.5b03962] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA methylation (5-methylcytosine, 5-mC) is the best characterized epigenetic mark that has regulatory roles in diverse biological processes. Recent investigation of RNA modifications also raises the possible functions of RNA adenine and cytosine methylations on gene regulation in the form of "RNA epigenetics." Previous studies demonstrated global DNA hypomethylation in tumor tissues compared to healthy controls. However, DNA and RNA methylation in circulating tumor cells (CTCs) that are derived from tumors are still a mystery due to the lack of proper analytical methods. In this respect, here we established an effective CTCs capture system conjugated with a combined strategy of sample preparation for the captured CTCs lysis, nucleic acids digestion, and nucleosides extraction in one tube. The resulting nucleosides were then further analyzed by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). With the developed method, we are able to detect DNA and RNA methylation (5-methyl-2'-deoxycytidine, 5-methylcytidine, and N(6)-methyladenosine) in a single cell. We then further successfully determined DNA and RNA methylation in CTCs from lung cancer patients. Our results demonstrated, for the first time, a significant decrease of DNA methylation (5-methyl-2'-deoxycytidine) and increase of RNA adenine and cytosine methylations (N(6)-methyladenosine and 5-methylcytidine) in CTCs compared with whole blood cells. The discovery of DNA hypomethylation and RNA hypermethylation in CTCs in the current study together with previous reports of global DNA hypomethylation in tumor tissues suggest that nucleic acid modifications play important roles in the formation and development of cancer cells. This work constitutes the first step for the investigation of DNA and RNA methylation in CTCs, which may facilitate uncovering the metastasis mechanism of cancers in the future.
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Affiliation(s)
- Wei Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Chu-Bo Qi
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China.,Department of Pathology, Hubei Cancer Hospital , Wuhan, Hubei 430079, Peoples' Republic of China
| | - Song-Wei Lv
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Min Xie
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Wei-Hua Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
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Pal M, Ebrahimi S, Oh G, Khare T, Zhang A, Kaminsky ZA, Wang SC, Petronis A. High Precision DNA Modification Analysis of HCG9 in Major Psychosis. Schizophr Bull 2016; 42:170-7. [PMID: 26078387 PMCID: PMC4681545 DOI: 10.1093/schbul/sbv079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
New epigenetic technologies may uncover etiopathogenic mechanisms of major psychosis. In this study, we applied padlock probe-based ultra-deep bisulfite sequencing for fine mapping of modified cytosines of the HLA complex group 9 (nonprotein coding) gene in the postmortem brains of individuals affected with schizophrenia or bipolar disorder and unaffected controls. Significant differences between patients and controls were detected in both CpG and CpH modifications. In addition, we identified epigenetic age effects, DNA modification differences between sense and anti-sense strands, and demonstrated how DNA modification data can be used in clustering of patient populations. Our findings revealed new epigenetic complexities but also highlighted the potential of DNA modification approaches in the search of heterogeneous causes of major psychiatric disease.
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Affiliation(s)
- Mrinal Pal
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, CAMH, Toronto, Ontario M5T 1R8, Canada
| | - Sasha Ebrahimi
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, CAMH, Toronto, Ontario M5T 1R8, Canada
| | - Gabriel Oh
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, CAMH, Toronto, Ontario M5T 1R8, Canada
| | - Tarang Khare
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, CAMH, Toronto, Ontario M5T 1R8, Canada
| | - Aiping Zhang
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, CAMH, Toronto, Ontario M5T 1R8, Canada
| | - Zachary A. Kaminsky
- The Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Sun-Chong Wang
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, CAMH, Toronto, Ontario M5T 1R8, Canada;,Institute of Systems Biology and Bioinformatics, National Central University, Chungli City 32001, Taiwan
| | - Arturas Petronis
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, CAMH, Toronto, Ontario M5T 1R8, Canada;
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Mendonça ADS, Guimarães ALS, da Silva NMA, Caetano AR, Dode MAN, Franco MM. Characterization of the IGF2 Imprinted Gene Methylation Status in Bovine Oocytes during Folliculogenesis. PLoS One 2015; 10:e0142072. [PMID: 26517264 PMCID: PMC4627647 DOI: 10.1371/journal.pone.0142072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/17/2015] [Indexed: 02/07/2023] Open
Abstract
DNA methylation reprogramming occurs during mammalian gametogenesis and embryogenesis. Sex-specific DNA methylation patterns at specific CpG islands controlling imprinted genes are acquired during this window of development. Characterization of the DNA methylation dynamics of imprinted genes acquired by oocytes during folliculogenesis is essential for understanding the physiological and genetic aspects of female gametogenesis and to determine the parameters for oocyte competence. This knowledge can be used to improve in vitro embryo production (IVP), specifically because oocyte competence is one of the most important aspects determining the success of IVP. Imprinted genes, such as IGF2, play important roles in embryo development, placentation and fetal growth. The aim of this study was to characterize the DNA methylation profile of the CpG island located in IGF2 exon 10 in oocytes during bovine folliculogenesis. The methylation percentages in oocytes from primordial follicles, final secondary follicles, small antral follicles, large antral follicles, MII oocytes and spermatozoa were 73.74 ± 2.88%, 58.70 ± 7.46%, 56.00 ± 5.58%, 65.77 ± 5.10%, 56.35 ± 7.45% and 96.04 ± 0.78%, respectively. Oocytes from primordial follicles showed fewer hypomethylated alleles (15.5%) than MII oocytes (34.6%) (p = 0.039); spermatozoa showed only hypermethylated alleles. Moreover, MII oocytes were less methylated than spermatozoa (p<0.001). Our results showed that the methylation pattern of this region behaves differently between mature oocytes and spermatozoa. However, while this region has a classical imprinted pattern in spermatozoa that is fully methylated, it was variable in mature oocytes, showing hypermethylated and hypomethylated alleles. Furthermore, our results suggest that this CpG island may have received precocious reprogramming, considering that the hypermethylated pattern was already found in growing oocytes from primordial follicles. These results may contribute to our understanding of the reprogramming of imprinted genes during bovine oogenesis.
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Affiliation(s)
- Anelise dos Santos Mendonça
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Ana Luíza Silva Guimarães
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- School of Agriculture and Veterinary Medicine, University of Brasília, Brasília, Distrito Federal, Brazil
| | | | | | - Margot Alves Nunes Dode
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- School of Agriculture and Veterinary Medicine, University of Brasília, Brasília, Distrito Federal, Brazil
| | - Maurício Machaim Franco
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
- School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
- * E-mail:
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47
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Methylation-sensitive restriction enzyme nested real time PCR, a potential approach for sperm DNA identification. J Forensic Leg Med 2015; 34:34-9. [DOI: 10.1016/j.jflm.2015.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/05/2015] [Accepted: 05/07/2015] [Indexed: 11/19/2022]
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48
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Aldape K, Zadeh G, Mansouri S, Reifenberger G, von Deimling A. Glioblastoma: pathology, molecular mechanisms and markers. Acta Neuropathol 2015; 129:829-48. [PMID: 25943888 DOI: 10.1007/s00401-015-1432-1] [Citation(s) in RCA: 433] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/14/2015] [Accepted: 04/22/2015] [Indexed: 12/30/2022]
Abstract
Recent advances in genomic technology have led to a better understanding of key molecular alterations that underlie glioblastoma (GBM). The current WHO-based classification of GBM is mainly based on histologic features of the tumor, which frequently do not reflect the molecular differences that describe the diversity in the biology of these lesions. The current WHO definition of GBM relies on the presence of high-grade astrocytic neoplasm with the presence of either microvascular proliferation and/or tumor necrosis. High-throughput analyses have identified molecular subtypes and have led to progress in more accurate classification of GBM. These findings, in turn, would result in development of more effective patient stratification, targeted therapeutics, and prediction of patient outcome. While consensus has not been reached on the precise nature and means to sub-classify GBM, it is clear that IDH-mutant GBMs are clearly distinct from GBMs without IDH1/2 mutation with respect to molecular and clinical features, including prognosis. In addition, recent findings in pediatric GBMs regarding mutations in the histone H3F3A gene suggest that these tumors may represent a 3rd major category of GBM, separate from adult primary (IDH1/2 wt), and secondary (IDH1/2 mut) GBMs. In this review, we describe major clinically relevant genetic and epigenetic abnormalities in GBM-such as mutations in IDH1/2, EGFR, PDGFRA, and NF1 genes-altered methylation of MGMT gene promoter, and mutations in hTERT promoter. These markers may be incorporated into a more refined classification system and applied in more accurate clinical decision-making process. In addition, we focus on current understanding of the biologic heterogeneity and classification of GBM and highlight some of the molecular signatures and alterations that characterize GBMs as histologically defined. We raise the question whether IDH-wild type high grade astrocytomas without microvascular proliferation or necrosis might best be classified as GBM, even if they lack the histologic hallmarks as required in the current WHO classification. Alternatively, an astrocytic tumor that fits the current histologic definition of GBM, but which shows an IDH mutation may in fact be better classified as a distinct entity, given that IDH-mutant GBM are quite distinct from a biological and clinical perspective.
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Affiliation(s)
- Kenneth Aldape
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, 101 College St., Toronto, ON, M5G 1L7, Canada,
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Hypermethylated Epidermal growth factor receptor (EGFR) promoter is associated with gastric cancer. Sci Rep 2015; 5:10154. [PMID: 25959250 PMCID: PMC4426697 DOI: 10.1038/srep10154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/01/2015] [Indexed: 01/28/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinases ErbB family and it is found to be overexpressed in gastric cancer. However, the mechanism of the regulation of the EGFR expression is still unknown. We used the Sequenom EpiTYPER assay to detect the methylation status of the EGFR promoter in normal and tumour tissues of 30 patients with gastric cancer. We also carried out quantitative real time PCR (qPCR) to detect the expression level of EGFR in our 30 patients. Notably, increased methylation level at EGFR promoter was found in tumour tissues than the corresponding adjacent noncancerous. In both Region I DMR and Region II DMR detected in our study, tumor tissues were significantly hypermethylated (P=2.7743E-10 and 2.1703E-05, respectively). Region I_⊿CpG_2 was also found to be associated with the presence of distant metastasis (P=0.0323). Furthermore, the results showed a strongly significant association between the relative EGFR expression and the EGFR methylation changes in both Region I and Region II (P=0.0004 and 0.0001, respectively). Our findings help to indicate the hypermethylation at EGFR promoter in gastric cancer and it could be a potential epigenetic biomarker for gastric cancer status and progression.
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50
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Perera BPU, Teruyama R, Kim J. Yy1 gene dosage effect and bi-allelic expression of Peg3. PLoS One 2015; 10:e0119493. [PMID: 25774914 PMCID: PMC4361396 DOI: 10.1371/journal.pone.0119493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/28/2015] [Indexed: 01/22/2023] Open
Abstract
In the current study, we tested the in vivo effects of Yy1 gene dosage on the Peg3 imprinted domain with various breeding schemes utilizing two sets of mutant alleles. The results indicated that a half dosage of Yy1 coincides with the up-regulation of Peg3 and Zim1, suggesting a repressor role of Yy1 in this imprinted domain. This repressor role of Yy1 is consistent with the observations derived from previous in vitro studies. The current study also provided an unexpected observation that the maternal allele of Peg3 is also normally expressed, and thus the expression of Peg3 is bi-allelic in the specific areas of the brain, including the choroid plexus, the PVN (Paraventricular Nucleus) and the SON (Supraoptic Nucleus) of the hypothalamus. The exact roles of the maternal allele of Peg3 in these cell types are currently unknown, but this new finding confirms the previous prediction that the maternal allele may be functional in specific cell types based on the lethality associated with the homozygotes for several mutant alleles of the Peg3 locus. Overall, these results confirm the repressor role of Yy1 in the Peg3 domain and also provide a new insight regarding the bi-allelic expression of Peg3 in mouse brain.
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Affiliation(s)
- Bambarendage P. U. Perera
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, United States of America
| | - Ryoichi Teruyama
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, United States of America
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, United States of America
- * E-mail:
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