1
|
Hilton BJ, Griffin JM, Fawcett JW, Bradke F. Neuronal maturation and axon regeneration: unfixing circuitry to enable repair. Nat Rev Neurosci 2024:10.1038/s41583-024-00849-3. [PMID: 39164450 DOI: 10.1038/s41583-024-00849-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2024] [Indexed: 08/22/2024]
Abstract
Mammalian neurons lose the ability to regenerate their central nervous system axons as they mature during embryonic or early postnatal development. Neuronal maturation requires a transformation from a situation in which neuronal components grow and assemble to one in which these components are fixed and involved in the machinery for effective information transmission and computation. To regenerate after injury, neurons need to overcome this fixed state to reactivate their growth programme. A variety of intracellular processes involved in initiating or sustaining neuronal maturation, including the regulation of gene expression, cytoskeletal restructuring and shifts in intracellular trafficking, have been shown to prevent axon regeneration. Understanding these processes will contribute to the identification of targets to promote repair after injury or disease.
Collapse
Affiliation(s)
- Brett J Hilton
- Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
- International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, British Columbia, Canada.
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Jarred M Griffin
- Laboratory for Axonal Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - James W Fawcett
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK.
- Centre for Reconstructive Neuroscience, Institute for Experimental Medicine Czech Academy of Science (CAS), Prague, Czechia.
| | - Frank Bradke
- Laboratory for Axonal Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| |
Collapse
|
2
|
Zhang J, Sheng H, Hu C, Li F, Cai B, Ma Y, Wang Y, Ma Y. Effects of DNA Methylation on Gene Expression and Phenotypic Traits in Cattle: A Review. Int J Mol Sci 2023; 24:11882. [PMID: 37569258 PMCID: PMC10419045 DOI: 10.3390/ijms241511882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
Gene expression in cells is determined by the epigenetic state of chromatin. Therefore, the study of epigenetic changes is very important to understand the regulatory mechanism of genes at the molecular, cellular, tissue and organ levels. DNA methylation is one of the most studied epigenetic modifications, which plays an important role in maintaining genome stability and ensuring normal growth and development. Studies have shown that methylation levels in bovine primordial germ cells, the rearrangement of methylation during embryonic development and abnormal methylation during placental development are all closely related to their reproductive processes. In addition, the application of bovine male sterility and assisted reproductive technology is also related to DNA methylation. This review introduces the principle, development of detection methods and application conditions of DNA methylation, with emphasis on the relationship between DNA methylation dynamics and bovine spermatogenesis, embryonic development, disease resistance and muscle and fat development, in order to provide theoretical basis for the application of DNA methylation in cattle breeding in the future.
Collapse
Affiliation(s)
- Junxing Zhang
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hui Sheng
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Chunli Hu
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Fen Li
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Bei Cai
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Yanfen Ma
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Yachun Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| |
Collapse
|
3
|
Irani D, Balasinor N, Bansal V, Tandon D, Patil A, Singh D. Whole genome bisulfite sequencing of sperm reveals differentially methylated regions in male partners of idiopathic recurrent pregnancy loss cases. Fertil Steril 2023; 119:420-432. [PMID: 36528109 DOI: 10.1016/j.fertnstert.2022.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To study the genome wide alterations in sperm DNA methylation in male partners of idiopathic recurrent pregnancy loss (iRPL) cases and note regions as potential diagnostic markers. DESIGN Case-control study and methylome analysis of human sperm. SETTING Obstetrics and Gynaecology clinics. PATIENT(S) Control group consists of apparently healthy fertile men having fathered a child within the last 2 years (n = 39); and case group consists of male partners of iRPL cases having ≥2 consecutive 1st trimester pregnancy losses (n = 47). INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Sperm DNA samples of controls and cases were selected for whole genome bisulfite sequencing analysis based on the previously set thresholds of global methylation levels and methylation levels of imprinted genes (KvDMR and ZAC). Whole genome bisulfite sequencing of selected sperm genomic DNA was performed to identify differentially methylated CpG sites of iRPL cases compared with fertile controls. Pathway analysis of all the differentially methylated genes was done by Database for Annotation, Visualization, and Integrated Discovery annotation tool and Kyoto Encyclopedia of Genes and Genomes tool. Differentially methylated CpGs within genes relevant to embryo and placenta development were selected to further validate their methylation levels in study population by pyrosequencing. RESULT(S) A total of 9497 differentially methylated CpGs with highest enrichment in intronic regions were obtained. In addition, 5352 differentially methylated regions and 2087 differentially methylated genes were noted. Signaling pathways involved in development were enriched on pathway analysis. Select CpGs within genes PPARG, KCNQ1, SETD2, and MAP3K4 showed distinct hypomethylated subpopulations within iRPL study population. CONCLUSION(S) Our study highlights the altered methylation landscape of iRPL sperm, and their possible implications in pathways of embryo and placental development. The CpG sites that are hypomethylated specifically in sperm of iRPL subpopulation can be further assessed as predictive biomarkers.
Collapse
Affiliation(s)
- Delna Irani
- Department of Neuroendocrinology, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Nafisa Balasinor
- Department of Neuroendocrinology, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Vandana Bansal
- Department of Obstetrics and Gynaecology, Nowrosjee Wadia Maternity Hospital, Mumbai, India
| | - Deepti Tandon
- Department of Clinical Research, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Anushree Patil
- Department of Clinical Research, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Dipty Singh
- Department of Neuroendocrinology, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India.
| |
Collapse
|
4
|
Zhou X, Torres VE. Emerging therapies for autosomal dominant polycystic kidney disease with a focus on cAMP signaling. Front Mol Biosci 2022; 9:981963. [PMID: 36120538 PMCID: PMC9478168 DOI: 10.3389/fmolb.2022.981963] [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: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), with an estimated genetic prevalence between 1:400 and 1:1,000 individuals, is the third most common cause of end stage kidney disease after diabetes mellitus and hypertension. Over the last 3 decades there has been great progress in understanding its pathogenesis. This allows the stratification of therapeutic targets into four levels, gene mutation and polycystin disruption, proximal mechanisms directly caused by disruption of polycystin function, downstream regulatory and signaling pathways, and non-specific pathophysiologic processes shared by many other diseases. Dysfunction of the polycystins, encoded by the PKD genes, is closely associated with disruption of calcium and upregulation of cyclic AMP and protein kinase A (PKA) signaling, affecting most downstream regulatory, signaling, and pathophysiologic pathways altered in this disease. Interventions acting on G protein coupled receptors to inhibit of 3',5'-cyclic adenosine monophosphate (cAMP) production have been effective in preclinical trials and have led to the first approved treatment for ADPKD. However, completely blocking cAMP mediated PKA activation is not feasible and PKA activation independently from cAMP can also occur in ADPKD. Therefore, targeting the cAMP/PKA/CREB pathway beyond cAMP production makes sense. Redundancy of mechanisms, numerous positive and negative feedback loops, and possibly counteracting effects may limit the effectiveness of targeting downstream pathways. Nevertheless, interventions targeting important regulatory, signaling and pathophysiologic pathways downstream from cAMP/PKA activation may provide additive or synergistic value and build on a strategy that has already had success. The purpose of this manuscript is to review the role of cAMP and PKA signaling and their multiple downstream pathways as potential targets for emergent therapies for ADPKD.
Collapse
Affiliation(s)
- Xia Zhou
- Mayo Clinic, Department of Nephrology, Rochester, MN, United States
| | | |
Collapse
|
5
|
Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nat Neurosci 2022; 25:1049-1058. [PMID: 35915179 PMCID: PMC9343253 DOI: 10.1038/s41593-022-01123-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022]
Abstract
Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.
Collapse
|
6
|
Hayashi T, Eto K, Kadoya Y. Downregulation of ten-eleven translocation-2 triggers epithelial differentiation during organogenesis. Differentiation 2022; 125:45-53. [DOI: 10.1016/j.diff.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 11/26/2022]
|
7
|
Choudhury J, Pandey D, Chaturvedi PK, Gupta S. Epigenetic regulation of epithelial to mesenchymal transition: a trophoblast perspective. Mol Hum Reprod 2022; 28:6572349. [PMID: 35451485 DOI: 10.1093/molehr/gaac013] [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: 02/11/2022] [Revised: 03/31/2022] [Indexed: 11/12/2022] Open
Abstract
Epigenetic changes alter expression of genes at both pre- and post-transcriptional levels without changing their DNA sequence. Accumulating evidence suggests that such changes can modify cellular behaviour and characteristics required during development and in response to various extracellular stimuli. Trophoblast cells develop from the outermost trophectoderm layer of the blastocyst and undergo many phenotypic changes as the placenta develops. One such phenotypic change is differentiation of the epithelial natured cytotrophoblasts into the mesenchymal natured extravillous trophoblasts. The extravillous trophoblasts are primarily responsible for invading into the maternal decidua and thus establishing connection with the maternal spiral arteries. Any dysregulation of this process can have adverse effects on the pregnancy outcome. Hence, tight regulation of this epithelial-mesenchymal transition is critical for successful pregnancy. This review summarizes the recent research on the epigenetic regulation of the epithelial-mesenchymal transition occurring in the trophoblast cells during placental development. The functional significance of chemical modifications of DNA and histone, which regulate transcription, as well as non-coding RNAs, which control gene expression post-transcriptionally, is discussed in relation to trophoblast biology.
Collapse
Affiliation(s)
- Jaganmoy Choudhury
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
| | - Deepak Pandey
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
| | - Pradeep Kumar Chaturvedi
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
| | - Surabhi Gupta
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
| |
Collapse
|
8
|
Domingo-Relloso A, Bozack A, Kiihl S, Rodriguez-Hernandez Z, Rentero-Garrido P, Casasnovas JA, Leon-Latre M, Garcia-Barrera T, Gomez-Ariza JL, Moreno B, Cenarro A, de Marco G, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Navas-Acien A, Gamble M, Tellez-Plaza M. Arsenic exposure and human blood DNA methylation and hydroxymethylation profiles in two diverse populations from Bangladesh and Spain. ENVIRONMENTAL RESEARCH 2022; 204:112021. [PMID: 34516978 PMCID: PMC8734953 DOI: 10.1016/j.envres.2021.112021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Associations of arsenic (As) with the sum of 5-mC and 5-hmC levels have been reported; however, As exposure-related differences of the separated 5-mC and 5-hmC markers have rarely been studied. METHODS In this study, we evaluated the association of arsenic exposure biomarkers and 5-mC and 5-hmC in 30 healthy men (43-55 years) from the Aragon Workers Health Study (AWHS) (Spain) and 31 healthy men (31-50 years) from the Folic Acid and Creatinine Trial (FACT) (Bangladesh). We conducted 5-mC and 5-hmC profiling using Infinium MethylationEPIC arrays, on paired standard and modified (ox-BS in AWHS and TAB in FACT) bisulfite converted blood DNA samples. RESULTS The median for the sum of urine inorganic and methylated As species (ΣAs) (μg/L) was 12.5 for AWHS and 89.6 for FACT. The median of blood As (μg/L) was 8.8 for AWHS and 10.2 for FACT. At a statistical significance p-value cut-off of 0.01, the differentially methylated (DMP) and hydroxymethylated (DHP) positions were mostly located in different genomic sites. Several DMPs and DHPs were consistently found in AWHS and FACT both for urine ΣAs and blood models, being of special interest those attributed to the DIP2C gene. Three DMPs (annotated to CLEC12A) for AWHS and one DHP (annotated to NPLOC4) for FACT remained statistically significant after false discovery rate (FDR) correction. Pathways related to chronic diseases including cardiovascular, cancer and neurological were enriched. CONCLUSIONS While we identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, differences in As-related epigenetic sites across the study populations may additionally reflect low and high As-specific associations. This work contributes a deeper understanding of potential epigenetic dysregulations of As. However, further research is needed to confirm biological consequences associated with DIP2C epigenetic regulation and to investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.
Collapse
Affiliation(s)
- Arce Domingo-Relloso
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain; Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA; Department of Statistics and Operations Research, University of Valencia, Spain
| | - Anne Bozack
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA; Department of Environmental Health Sciences, School of Public Health, University of California, Berkeley, USA
| | - Samara Kiihl
- Department of Statistics, State University of Campinas, Brazil
| | - Zulema Rodriguez-Hernandez
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Pilar Rentero-Garrido
- Precision Medicine Unit, Biomedical Research Institute Hospital Clinic de Valencia INCLIVA, Valencia, Spain
| | - J Antonio Casasnovas
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Montserrat Leon-Latre
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Tamara Garcia-Barrera
- Research Center on Natural Resources, Health and the Environment, Department of Chemistry, University of Huelva, Huelva, Spain
| | - J Luis Gomez-Ariza
- Research Center on Natural Resources, Health and the Environment, Department of Chemistry, University of Huelva, Huelva, Spain
| | - Belen Moreno
- Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Ana Cenarro
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Griselda de Marco
- Genomics Area, Foundation for the Promotion of Health and Biomedical Research of the Valencian Region (FISABIO), Valencia, Spain
| | - Faruque Parvez
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Abu B Siddique
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Hasan Shahriar
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Mohammad N Uddin
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Tariqul Islam
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Mary Gamble
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Maria Tellez-Plaza
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
9
|
Abstract
Osteoporosis, characterised by low bone mass, poor bone structure, and an increased risk of fracture, is a major public health problem. There is increasing evidence that the influence of the environment on gene expression, through epigenetic processes, contributes to variation in BMD and fracture risk across the lifecourse. Such epigenetic processes include DNA methylation, histone and chromatin modifications and non-coding RNAs. Examples of associations with phenotype include DNA methylation in utero linked to maternal vitamin D status, and to methylation of target genes such as OPG and RANKL being associated with osteoporosis in later life. Epigenome-wide association studies and multi-omics technologies have further revealed susceptibility loci, and histone acetyltransferases, deacetylases and methylases are being considered as therapeutic targets. This review encompasses recent advances in our understanding of epigenetic mechanisms in the regulation of bone mass and osteoporosis development, and outlines possible diagnostic and prognostic biomarker applications.
Collapse
Affiliation(s)
| | | | - Cyrus Cooper
- MRC Lifecourse Epidemiology Centre, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK; NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Centre, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.
| |
Collapse
|
10
|
Fritz AJ, El Dika M, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype. Results Probl Cell Differ 2022; 70:339-373. [PMID: 36348114 PMCID: PMC9753575 DOI: 10.1007/978-3-031-06573-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epigenetic gene regulatory mechanisms play a central role in the biological control of cell and tissue structure, function, and phenotype. Identification of epigenetic dysregulation in cancer provides mechanistic into tumor initiation and progression and may prove valuable for a variety of clinical applications. We present an overview of epigenetically driven mechanisms that are obligatory for physiological regulation and parameters of epigenetic control that are modified in tumor cells. The interrelationship between nuclear structure and function is not mutually exclusive but synergistic. We explore concepts influencing the maintenance of chromatin structures, including phase separation, recognition signals, factors that mediate enhancer-promoter looping, and insulation and how these are altered during the cell cycle and in cancer. Understanding how these processes are altered in cancer provides a potential for advancing capabilities for the diagnosis and identification of novel therapeutic targets.
Collapse
Affiliation(s)
- Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | |
Collapse
|
11
|
Differential Epigenetic Signature of Corticospinal Motor Neurons in ALS. Brain Sci 2021; 11:brainsci11060754. [PMID: 34200232 PMCID: PMC8230084 DOI: 10.3390/brainsci11060754] [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: 04/17/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 11/26/2022] Open
Abstract
Corticospinal motor neurons (CSMN) are an indispensable neuron population for the motor neuron circuitry. They are excitatory projection neurons, which collect information from different regions of the brain and transmit it to spinal cord targets, initiating and controlling motor function. CSMN degeneration is pronounced cellular event in motor neurons diseases, such as amyotrophic lateral sclerosis (ALS). Genetic mutations contribute to only about ten percent of ALS. Thus understanding the involvement of other factors, such as epigenetic controls, is immensely valuable. Here, we investigated epigenomic signature of CSMN that become diseased due to misfolded SOD1 toxicity and TDP-43 pathology, by performing quantitative analysis of 5-methylcytosine (5mC) and 5-hydroxymethycytosine (5hmC) expression profiles during end-stage of the disease in hSOD1G93A, and prpTDP-43A315T mice. Our analysis revealed that expression of 5mC was specifically reduced in CSMN of both hSOD1G93A and prpTDP-43A315T mice. However, 5hmC expression was increased in the CSMN that becomes diseased due to misfolded SOD1 and decreased in CSMN that degenerates due to TDP-43 pathology. These results suggest the presence of a distinct difference between different underlying causes. These differential epigenetic events might modulate the expression profiles of select genes, and ultimately contribute to the different paths that lead to CSMN vulnerability in ALS.
Collapse
|
12
|
Cao X, Lintelmann J, Padoan S, Bauer S, Huber A, Mudan A, Oeder S, Adam T, Di Bucchianico S, Zimmermann R. Adenine derivatization for LC-MS/MS epigenetic DNA modifications studies on monocytic THP-1 cells exposed to reference particulate matter. Anal Biochem 2021; 618:114127. [PMID: 33571488 DOI: 10.1016/j.ab.2021.114127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 11/18/2022]
Abstract
The aim of this study was to explore the impact of three different standard reference particulate matter (ERM-CZ100, SRM-1649, and SRM-2975) on epigenetic DNA modifications including cytosine methylation, cytosine hydroxymethylation, and adenine methylation. For the determination of low levels of adenine methylation, we developed and applied a novel DNA nucleobase chemical derivatization and combined it with liquid chromatography tandem mass spectrometry. The developed method was applied for the analysis of epigenetic modifications in monocytic THP-1 cells exposed to the three different reference particulate matter for 24 h and 48 h. The mass fraction of epigenetic active elements As, Cd, and Cr was analyzed by inductively coupled plasma mass spectrometry. The exposure to fine dust ERM-CZ100 and urban dust SRM-1649 decreased cytosine methylation after 24 h exposure, whereas all 3 p.m. increased cytosine hydoxymethylation following 24 h exposure, and the epigenetic effects induced by SRM-1649 and diesel SRM-2975 were persistent up to 48 h exposure. The road tunnel dust ERM-CZ100 significantly increased adenine methylation following the shorter exposure time. Two-dimensional scatters analysis between different epigenetic DNA modifications were used to depict a significantly negative correlation between cytosine methylation and cytosine hydroxymethylation supporting their possible functional relationship. Metals and polycyclic aromatic hydrocarbons differently shapes epigenetic DNA modifications.
Collapse
Affiliation(s)
- Xin Cao
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Jutta Lintelmann
- Research Unit of Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Sara Padoan
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Neubiberg, Germany
| | - Stefanie Bauer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany
| | - Anja Huber
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany
| | - Ajit Mudan
- University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Neubiberg, Germany
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Adam
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Neubiberg, Germany
| | - Sebastiano Di Bucchianico
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany.
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| |
Collapse
|
13
|
Addressing the challenges of E-cigarette safety profiling by assessment of pulmonary toxicological response in bronchial and alveolar mucosa models. Sci Rep 2020; 10:20460. [PMID: 33235237 PMCID: PMC7686373 DOI: 10.1038/s41598-020-77452-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Limited toxicity data on electronic cigarette (ECIG) impede evidence-based policy recommendations. We compared two popular mixed fruit flavored ECIG-liquids with and without nicotine aerosolized at 40 W (E-smoke) with respect to particle number concentrations, chemical composition, and response on physiologically relevant human bronchial and alveolar lung mucosa models cultured at air–liquid interface. E-smoke was characterized by significantly increased particle number concentrations with increased wattage (25, 40, and 55 W) and nicotine presence. The chemical composition of E-smoke differed across the two tested flavors in terms of cytotoxic compounds including p-benzoquinone, nicotyrine, and flavoring agents (for example vanillin, ethyl vanillin). Significant differences in the expression of markers for pro-inflammation, oxidative stress, tissue injury/repair, alarm anti-protease, anti-microbial defense, epithelial barrier function, and epigenetic modification were observed between the flavors, nicotine content, and/ or lung models (bronchial or alveolar). Our findings indicate that ECIG toxicity is influenced by combination of multiple factors including flavor, nicotine content, vaping regime, and the region of respiratory tree (bronchial or alveolar). Toxic chemicals and flavoring agents detected in high concentrations in the E-smoke of each flavor warrant independent evaluation for their specific role in imparting toxicity. Therefore, multi-disciplinary approaches are warranted for comprehensive safety profiling of ECIG.
Collapse
|
14
|
Ouni M, Saussenthaler S, Eichelmann F, Jähnert M, Stadion M, Wittenbecher C, Rönn T, Zellner L, Gottmann P, Ling C, Schulze MB, Schürmann A. Epigenetic Changes in Islets of Langerhans Preceding the Onset of Diabetes. Diabetes 2020; 69:2503-2517. [PMID: 32816961 PMCID: PMC7576562 DOI: 10.2337/db20-0204] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/09/2020] [Indexed: 12/19/2022]
Abstract
The identification of individuals with a high risk of developing type 2 diabetes (T2D) is fundamental for prevention. Here, we used a translational approach and prediction criteria to identify changes in DNA methylation visible before the development of T2D. Islets of Langerhans were isolated from genetically identical 10-week-old female New Zealand Obese mice, which differ in their degree of hyperglycemia and in liver fat content. The application of a semiexplorative approach identified 497 differentially expressed and methylated genes (P = 6.42e-09, hypergeometric test) enriched in pathways linked to insulin secretion and extracellular matrix-receptor interaction. The comparison of mouse data with DNA methylation levels of incident T2D cases from the prospective European Prospective Investigation of Cancer (EPIC)-Potsdam cohort, revealed 105 genes with altered DNA methylation at 605 cytosine-phosphate-guanine (CpG) sites, which were associated with future T2D. AKAP13, TENM2, CTDSPL, PTPRN2, and PTPRS showed the strongest predictive potential (area under the receiver operating characteristic curve values 0.62-0.73). Among the new candidates identified in blood cells, 655 CpG sites, located in 99 genes, were differentially methylated in islets of humans with T2D. Using correction for multiple testing detected 236 genes with an altered DNA methylation in blood cells and 201 genes in diabetic islets. Thus, the introduced translational approach identified novel putative biomarkers for early pancreatic islet aberrations preceding T2D.
Collapse
Affiliation(s)
- Meriem Ouni
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sophie Saussenthaler
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Fabian Eichelmann
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
| | - Markus Jähnert
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Mandy Stadion
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Clemens Wittenbecher
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Tina Rönn
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Lisa Zellner
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Pascal Gottmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Matthias B Schulze
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| |
Collapse
|
15
|
Chen X, Lin Q, Wen J, Lin W, Liang J, Huang H, Li L, Huang J, Chen F, Liu D, Chen G. Whole genome bisulfite sequencing of human spermatozoa reveals differentially methylated patterns from type 2 diabetic patients. J Diabetes Investig 2020; 11:856-864. [PMID: 31869513 PMCID: PMC7378413 DOI: 10.1111/jdi.13201] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/15/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
AIMS/INTRODUCTION The incidence of type 2 diabetes mellitus is increasing worldwide, and it might partly cause metabolic disorder and type 2 diabetes mellitus susceptibility in patients' offspring through epigenetic modification. However, the underlying mechanisms remain largely unclear. Recent studies have shown a potential link between deoxyribonucleic acid methylation in paternal sperm and susceptibility to type 2 diabetes mellitus in offspring, so this article focuses on whether the whole-genome methylation profiles of spermatozoa in type 2 diabetes mellitus patients have changed. MATERIALS AND METHODS We investigated the genome-wide deoxyribonucleic acid methylation profiles in spermatozoa by comparing eight individuals with type 2 diabetes mellitus and nine non-diabetic controls using whole-genome bisulfite sequencing method. RESULTS First, we found that the proportion of methylated cytosine in the whole genome of the type 2 diabetes mellitus group was slightly lower than that of the control group. Interestingly, the proportion of methylated cytosines in the CG context decreased, and the proportion of methylated cytosines in the CHG context (H = A, T or C) increased in the type 2 diabetes mellitus group, but the proportion of methylated cytosines in the CHH context (H = A, T or C) barely changed. The methylated cytosines in the CG context were mainly distributed at the high methylated level, whereas methylated cytosines in the CHG context and methylated cytosines in the CHH context were mainly distributed at the low and middle methylated level in both groups. Second, functional enrichment analysis showed that differentially methylated genes played a significant role in nervous system development and cell metabolism. Finally, we identified 10 top type 2 diabetes mellitus-related differentially methylated genes, including IRS1, PRKCE, FTO, PPARGC1A, KCNQ1, ATP10A, GHR, CREB1, PRKAR1A and HNF1B. CONCLUSIONS Our study provides the first evidence for deoxyribonucleic acid methylation reprogramming in spermatozoa of type 2 diabetes mellitus patients, and provides a new basis for explaining the complex mechanism of type 2 diabetes mellitus susceptibility in offspring.
Collapse
Affiliation(s)
- Xiongfeng Chen
- Department of Scientific ResearchFujian Provincial HospitalFuzhouFujianChina
| | - Qinghua Lin
- Department of Scientific ResearchFujian Academy of Medical SciencesFuzhouFujianChina
| | - Junping Wen
- Department of Endocrinology and MetabolismFujian Provincial HospitalShengli Clinical Medical College of Fujian Medical UniversityFuzhouFujianChina
| | - Wei Lin
- Department of Endocrinology and MetabolismFujian Provincial HospitalShengli Clinical Medical College of Fujian Medical UniversityFuzhouFujianChina
| | - Jixing Liang
- Department of Endocrinology and MetabolismFujian Provincial HospitalShengli Clinical Medical College of Fujian Medical UniversityFuzhouFujianChina
| | - Huibin Huang
- Department of Endocrinology and MetabolismFujian Provincial HospitalShengli Clinical Medical College of Fujian Medical UniversityFuzhouFujianChina
| | - Liantao Li
- Department of Endocrinology and MetabolismFujian Provincial HospitalShengli Clinical Medical College of Fujian Medical UniversityFuzhouFujianChina
| | - Jianxin Huang
- Department of Clinical LaboratoryFujian Provincial HospitalFuzhouFujianChina
| | - Falin Chen
- Department of Clinical LaboratoryFujian Provincial HospitalFuzhouFujianChina
| | - Deli Liu
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational BiomedicineNew York CityNew YorkUSA
| | - Gang Chen
- Department of Scientific ResearchFujian Academy of Medical SciencesFuzhouFujianChina
- Department of Endocrinology and MetabolismFujian Provincial HospitalShengli Clinical Medical College of Fujian Medical UniversityFuzhouFujianChina
| |
Collapse
|
16
|
Li Y, Hamilton KJ, Perera L, Wang T, Gruzdev A, Jefferson TB, Zhang AX, Mathura E, Gerrish KE, Wharey L, Martin NP, Li JL, Korach KS. ESR1 Mutations Associated With Estrogen Insensitivity Syndrome Change Conformation of Ligand-Receptor Complex and Altered Transcriptome Profile. Endocrinology 2020; 161:bqaa050. [PMID: 32242619 PMCID: PMC7947601 DOI: 10.1210/endocr/bqaa050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/01/2020] [Indexed: 11/19/2022]
Abstract
Estrogen insensitivity syndrome (EIS) arises from rare mutations in estrogen receptor-α (ERα, encoded by ESR1 gene) resulting in the inability of estrogen to exert its biological effects. Due to its rarity, mutations in ESR1 gene and the underlying molecular mechanisms of EIS have not been thoroughly studied. Here, we investigate known ESR1 mutants, Q375H and R394H, associated with EIS patients using in vitro and in vivo systems. Comparison of the transcriptome and deoxyribonucleic acid methylome from stable cell lines of both Q375H and R394H clinical mutants shows a differential profile compared with wild-type ERα, resulting in loss of estrogen responsiveness. Molecular dynamic simulation shows that both ESR1 mutations change the ERα conformation of the ligand-receptor complexes. Furthermore, we generated a mouse model Esr1-Q harboring the human mutation using CRISPR/Cas9 genome editing. Female and male Esr1-Q mice are infertile and have similar phenotypes to αERKO mice. Overall phenotypes of the Esr1-Q mice correspond to those observed in the patient with Q375H. Finally, we explore the effects of a synthetic progestogen and a gonadotropin-releasing hormone inhibitor in the Esr1-Q mice for potentially reversing the impaired female reproductive tract function. These findings provide an important basis for understanding the molecular mechanistic consequences associated with EIS.
Collapse
Affiliation(s)
- Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Katherine J Hamilton
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Tianyuan Wang
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Artiom Gruzdev
- Molecular Genomics Core Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Tanner B Jefferson
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Austin X Zhang
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Emilie Mathura
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Kevin E Gerrish
- Knockout Mouse Core Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Laura Wharey
- Knockout Mouse Core Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Negin P Martin
- Viral Vector Core Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Jian-Liang Li
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Kenneth S Korach
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| |
Collapse
|
17
|
Dimauro I, Paronetto MP, Caporossi D. Exercise, redox homeostasis and the epigenetic landscape. Redox Biol 2020; 35:101477. [PMID: 32127290 PMCID: PMC7284912 DOI: 10.1016/j.redox.2020.101477] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/23/2020] [Indexed: 02/07/2023] Open
Abstract
Physical exercise represents one of the strongest physiological stimuli capable to induce functional and structural modifications in all biological systems. Indeed, beside the traditional genetic mechanisms, physical exercise can modulate gene expression through epigenetic modifications, namely DNA methylation, post-translational histone modification and non-coding RNA transcripts. Initially considered as merely damaging molecules, it is now well recognized that both reactive oxygen (ROS) and nitrogen species (RNS) produced under voluntary exercise play an important role as regulatory mediators in signaling processes. While robust scientific evidences highlight the role of exercise-associated redox modifications in modulating gene expression through the genetic machinery, the understanding of their specific impact on epigenomic profile is still at an early stage. This review will provide an overview of the role of ROS and RNS in modulating the epigenetic landscape in the context of exercise-related adaptations. Physical exercise can modulate gene expression through epigenetic modifications. Epigenetic regulation of ROS/RNS generating, sensing and neutralizing enzymes can impact the cellular levels of ROS and RNS. ROS might act as modulators of epigenetic machinery, interfering with DNA methylation, hPTMs and ncRNAs expression. Redox homeostasis might hold a relevant role in the epigenetic landscape modulating exercise-related adaptations.
Collapse
Affiliation(s)
- Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Maria Paola Paronetto
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy; Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, Via Del Fosso di Fiorano, Rome, Italy
| | - Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy.
| |
Collapse
|
18
|
Rauluseviciute I, Drabløs F, Rye MB. DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis. Clin Epigenetics 2019; 11:193. [PMID: 31831061 PMCID: PMC6909609 DOI: 10.1186/s13148-019-0795-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/04/2019] [Indexed: 02/06/2023] Open
Abstract
Sequencing technologies have changed not only our approaches to classical genetics, but also the field of epigenetics. Specific methods allow scientists to identify novel genome-wide epigenetic patterns of DNA methylation down to single-nucleotide resolution. DNA methylation is the most researched epigenetic mark involved in various processes in the human cell, including gene regulation and development of diseases, such as cancer. Increasing numbers of DNA methylation sequencing datasets from human genome are produced using various platforms-from methylated DNA precipitation to the whole genome bisulfite sequencing. Many of those datasets are fully accessible for repeated analyses. Sequencing experiments have become routine in laboratories around the world, while analysis of outcoming data is still a challenge among the majority of scientists, since in many cases it requires advanced computational skills. Even though various tools are being created and published, guidelines for their selection are often not clear, especially to non-bioinformaticians with limited experience in computational analyses. Separate tools are often used for individual steps in the analysis, and these can be challenging to manage and integrate. However, in some instances, tools are combined into pipelines that are capable to complete all the essential steps to achieve the result. In the case of DNA methylation sequencing analysis, the goal of such pipeline is to map sequencing reads, calculate methylation levels, and distinguish differentially methylated positions and/or regions. The objective of this review is to describe basic principles and steps in the analysis of DNA methylation sequencing data that in particular have been used for mammalian genomes, and more importantly to present and discuss the most pronounced computational pipelines that can be used to analyze such data. We aim to provide a good starting point for scientists with limited experience in computational analyses of DNA methylation and hydroxymethylation data, and recommend a few tools that are powerful, but still easy enough to use for their own data analysis.
Collapse
Affiliation(s)
- Ieva Rauluseviciute
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, NO-7491, Trondheim, Norway.
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, NO-7491, Trondheim, Norway
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, NO-7491, Trondheim, Norway.,Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, NO-7030, Trondheim, Norway
| |
Collapse
|
19
|
Goel D, Un Nisa K, Reza MI, Rahman Z, Aamer S. Aberrant DNA Methylation Pattern may Enhance Susceptibility to Migraine: A Novel Perspective. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2019; 18:504-515. [DOI: 10.2174/1871527318666190809162631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/04/2019] [Accepted: 07/27/2019] [Indexed: 12/17/2022]
Abstract
In today’s world, migraine is one of the most frequent disorders with an estimated world prevalence of 14.7% characterized by attacks of a severe headache making people enfeebled and imposing a big socioeconomic burden. The pathophysiology of a migraine is not completely understood however there are pieces of evidence that epigenetics performs a primary role in the pathophysiology of migraine. Here, in this review, we highlight current evidence for an epigenetic link with migraine in particular DNA methylation of numerous genes involved in migraine pathogenesis. Outcomes of various studies have explained the function of DNA methylation of a several migraine related genes such as RAMP1, CALCA, NOS1, ESR1, MTHFR and NR4A3 in migraine pathogenesis. Mentioned data suggested there exist a strong association of DNA methylation of migraine-related genes in migraine. Although we now have a general understanding of the role of epigenetic modifications of a numerous migraine associated genes in migraine pathogenesis, there are many areas of active research are of key relevance to medicine. Future studies into the complexities of epigenetic modifications will bring a new understanding of the mechanisms of migraine processes and open novel approaches towards therapeutic intervention.
Collapse
Affiliation(s)
- Divya Goel
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, Guwahati, India
| | - Kaiser Un Nisa
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
| | - Mohammad Irshad Reza
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
| | - Ziaur Rahman
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
| | - Shaikh Aamer
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
| |
Collapse
|
20
|
Blanquart C, Linot C, Cartron PF, Tomaselli D, Mai A, Bertrand P. Epigenetic Metalloenzymes. Curr Med Chem 2019; 26:2748-2785. [PMID: 29984644 DOI: 10.2174/0929867325666180706105903] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Abstract
Epigenetics controls the expression of genes and is responsible for cellular phenotypes. The fundamental basis of these mechanisms involves in part the post-translational modifications (PTMs) of DNA and proteins, in particular, the nuclear histones. DNA can be methylated or demethylated on cytosine. Histones are marked by several modifications including acetylation and/or methylation, and of particular importance are the covalent modifications of lysine. There exists a balance between addition and removal of these PTMs, leading to three groups of enzymes involved in these processes: the writers adding marks, the erasers removing them, and the readers able to detect these marks and participating in the recruitment of transcription factors. The stimulation or the repression in the expression of genes is thus the result of a subtle equilibrium between all the possibilities coming from the combinations of these PTMs. Indeed, these mechanisms can be deregulated and then participate in the appearance, development and maintenance of various human diseases, including cancers, neurological and metabolic disorders. Some of the key players in epigenetics are metalloenzymes, belonging mostly to the group of erasers: the zinc-dependent histone deacetylases (HDACs), the iron-dependent lysine demethylases of the Jumonji family (JMJ or KDM) and for DNA the iron-dependent ten-eleven-translocation enzymes (TET) responsible for the oxidation of methylcytosine prior to the demethylation of DNA. This review presents these metalloenzymes, their importance in human disease and their inhibitors.
Collapse
Affiliation(s)
- Christophe Blanquart
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Camille Linot
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.,Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Philippe Bertrand
- Réseau Epigénétique du Cancéropôle Grand Ouest, France.,Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B27, 86073, Poitiers cedex 09, France
| |
Collapse
|
21
|
Okamura K, Nakabayashi K, Kawai T, Suzuki T, Sano T, Hata K, Nohara K. DNA methylation changes involved in the tumor increase in F2 males born to gestationally arsenite-exposed F1 male mice. Cancer Sci 2019; 110:2629-2642. [PMID: 31215104 PMCID: PMC6676110 DOI: 10.1111/cas.14104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/08/2023] Open
Abstract
Multigenerational adverse effects from the environment such as nutrition and chemicals are among important concerns in environmental health issues. Previously, we have found that arsenite exposure of only F0 females during their pregnancy increases hepatic tumors in the F2 males in C3H mice. In the current study, we investigated the association of DNA methylation with the hepatic tumor increase in the F2 males of the arsenite group. Reduced-representation bisulfite sequencing analysis newly identified that DNA methylation levels of regions around the transcriptional start sites of Tmem54 and Cd74 were decreased and the expression of these genes were significantly increased in the hepatic tumors of F2 males of the arsenite group. The associations between DNA methylation in these regions and gene expression changes were confirmed by treatment of murine hepatoma cell lines and hepatic stellate cell line with 5-aza-2'-deoxycytidine. Overexpression of Cd74 in Hepa1c1c7 cells increased Trib3 expression and suppressed the expression of tumor suppressor genes Id3 and Atoh8. Human database analysis using the Cancer Genome Atlas indicated that TMEM54, CD74, and TRIB3 were significantly increased and that ATOH8 was decreased in hepatocellular carcinoma. The data also showed that high expression of TMEM54 and TRIB3 and low expression of ATOH8 were associated with poor survival. These results suggested that an increase in Tmem54 and Cd74 expression via DNA methylation reduction was involved in the tumor increase in the F2 male offspring by gestational arsenite exposure of F0 females. This study also suggested that genes downstream of Cd74 were involved in tumorigenesis.
Collapse
Affiliation(s)
- Kazuyuki Okamura
- Center for Health and Environmental Risk ResearchNational Institute for Environmental StudiesTsukubaIbarakiJapan
| | - Kazuhiko Nakabayashi
- Department of Maternal‐Fetal BiologyNational Research Institute for Child Health and DevelopmentSetagaya, TokyoJapan
| | - Tomoko Kawai
- Department of Maternal‐Fetal BiologyNational Research Institute for Child Health and DevelopmentSetagaya, TokyoJapan
| | - Takehiro Suzuki
- Center for Health and Environmental Risk ResearchNational Institute for Environmental StudiesTsukubaIbarakiJapan
| | - Tomoharu Sano
- Center for Environmental Measurement and AnalysisNational Institute for Environmental StudiesTsukubaIbarakiJapan
| | - Kenichiro Hata
- Department of Maternal‐Fetal BiologyNational Research Institute for Child Health and DevelopmentSetagaya, TokyoJapan
| | - Keiko Nohara
- Center for Health and Environmental Risk ResearchNational Institute for Environmental StudiesTsukubaIbarakiJapan
| |
Collapse
|
22
|
Jacques M, Hiam D, Craig J, Barrès R, Eynon N, Voisin S. Epigenetic changes in healthy human skeletal muscle following exercise- a systematic review. Epigenetics 2019; 14:633-648. [PMID: 31046576 PMCID: PMC6557592 DOI: 10.1080/15592294.2019.1614416] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 12/20/2022] Open
Abstract
Exercise training is continually challenging whole-body homeostasis, leading to improvements in performance and health. Adaptations to exercise training are complex and are influenced by both environmental and genetic factors. Epigenetic factors regulate gene expression in a tissue-specific manner and constitute a link between the genotype and the environment. Moreover, epigenetic factors are emerging as potential biomarkers that could predict the response to exercise training. This systematic review aimed to identify epigenetic changes that have been reported in skeletal muscle following exercise training in healthy populations. A literature search of five databases (PUBMED, MEDLINE, CINHAL, SCOPUS and SportDiscuss) was conducted in November 2018. Articles were included if they examined epigenetic modifications (DNA methylation, histone modifications and non-coding RNAs) in skeletal muscle, following either an acute bout of exercise, an exercise intervention in a pre/post design, or a case/control type of study. Twenty-two studies met the inclusion criteria. Several epigenetic markers including DNA methylation of genes known to be differentially expressed after exercise and myomiRs were reported to be modified after exercise. Several epigenetic marks were identified to be altered in response to exercise, with potential influence on skeletal muscle metabolism. However, whether these epigenetic marks play a role in the physiological impact of exercise is unclear. Exercise epigenetics is still a very young research field, and it is expected that in the future the causality of such changes will be elucidated via the utilization of emerging experimental models able to target the epigenome.
Collapse
Affiliation(s)
- Macsue Jacques
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Danielle Hiam
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Jeffrey Craig
- Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
- Environmental & Genetic Epidemiology Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| |
Collapse
|
23
|
Apicella C, Ruano CSM, Méhats C, Miralles F, Vaiman D. The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia. Int J Mol Sci 2019; 20:ijms20112837. [PMID: 31212604 PMCID: PMC6600551 DOI: 10.3390/ijms20112837] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022] Open
Abstract
In this review, we comprehensively present the function of epigenetic regulations in normal placental development as well as in a prominent disease of placental origin, preeclampsia (PE). We describe current progress concerning the impact of DNA methylation, non-coding RNA (with a special emphasis on long non-coding RNA (lncRNA) and microRNA (miRNA)) and more marginally histone post-translational modifications, in the processes leading to normal and abnormal placental function. We also explore the potential use of epigenetic marks circulating in the maternal blood flow as putative biomarkers able to prognosticate the onset of PE, as well as classifying it according to its severity. The correlation between epigenetic marks and impacts on gene expression is systematically evaluated for the different epigenetic marks analyzed.
Collapse
Affiliation(s)
- Clara Apicella
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Camino S M Ruano
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Céline Méhats
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Francisco Miralles
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Daniel Vaiman
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| |
Collapse
|
24
|
Fu X, Li C, Liu Q, McMillin KW. GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: The regulation of beef quality by resident progenitor cells1. J Anim Sci 2019; 97:2658-2673. [PMID: 30982893 PMCID: PMC6541817 DOI: 10.1093/jas/skz111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/01/2019] [Indexed: 12/11/2022] Open
Abstract
The intramuscular adipose tissue deposition in the skeletal muscle of beef cattle is a highly desired trait essential for high-quality beef. In contrast, the excessive accumulation of crosslinked collagen in intramuscular connective tissue contributes to beef toughness. Recent studies revealed that adipose tissue and connective tissue share an embryonic origin in mice and may be derived from a common immediate bipotent precursor in mice and humans. Having the same linkages in the development of adipose tissue and connective tissue in beef, the lineage commitment and differentiation of progenitor cells giving rise to these tissues may directly affect beef quality. It has been shown that these processes are regulated by some key transcription regulators and are subjective to epigenetic modifications such as DNA methylation, histone modifications, and microRNAs. Continued exploration of relevant regulatory pathways is very important for the identification of mechanisms influencing meat quality and the development of proper management strategies for beef quality improvement.
Collapse
Affiliation(s)
- Xing Fu
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Chaoyang Li
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Qianglin Liu
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Kenneth W McMillin
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
| |
Collapse
|
25
|
Jang HO, Lee HN, Woo JH, Lee JY, Kim A, Lee JK, Kim DH, Surh YJ, Na HK. 15-Deoxy-Δ12,14-prostaglandin J2 up-regulates the expression of 15-hydroxyprostaglandin dehydrogenase through DNA methyltransferase 1 inactivation. Free Radic Res 2019; 53:335-347. [DOI: 10.1080/10715762.2019.1576867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hye-Ok Jang
- Department of Molecular Medicine and Biopharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Ha-Na Lee
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Jeong-Hwa Woo
- Department of Food and Nutrition, College of Health & Wellness, Sungshin Women’s University, Seoul, South Korea
| | - Ja-Young Lee
- Department of Food and Nutrition, College of Health & Wellness, Sungshin Women’s University, Seoul, South Korea
| | - Areumnuri Kim
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Seoul, South Korea
| | - Jin Kyung Lee
- KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Seoul, South Korea
| | - Do-Hee Kim
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Young-Joon Surh
- Department of Molecular Medicine and Biopharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Hye-Kyung Na
- Department of Food and Nutrition, College of Health & Wellness, Sungshin Women’s University, Seoul, South Korea
- Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women’s University, Seoul, South Korea
| |
Collapse
|
26
|
Cao Y, Wang B, Wang D, Zhan D, Mai C, Wang P, Wei Q, Liu Y, Wang H, He W, Xu L. Expression of Sclerostin in Osteoporotic Fracture Patients Is Associated with DNA Methylation in the CpG Island of the SOST Gene. Int J Genomics 2019; 2019:7076513. [PMID: 30729116 PMCID: PMC6341240 DOI: 10.1155/2019/7076513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/26/2018] [Accepted: 10/11/2018] [Indexed: 01/17/2023] Open
Abstract
PURPOSE SOST gene is one of the key factors in regulating bone absorption. Although there are reports showing diverse transcription factors, epigenetic modification could be responsible for regulating SOST gene expression. There is still little exploration on promoter methylation status of SOST gene in osteoporotic bone tissues. The aim of this study is to investigate the involvement of CpG methylation in regulation of SOST expression in patients with primary osteoporosis. METHODS The diagnosis of osteoporosis was established on the basis of dual energy X-ray absorptiometry to measure BMD. All femoral bone tissues were separated in surgeries. After extracting total RNA and protein, we checked the relative expression levels of SOST by quantitative real-time PCR and western blot. Also, immunohistochemical staining was performed to observe the expression of SOST protein in the bone samples. The genomic DNA of non-OPF (non-osteoporotic fracture bone tissues) and OPF (osteoporotic fracture bone tissues) were treated by bisulfite modification, and methylation status of CpG sites in the CpG island of SOST gene promoter was determined by DNA sequencing. RESULTS SOST gene expression in the non-OPF group was lower than that in OPF group. Bisulfite sequencing result showed that SOST gene promoter was slightly demethylated in the OPF group, as compared with non-OPF group. CONCLUSION Our study demonstrated that DNA methylation influenced the transcriptional expression of SOST gene, which probably may play an important role in the pathogenesis of primary osteoporosis.
Collapse
Affiliation(s)
- Yanming Cao
- Department of Orthopedics, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bin Wang
- Department of Orthopedics, People's Hospital of Sanshui, Foshan, China
| | - Ding Wang
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongxiang Zhan
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Caiyuan Mai
- Department of Obstetrics, Guangdong Women and Children's Hospital, Guangzhou 510010, China
| | - Peng Wang
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiushi Wei
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yamei Liu
- Departments of Diagnostics of Traditional Chinese Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Haibin Wang
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei He
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liangliang Xu
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Laboratory of Orthopaedics & Traumatology, Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| |
Collapse
|
27
|
Asenso J, Wang L, Du Y, Liu QH, Xu BJ, Guo MZ, Tang DQ. Advances in detection and quantification of methylcytosine and its derivatives. J Sep Sci 2018; 42:1105-1116. [PMID: 30575277 DOI: 10.1002/jssc.201801100] [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: 10/21/2018] [Revised: 11/21/2018] [Accepted: 12/16/2018] [Indexed: 11/08/2022]
Abstract
Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification of four cytosine modifications, based on which, the development, diagnosis, and prognosis of diseases could be monitored through non-invasive procedures.
Collapse
Affiliation(s)
- James Asenso
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, P. R. China
| | - Yan Du
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Qing-Hua Liu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Bing-Ju Xu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Meng-Zhe Guo
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Dao-Quan Tang
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| |
Collapse
|
28
|
Xue J, Gharaibeh RZ, Pietryk EW, Brouwer C, Tarantino LM, Valdar W, Ideraabdullah FY. Impact of vitamin D depletion during development on mouse sperm DNA methylation. Epigenetics 2018; 13:959-974. [PMID: 30239288 DOI: 10.1080/15592294.2018.1526027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Suboptimal environmental conditions during development can substantially alter the epigenome. Stable environmentally-induced changes to the germline epigenome, in particular, have important implications for the health of the next generation. We showed previously that developmental vitamin D depletion (DVD) resulted in loss of DNA methylation at several imprinted loci over two generations. Here, we assessed the impact of DVD on genome-wide methylation in mouse sperm in order to characterize the number, extent and distribution of methylation changes in response to DVD and to find genes that may be susceptible to this prevalent environmental perturbation. We detected 15,827 loci that were differentially methylated in DVD mouse sperm vs. controls. Most epimutations (69%) were loss of methylation, and the extent of methylation change and number of CpGs affected in a region were associated with genic location and baseline methylation state. Methylation response to DVD at validated loci was only detected in offspring that exhibited a phenotypic response to DVD (increased body and testes weight) suggesting the two types of responses are linked, though a causal relationship is unclear. Epimutations localized to regions enriched for developmental and metabolic genes and pathway analyses showed enrichment for Cadherin, Wnt, PDGF and Integrin signaling pathways. These findings show for the first time that vitamin D status during development leads to substantial DNA methylation changes across the sperm genome and that locus susceptibility is linked to genomic and epigenomic context.
Collapse
Affiliation(s)
- Jing Xue
- a Department of Genetics, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA
| | - Raad Z Gharaibeh
- c Department of Bioinformatics and Genomics , University of North Carolina at Charlotte , Charlotte , NC , USA.,d UNC Charlotte Bioinformatics Service Division , North Carolina Research Campus , Kannapolis , NC , USA.,e Department of Medicine, Division of Gastroenterology , University of Florida , Gainesville , FL , USA
| | - Edward W Pietryk
- a Department of Genetics, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA
| | - Cory Brouwer
- c Department of Bioinformatics and Genomics , University of North Carolina at Charlotte , Charlotte , NC , USA.,d UNC Charlotte Bioinformatics Service Division , North Carolina Research Campus , Kannapolis , NC , USA
| | - Lisa M Tarantino
- b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA.,f Department of Psychiatry, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,g Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - William Valdar
- b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA.,h Lineberger Comprehensive Cancer Center , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - Folami Y Ideraabdullah
- a Department of Genetics, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA.,i Department of Nutrition, Gillings School of Public Health , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| |
Collapse
|
29
|
Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, Ecker JR, Goll M, Panning B. OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. eLife 2018; 7:34870. [PMID: 30325306 PMCID: PMC6214653 DOI: 10.7554/elife.34870] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 10/15/2018] [Indexed: 12/11/2022] Open
Abstract
TET enzymes convert 5-methylcytosine to 5-hydroxymethylcytosine and higher oxidized derivatives. TETs stably associate with and are post-translationally modified by the nutrient-sensing enzyme OGT, suggesting a connection between metabolism and the epigenome. Here, we show for the first time that modification by OGT enhances TET1 activity in vitro. We identify a TET1 domain that is necessary and sufficient for binding to OGT and report a point mutation that disrupts the TET1-OGT interaction. We show that this interaction is necessary for TET1 to rescue hematopoetic stem cell production in tet mutant zebrafish embryos, suggesting that OGT promotes TET1’s function during development. Finally, we show that disrupting the TET1-OGT interaction in mouse embryonic stem cells changes the abundance of TET2 and 5-methylcytosine, which is accompanied by alterations in gene expression. These results link metabolism and epigenetic control, which may be relevant to the developmental and disease processes regulated by these two enzymes.
Collapse
Affiliation(s)
- Joel Hrit
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Leeanne Goodrich
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Cheng Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology (BCMB Allied program), Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Bang-An Wang
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Ji Nie
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Xiaolong Cui
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Elizabeth Allene Martin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Eric Simental
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Jenna Fernandez
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Monica Yun Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Joseph R Nery
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Rosa Castanon
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Rahul M Kohli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Chuan He
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Mary Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Barbara Panning
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States
| |
Collapse
|
30
|
Montagud-Romero S, Blanco-Gandía MC, Reguilón MD, Ferrer-Pérez C, Ballestín R, Miñarro J, Rodríguez-Arias M. Social defeat stress: Mechanisms underlying the increase in rewarding effects of drugs of abuse. Eur J Neurosci 2018; 48:2948-2970. [PMID: 30144331 DOI: 10.1111/ejn.14127] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/11/2018] [Accepted: 08/14/2018] [Indexed: 12/27/2022]
Abstract
Social interaction is known to be the main source of stress in human beings, which explains the translational importance of this research in animals. Evidence reported over the last decade has revealed that, when exposed to social defeat experiences (brief episodes of social confrontations during adolescence and adulthood), the rodent brain undergoes remodeling and functional modifications, which in turn lead to an increase in the rewarding and reinstating effects of different drugs of abuse. The mechanisms by which social stress cause changes in the brain and behavior are unknown, and so the objective of this review is to contemplate how social defeat stress induces long-lasting consequences that modify the reward system. First of all, we will describe the most characteristic results of the short- and long-term consequences of social defeat stress on the rewarding effects of drugs of abuse such as psychostimulants and alcohol. Secondly, and throughout the review, we will carefully assess the neurobiological mechanisms underlying these effects, including changes in the dopaminergic system, corticotrophin releasing factor signaling, epigenetic modifications and the neuroinflammatory response. To conclude, we will consider the advantages and disadvantages and the translational value of the social defeat stress model, and will discuss challenges and future directions.
Collapse
Affiliation(s)
- Sandra Montagud-Romero
- Department of Psychobiology, Facultad de Psicología, Universitat de Valencia, Valencia, Spain
| | | | - Marina D Reguilón
- Department of Psychobiology, Facultad de Psicología, Universitat de Valencia, Valencia, Spain
| | - Carmen Ferrer-Pérez
- Department of Psychobiology, Facultad de Psicología, Universitat de Valencia, Valencia, Spain
| | - Raul Ballestín
- Department of Psychobiology, Facultad de Psicología, Universitat de Valencia, Valencia, Spain
| | - Jose Miñarro
- Department of Psychobiology, Facultad de Psicología, Universitat de Valencia, Valencia, Spain
| | - Marta Rodríguez-Arias
- Department of Psychobiology, Facultad de Psicología, Universitat de Valencia, Valencia, Spain
| |
Collapse
|
31
|
De Sa Nogueira D, Merienne K, Befort K. Neuroepigenetics and addictive behaviors: Where do we stand? Neurosci Biobehav Rev 2018; 106:58-72. [PMID: 30205119 DOI: 10.1016/j.neubiorev.2018.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/28/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022]
Abstract
Substance use disorders involve long-term changes in the brain that lead to compulsive drug seeking, craving, and a high probability of relapse. Recent findings have highlighted the role of epigenetic regulations in controlling chromatin access and regulation of gene expression following exposure to drugs of abuse. In the present review, we focus on data investigating genome-wide epigenetic modifications in the brain of addicted patients or in rodent models exposed to drugs of abuse, with a particular focus on DNA methylation and histone modifications associated with transcriptional studies. We highlight critical factors for epigenomic studies in addiction. We discuss new findings related to psychostimulants, alcohol, opiate, nicotine and cannabinoids. We examine the possible transmission of these changes across generations. We highlight developing tools, specifically those that allow investigation of structural reorganization of the chromatin. These have the potential to increase our understanding of alteration of chromatin architecture at gene regulatory regions. Neuroepigenetic mechanisms involved in addictive behaviors could explain persistent phenotypic effects of drugs and, in particular, vulnerability to relapse.
Collapse
Affiliation(s)
- David De Sa Nogueira
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 3 « Abuse of Drugs and Neuroadaptations », Faculté de Psychologie, 12 rue Goethe, F-67000, France
| | - Karine Merienne
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 1 « Dynamics of Memory and Epigenetics », Faculté de Psychologie, 12 rue Goethe, F-67000, France
| | - Katia Befort
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 3 « Abuse of Drugs and Neuroadaptations », Faculté de Psychologie, 12 rue Goethe, F-67000, France.
| |
Collapse
|
32
|
Storebjerg TM, Strand SH, Høyer S, Lynnerup AS, Borre M, Ørntoft TF, Sørensen KD. Dysregulation and prognostic potential of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) levels in prostate cancer. Clin Epigenetics 2018; 10:105. [PMID: 30086793 PMCID: PMC6081903 DOI: 10.1186/s13148-018-0540-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/29/2018] [Indexed: 12/13/2022] Open
Abstract
Background Prognostic tools for prostate cancer (PC) are inadequate and new molecular biomarkers may improve risk stratification. The epigenetic mark 5-hydroxymethylcytosine (5hmC) has recently been proposed as a novel candidate prognostic biomarker in several malignancies including PC. 5hmC is an oxidized derivative of 5-methylcytosine (5mC) and can be further oxidized to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The present study is the first to investigate the biomarker potential in PC for all four DNA methylation marks in parallel. Thus, we determined 5mC, 5hmC, 5fC, and 5caC levels in non-malignant (NM) and PC tissue samples from a large radical prostatectomy (RP) patient cohort (n = 546) by immunohistochemical (IHC) analysis of serial sections of a tissue microarray. Possible associations between methylation marks, routine clinicopathological parameters, ERG status, and biochemical recurrence (BCR) after RP were investigated. Results 5mC and 5hmC levels were significantly reduced in PC compared to NM prostate tissue samples (p ≤ 0.027) due to a global loss of both marks specifically in ERG− PCs. 5fC levels were significantly increased in ERG+ PCs (p = 0.004), whereas 5caC levels were elevated in both ERG− and ERG+ PCs compared with NM prostate tissue samples (p ≤ 0.019). Positive correlations were observed between 5mC, 5fC, and 5caC levels in both NM and PC tissues (p < 0.001), while 5hmC levels were only weakly positively correlated to 5mC in the PC subset (p = 0.030). There were no significant associations between 5mC, 5fC, or ERG status and time to BCR in this RP cohort. In contrast, high 5hmC levels were associated with BCR in ERG− PCs (p = 0.043), while high 5caC levels were associated with favorable prognosis in ERG+ PCs (p = 0.011) and were borderline significantly associated with worse prognosis in ERG− PCs (p = 0.058). Moreover, a combined high-5hmC/high-5caC score was a significant adverse predictor of post-operative BCR beyond routine clinicopathological variables in ERG− PCs (hazard ratio 3.18 (1.54–6.56), p = 0.002, multivariate Cox regression). Conclusions This is the first comprehensive study of 5mC, 5hmC, 5fC, and 5caC levels in PC and the first report of a significant prognostic potential for 5caC in PC. Electronic supplementary material The online version of this article (10.1186/s13148-018-0540-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tine Maj Storebjerg
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark.,Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Anne-Sofie Lynnerup
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark.,Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
| |
Collapse
|
33
|
Curtis EM, Suderman M, Phillips CM, Relton C, Harvey NC. Early-life dietary and epigenetic influences on childhood musculoskeletal health: Update on the UK component of the ALPHABET project. NUTR BULL 2018. [DOI: 10.1111/nbu.12322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- E. M. Curtis
- MRC Lifecourse Epidemiology Unit, University of Southampton; Southampton UK
| | - M. Suderman
- MRC Integrative Epidemiology Unit, University of Bristol; Bristol UK
| | - C. M. Phillips
- HRB Centre for Diet and Health Research, University College Dublin; Dublin Ireland
| | - C. Relton
- MRC Integrative Epidemiology Unit, University of Bristol; Bristol UK
| | - N. C. Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton; Southampton UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust; Southampton UK
| |
Collapse
|
34
|
DNA methylation and transcriptome aberrations mediated by ERα in mouse seminal vesicles following developmental DES exposure. Proc Natl Acad Sci U S A 2018; 115:E4189-E4198. [PMID: 29666266 DOI: 10.1073/pnas.1719010115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Early transient developmental exposure to an endocrine active compound, diethylstilbestrol (DES), a synthetic estrogen, causes late-stage effects in the reproductive tract of adult mice. Estrogen receptor alpha (ERα) plays a role in mediating these developmental effects. However, the developmental mechanism is not well known in male tissues. Here, we present genome-wide transcriptome and DNA methylation profiling of the seminal vesicles (SVs) during normal development and after DES exposure. ERα mediates aberrations of the mRNA transcriptome in SVs of adult mice following neonatal DES exposure. This developmental exposure impacts differential diseases between male (SVs) and female (uterus) tissues when mice reach adulthood due to most DES-altered genes that appear to be tissue specific during mouse development. Certain estrogen-responsive gene changes in SVs are cell-type specific. DNA methylation dynamically changes during development in the SVs of wild-type (WT) and ERα-knockout (αERKO) mice, which increases both the loss and gain of differentially methylated regions (DMRs). There are more gains of DMRs in αERKO compared with WT. Interestingly, the methylation changes between the two genotypes are in different genomic loci. Additionally, the expression levels of a subset of DES-altered genes are associated with their DNA methylation status following developmental DES exposure. Taken together, these findings provide an important basis for understanding the molecular and cellular mechanism of endocrine-disrupting chemicals (EDCs), such as DES, during development in the male mouse tissues. This unique evidence contributes to our understanding of developmental actions of EDCs in human health.
Collapse
|
35
|
De Majo F, Calore M. Chromatin remodelling and epigenetic state regulation by non-coding RNAs in the diseased heart. Noncoding RNA Res 2018; 3:20-28. [PMID: 30159436 PMCID: PMC6084839 DOI: 10.1016/j.ncrna.2018.02.003] [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: 11/16/2017] [Revised: 02/08/2018] [Accepted: 02/26/2018] [Indexed: 02/06/2023] Open
Abstract
Epigenetics refers to all the changes in phenotype and gene expression which are not due to alterations in the DNA sequence. These mechanisms have a pivotal role not only in the development but also in the maintenance during adulthood of a physiological phenotype of the heart. Because of the crucial role of epigenetic modifications, their alteration can lead to the arise of pathological conditions. Heart failure affects an estimated 23 million people worldwide and leads to substantial numbers of hospitalizations and health care costs: ischemic heart disease, hypertension, rheumatic fever and other valve diseases, cardiomyopathy, cardiopulmonary disease, congenital heart disease and other factors may all lead to heart failure, either alone or in concert with other risk factors. Epigenetic alterations have recently been included among these risk factors as they can affect gene expression in response to external stimuli. In this review, we provide an overview of all the major classes of chromatin remodellers, providing examples of how their disregulation in the adult heart alters specific gene programs with subsequent development of major cardiomyopathies. Understanding the functional significance of the different epigenetic marks as points of genetic control may be useful for developing promising future therapeutic tools.
Collapse
Affiliation(s)
| | - M. Calore
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6229 ER Maastricht, The Netherlands
| |
Collapse
|
36
|
Boschen KE, Keller SM, Roth TL, Klintsova AY. Epigenetic mechanisms in alcohol- and adversity-induced developmental origins of neurobehavioral functioning. Neurotoxicol Teratol 2018; 66:63-79. [PMID: 29305195 DOI: 10.1016/j.ntt.2017.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/11/2017] [Accepted: 12/26/2017] [Indexed: 12/13/2022]
Abstract
The long-term effects of developmental alcohol and stress exposure are well documented in both humans and non-human animal models. Damage to the brain and attendant life-long impairments in cognition and increased risk for psychiatric disorders are debilitating consequences of developmental exposure to alcohol and/or psychological stress. Here we discuss evidence for a role of epigenetic mechanisms in mediating these consequences. While we highlight some of the common ways in which stress or alcohol impact the epigenome, we point out that little is understood of the epigenome's response to experiencing both stress and alcohol exposure, though stress is a contributing factor as to why women drink during pregnancy. Advancing our understanding of this relationship is of critical concern not just for the health and well-being of individuals directly exposed to these teratogens, but for generations to come.
Collapse
Affiliation(s)
- K E Boschen
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, NC 27599, United States
| | - S M Keller
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE 19716, United States
| | - T L Roth
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE 19716, United States.
| | - A Y Klintsova
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE 19716, United States.
| |
Collapse
|
37
|
Jung M, Kristiansen G, Dietrich D. DNA Methylation Analysis of Free-Circulating DNA in Body Fluids. Methods Mol Biol 2018; 1708:621-641. [PMID: 29224167 DOI: 10.1007/978-1-4939-7481-8_32] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration. However, free-circulating DNA is generally low concentrated. Therefore, high volumes of body fluids need to be analyzed. This high volume needs to be reduced in order to facilitate the bisulfite conversion. In addition, disease-related free-circulating DNA is even less abundant than normal DNA in the total amount of free-circulating DNA. Accordingly, analytical and pre-analytical methods are needed, which permit an accurate and sensitive quantification of single methylated DNA copies in the presence of unmethylated DNA in abundance.This protocol describes two methods for DNA enrichment from body fluids: DNA extraction by means of magnetic beads and polymer-mediated enrichment of DNA. Subsequent bisulfite conversion is achieved by means of a high-speed conversion protocol. Adaptions of the workflow required for the analysis of hydroxymethylation via oxidation 5-hydroxymethylcytosines to 5-formylcytosines prior to the bisulfite conversion are introduced. A quantitative real-time PCR based on the methylation-specific and HeavyMethyl PCR methodologies is introduced. This qPCR assay allows for an accurate and sensitive quantification of single copies of the DNA methylation biomarkers SHOX2 and SEPT9 in blood plasma. Specific issues regarding the analysis of body fluids and respective trouble shooting approaches are discussed.
Collapse
Affiliation(s)
- Maria Jung
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
| |
Collapse
|
38
|
Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
Collapse
Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
| |
Collapse
|
39
|
Abstract
DNA methylation is a dynamic epigenetic mark that characterizes different cellular developmental stages, including tissue-specific profiles. This CpG dinucleotide modification cooperates in the regulation of the output of the cellular genetic content, in both healthy and pathological conditions. According to endogenous and exogenous stimuli, DNA methylation is involved in gene transcription, alternative splicing, imprinting, X-chromosome inactivation, and control of transposable elements. When these dinucleotides are organized in dense regions are called CpG islands (CGIs), being commonly known as transcriptional regulatory regions frequently associated with the promoter region of several genes. In cancer, promoter DNA hypermethylation events sustained the mechanistic hypothesis of epigenetic transcriptional silencing of an increasing number of tumor suppressor genes. CGI hypomethylation-mediated reactivation of oncogenes was also documented in several cancer types. In this chapter, we aim to summarize the functional consequences of the differential DNA methylation at CpG dinucleotides in cancer, focused in CGIs. Interestingly, cancer methylome is being recently explored, looking for biomarkers for diagnosis, prognosis, and predictors of drug response.
Collapse
Affiliation(s)
- Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.
| |
Collapse
|
40
|
Miozzo F, Arnould H, de Thonel A, Schang AL, Sabéran-Djoneidi D, Baudry A, Schneider B, Mezger V. Alcohol exposure promotes DNA methyltransferase DNMT3A upregulation through reactive oxygen species-dependent mechanisms. Cell Stress Chaperones 2018; 23:115-126. [PMID: 28712054 PMCID: PMC5741586 DOI: 10.1007/s12192-017-0829-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 12/12/2022] Open
Abstract
Abundant evidence has accumulated showing that fetal alcohol exposure broadly modifies DNA methylation profiles in the brain. DNA methyltransferases (DNMTs), the enzymes responsible for DNA methylation, are likely implicated in this process. However, their regulation by ethanol exposure has been poorly addressed. Here, we show that alcohol exposure modulates DNMT protein levels through multiple mechanisms. Using a neural precursor cell line and primary mouse embryonic fibroblasts (MEFs), we found that ethanol exposure augments the levels of Dnmt3a, Dnmt3b, and Dnmt3l transcripts. We also unveil similar elevation of mRNA levels for other epigenetic actors upon ethanol exposure, among which the induction of lysine demethylase Kdm6a shows heat shock factor dependency. Furthermore, we show that ethanol exposure leads to specific increase in DNMT3A protein levels. This elevation not only relies on the upregulation of Dnmt3a mRNA but also depends on posttranscriptional mechanisms that are mediated by NADPH oxidase-dependent production of reactive oxygen species (ROS). Altogether, our work underlines complex regulation of epigenetic actors in response to alcohol exposure at both transcriptional and posttranscriptional levels. Notably, the upregulation of DNMT3A emerges as a prominent molecular event triggered by ethanol, driven by the generation of ROS.
Collapse
Affiliation(s)
- Federico Miozzo
- CNRS, UMR7216 Épigénétique et Destin Cellulaire, F-75205, Paris Cedex 13, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
- Département Hospitalo-Universitaire PROTECT, Paris, France
- Department of Genetics and Evolution, Sciences III, University of Geneva, Geneva, Switzerland
| | - Hélène Arnould
- INSERM UMR-S1124, Paris Cedex 6, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris Cedex 6, France
| | - Aurélie de Thonel
- CNRS, UMR7216 Épigénétique et Destin Cellulaire, F-75205, Paris Cedex 13, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
- Département Hospitalo-Universitaire PROTECT, Paris, France
| | - Anne-Laure Schang
- CNRS, UMR7216 Épigénétique et Destin Cellulaire, F-75205, Paris Cedex 13, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
- Département Hospitalo-Universitaire PROTECT, Paris, France
- UMR CNRS 8638-Chimie Toxicologie Analytique et Cellulaire, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie de Paris, 4 Avenue de l'Observatoire, 75006, Paris, France
| | - Délara Sabéran-Djoneidi
- CNRS, UMR7216 Épigénétique et Destin Cellulaire, F-75205, Paris Cedex 13, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
- Département Hospitalo-Universitaire PROTECT, Paris, France
| | - Anne Baudry
- INSERM UMR-S1124, Paris Cedex 6, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris Cedex 6, France
| | - Benoît Schneider
- INSERM UMR-S1124, Paris Cedex 6, France.
- Université Paris Descartes, Sorbonne Paris Cité, Paris Cedex 6, France.
| | - Valérie Mezger
- CNRS, UMR7216 Épigénétique et Destin Cellulaire, F-75205, Paris Cedex 13, France.
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France.
- Département Hospitalo-Universitaire PROTECT, Paris, France.
| |
Collapse
|
41
|
A cellular and molecular view of T helper 17 cell plasticity in autoimmunity. J Autoimmun 2017; 87:1-15. [PMID: 29275836 DOI: 10.1016/j.jaut.2017.12.007] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023]
Abstract
Since the original identification of the T helper 17 (Th17) subset in 2005, it has become evident that these cells do not only contribute to host defence against pathogens, such as bacteria and fungi, but that they are also critically involved in the pathogenesis of many autoimmune diseases. In contrast to the classic Th1 and Th2 cells, which represent rather stably polarized subsets, Th17 cells display remarkable heterogeneity and plasticity. This has been attributed to the characteristics of the key transcription factor that guides Th17 differentiation, retinoic acid receptor-related orphan nuclear receptor gamma (RORγ). Unlike the 'master regulators' T-bet and GATA3 that orchestrate Th1 and Th2 differentiation, respectively, RORγ controls transcription at relatively few loci in Th17 cells. Moreover, its expression is not stabilized by positive feedback loops but rather influenced by environmental cues, allowing for substantial functional plasticity. Importantly, a subset of IL-17/IFNγ double-producing Th17 cells was identified in both human and mouse models. Evidence is accumulating that these IL-17/IFNγ double-producing cells are pathogenic drivers in autoimmune diseases, including rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. In addition, IL-17/IFNγ double-producing cells have been identified in disorders in which the role of autoimmunity remains unclear, such as sarcoidosis. The observed plasticity of Th17 cells towards the Th1 phenotype can be explained by extensive epigenetic priming of the IFNG locus in Th17 cells. In fact, Th17 cells display an IFNG chromatin landscape that is remarkably similar to that of Th1 cells. On the other hand, pathogenic capabilities of Th17 cells can be restrained by stimulating IL-10 production and transdifferentiation into IL-10 producing T regulatory type 1 (Tr1) cells. In this review, we discuss recent advances in our knowledge on the cellular and molecular mechanisms involved in Th17 differentiation, heterogeneity and plasticity. We focus on transcriptional regulation of the Th17 expression program, the epigenetic dynamics involved, and how genetic variants associated with autoimmunity may affect immune responses through distal gene regulatory elements. Finally, the implications of Th17 cell plasticity for the pathogenesis and treatment of human autoimmune diseases will be discussed.
Collapse
|
42
|
Sharifi-Zarchi A, Gerovska D, Adachi K, Totonchi M, Pezeshk H, Taft RJ, Schöler HR, Chitsaz H, Sadeghi M, Baharvand H, Araúzo-Bravo MJ. DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. BMC Genomics 2017; 18:964. [PMID: 29233090 PMCID: PMC5727985 DOI: 10.1186/s12864-017-4353-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. Results We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci. We hypothesized “seesaw” dynamics between H3K4me1 and H3K4me3 in the low and intermediate DNA methylation range, in which DNA methylation discriminates between enhancers and promoters, marked by H3K4me1 and H3K4me3, respectively. Low methylated regions are H3K4me3 enriched, while those with intermediate DNA methylation levels are progressively H3K4me1 enriched. Additionally, the enrichment of H3K27ac, distinguishing active from primed enhancers, follows a plateau in the lower range of the intermediate DNA methylation level, corresponding to active enhancers, and decreases linearly in the higher range of the intermediate DNA methylation. Thus, the decrease of the DNA methylation switches smoothly the state of the enhancers from a primed to an active state. We summarize these observations into a rule of thumb of one-out-of-three methylation marks: “In each genomic region only one out of these three methylation marks {DNA methylation, H3K4me1, H3K4me3} is high. If it is the DNA methylation, the region is inactive. If it is H3K4me1, the region is an enhancer, and if it is H3K4me3, the region is a promoter”. To test our model, we used available genome-wide datasets of H3K4 methyltransferases knockouts. Our analysis suggests that CXXC proteins, as readers of non-methylated CpGs would regulate the “seesaw” mechanism that focuses H3K4me3 to unmethylated sites, while being repulsed from H3K4me1 decorated enhancers and CpG island shores. Conclusions Our results show that DNA methylation discriminates promoters from enhancers through H3K4me1-H3K4me3 seesaw mechanism, and suggest its possible function in the inheritance of chromatin marks after cell division. Our analyses suggest aberrant formation of promoter-like regions and ectopic transcription of hypomethylated regions of DNA. Such mechanism process can have important implications in biological process in where it has been reported abnormal DNA methylation status such as cancer and aging. Electronic supplementary material The online version of this article (10.1186/s12864-017-4353-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ali Sharifi-Zarchi
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Computer Science Department, Colorado State University, Fort Collins, CO, USA.,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Mehdi Totonchi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hamid Pezeshk
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | | | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Münster, Germany
| | - Hamidreza Chitsaz
- Computer Science Department, Colorado State University, Fort Collins, CO, USA
| | - Mehdi Sadeghi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.,National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran. .,Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
| | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain. .,Computational Biology and Bioinformatics Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany. .,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain.
| |
Collapse
|
43
|
Xu J, Bao X, Peng Z, Wang L, Du L, Niu W, Sun Y. Comprehensive analysis of genome-wide DNA methylation across human polycystic ovary syndrome ovary granulosa cell. Oncotarget 2017; 7:27899-909. [PMID: 27056885 PMCID: PMC5053696 DOI: 10.18632/oncotarget.8544] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/28/2016] [Indexed: 01/11/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) affects approximately 7% of the reproductive-age women. A growing body of evidence indicated that epigenetic mechanisms contributed to the development of PCOS. The role of DNA modification in human PCOS ovary granulosa cell is still unknown in PCOS progression. Global DNA methylation and hydroxymethylation were detected between PCOS’ and controls’ granulosa cell. Genome-wide DNA methylation was profiled to investigate the putative function of DNA methylaiton. Selected genes expressions were analyzed between PCOS’ and controls’ granulosa cell. Our results showed that the granulosa cell global DNA methylation of PCOS patients was significant higher than the controls’. The global DNA hydroxymethylation showed low level and no statistical difference between PCOS and control. 6936 differentially methylated CpG sites were identified between control and PCOS-obesity. 12245 differential methylated CpG sites were detected between control and PCOS-nonobesity group. 5202 methylated CpG sites were significantly differential between PCOS-obesity and PCOS-nonobesity group. Our results showed that DNA methylation not hydroxymethylation altered genome-wide in PCOS granulosa cell. The different methylation genes were enriched in development protein, transcription factor activity, alternative splicing, sequence-specific DNA binding and embryonic morphogenesis. YWHAQ, NCF2, DHRS9 and SCNA were up-regulation in PCOS-obesity patients with no significance different between control and PCOS-nonobesity patients, which may be activated by lower DNA methylaiton. Global and genome-wide DNA methylation alteration may contribute to different genes expression and PCOS clinical pathology.
Collapse
Affiliation(s)
- Jiawei Xu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Xiao Bao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Zhaofeng Peng
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Linlin Wang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Linqing Du
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Wenbin Niu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Yingpu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| |
Collapse
|
44
|
Abstract
PURPOSE OF REVIEW Next generation sequencing and large-scale analysis of patient specimens has created a more complete picture of multiple myeloma (MM) revealing that epigenetic deregulation is a prominent factor in MM pathogenesis. RECENT FINDINGS Over half of MM patients have mutations in genes encoding epigenetic modifier enzymes. The DNA methylation profile of MM is related to the stage of the disease and certain classes of mutations in epigenetic modifiers are more prevalent upon disease relapse, suggesting a role in disease progression. Many small molecules targeting regulators of epigenetic machinery have been developed and clinical trials are underway for some of these in MM. SUMMARY Recent findings suggest that epigenetic targeting drugs could be an important strategy to cure MM. Combining these agents along with other strategies to affect the MM cell such as immunomodulatory drugs and proteasome inhibitors may enhance efficacy of combination regimens in MM.
Collapse
|
45
|
Westphal N, Theis T, Loers G, Schachner M, Kleene R. Nuclear fragments of the neural cell adhesion molecule NCAM with or without polysialic acid differentially regulate gene expression. Sci Rep 2017; 7:13631. [PMID: 29051583 PMCID: PMC5648764 DOI: 10.1038/s41598-017-14056-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/04/2017] [Indexed: 02/05/2023] Open
Abstract
The neural cell adhesion molecule (NCAM) is the major carrier of polysialic acid (PSA) which modulates NCAM functions of neural cells at the cell surface. In previous studies, we have shown that stimulation of cultured neurons with surrogate NCAM ligands leads to the generation and nuclear import of PSA-lacking and -carrying NCAM fragments. Here, we show that the nuclear import of the PSA-carrying NCAM fragment is mediated by positive cofactor 4 and cofilin, which we identified as novel PSA-binding proteins. In the nucleus, the PSA-carrying NCAM fragment interacts via PSA with PC4 and cofilin, which are involved in RNA polymerase II-dependent transcription. Microarray analysis revealed that the nuclear PSA-carrying and -lacking NCAM fragments affect expression of different genes. By qPCR and immunoblot analysis we verified that the nuclear PSA-carrying NCAM fragment increases mRNA and protein expression of nuclear receptor subfamily 2 group F member 6, whereas the PSA-lacking NCAM fragment increases mRNA and protein expression of low density lipoprotein receptor-related protein 2 and α-synuclein. Differential gene expression evoked by nuclear NCAM fragments without and with PSA indicates that PSA-carrying and -lacking NCAM play different functional roles in the nervous system.
Collapse
Affiliation(s)
- Nina Westphal
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Thomas Theis
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Gabriele Loers
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Melitta Schachner
- Center for Neuroscience, Shantou University Medical College, 22 Xin Ling Road, Shantou, Guangdong, 515041, China.
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Piscataway, NJ, 08854, USA.
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| |
Collapse
|
46
|
Chappell GA, Rager JE. Epigenetics in chemical-induced genotoxic carcinogenesis. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
47
|
Schang AL, Sabéran-Djoneidi D, Mezger V. The impact of epigenomic next-generation sequencing approaches on our understanding of neuropsychiatric disorders. Clin Genet 2017; 93:467-480. [DOI: 10.1111/cge.13097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/31/2022]
Affiliation(s)
- A.-L. Schang
- CNRS; UMR7216 Épigénétique et Destin Cellulaire; F-75205 Paris Cedex 13 France
- Univ Paris Diderot; Sorbonne Paris Cité, F-75205 Paris Cedex 13 France
- Département Hospitalo-Universitaire PROTECT; Paris France
| | - D. Sabéran-Djoneidi
- CNRS; UMR7216 Épigénétique et Destin Cellulaire; F-75205 Paris Cedex 13 France
- Univ Paris Diderot; Sorbonne Paris Cité, F-75205 Paris Cedex 13 France
| | - V. Mezger
- CNRS; UMR7216 Épigénétique et Destin Cellulaire; F-75205 Paris Cedex 13 France
- Univ Paris Diderot; Sorbonne Paris Cité, F-75205 Paris Cedex 13 France
| |
Collapse
|
48
|
Baronchelli S, La Spada A, Ntai A, Barbieri A, Conforti P, Jotti GS, Redaelli S, Bentivegna A, De Blasio P, Biunno I. Epigenetic and transcriptional modulation of WDR5, a chromatin remodeling protein, in Huntington's disease human induced pluripotent stem cell (hiPSC) model. Mol Cell Neurosci 2017; 82:46-57. [PMID: 28476540 DOI: 10.1016/j.mcn.2017.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 04/04/2017] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
DNA methylation (DNAm) changes are of increasing relevance to neurodegenerative disorders, including Huntington's disease (HD). We performed genome-wide screening of possible DNAm changes occurring during striatal differentiation in human induced pluripotent stem cells derived from a HD patient (HD-hiPSCs) as cellular model. We identified 240 differentially methylated regions (DMRs) at promoters in fully differentiated HD-hiPSCs. Subsequently, we focused on the methylation differences in a subcluster of genes related to Jumonji Domain Containing 3 (JMJD3), a demethylase that epigenetically regulates neuronal differentiation and activates neuronal progenitor associated genes, which are indispensable for neuronal fate acquisition. Noticeably among these genes, WD repeat-containing protein 5 (WDR5) promoter was found hypermethylated in HD-hiPSCs, resulting in a significant down-modulation in its expression and of the encoded protein. A similar WDR5 expression decrease was seen in a small series of HD-hiPSC lines characterized by different CAG length. The decrease in WDR5 expression was particularly evident in HD-hiPSCs compared to hESCs and control-hiPSCs from healthy subjects. WDR5 is a core component of the MLL/SET1 chromatin remodeling complexes essential for H3K4me3, previously reported to play an important role in stem cells self-renewal and differentiation. These results suggest the existence of epigenetic mechanisms in HD and the identification of genes, which are able to modulate HD phenotype, is important both for biomarker discovery and therapeutic interventions.
Collapse
Affiliation(s)
- Simona Baronchelli
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Alberto La Spada
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Aikaterini Ntai
- Integrated Systems Engineering Srl, Via Fantoli 16/15, 20138 Milano, Italy
| | - Andrea Barbieri
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Paola Conforti
- Department of Biosciences, University of Milan and Istituto Nazionale di Genetica Molecolare Padiglione Invernizzi, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Gloria Saccani Jotti
- Department of Biological Science, Biotechnology and Translational - S.Bi.Bi.T., University of Parma, Via Gramsci 14, 43121 Parma, Italy
| | - Serena Redaelli
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Milan, Italy
| | - Angela Bentivegna
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Milan, Italy; NeuroMI, Milan Center of Neuroscience, via Pergolesi 33, 20900 Monza, Italy
| | - Pasquale De Blasio
- Integrated Systems Engineering Srl, Via Fantoli 16/15, 20138 Milano, Italy
| | - Ida Biunno
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy; IRCCS Multimedica, via Fantoli 16/15, 20138 Milano, Italy.
| |
Collapse
|
49
|
Cimarelli G, Virányi Z, Turcsán B, Rónai Z, Sasvári-Székely M, Bánlaki Z. Social Behavior of Pet Dogs Is Associated with Peripheral OXTR Methylation. Front Psychol 2017; 8:549. [PMID: 28443051 PMCID: PMC5385375 DOI: 10.3389/fpsyg.2017.00549] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/24/2017] [Indexed: 01/12/2023] Open
Abstract
Oxytocin is a key modulator of emotional processing and social cognitive function. In line with this, polymorphisms of genes involved in oxytocin signaling, like the oxytocin receptor (OXTR) gene, are known to influence social behavior in various species. However, to date, no study has investigated environmental factors possibly influencing the epigenetic variation of the OXTR gene and its behavioral effects in dogs. Pet dogs form individualized and strong relationships with their owners who are central figures in the social environment of their dogs and therefore might influence the methylation levels of their OXTR gene. Here we set out to investigate whether DNA methylation within the OXTR promoter region of pet dogs is linked to their owner's interaction style and to the social behavior of the dogs. To be able to do so, we collected buccal epithelial cells and, in Study 1, we used pyrosequencing techniques to look for differentially methylated CpG sites in the canine OXTR promoter region on a heterogeneous sample of dogs and wolves of different ages and keeping conditions. Four identified sites (at positions -727, -751, -1371, and -1383 from transcription start site) showing more than 10% methylation variation were then, in Study 2, measured in triplicate in 217 pet Border Collies previously tested for reactions to an adverse social situation (i.e., approach by a threatening human) and with available data on their owners' interaction styles. We found that CpG methylation was significantly associated with the behavior of the dogs, in particular with the likelihood that dogs would hide behind their owner or remain passive when approached by a threatening human. On the other hand, CpG methylation was not related to the owners' behavior but to dog sex (at position -1371). Our findings underpin the complex relationship between epigenetics and behavior and highlight the importance of including epigenetic methods in the analysis of dog behavioral development. Further research is needed to investigate which environmental factors influence the epigenetic variation of the OXTR gene.
Collapse
Affiliation(s)
- Giulia Cimarelli
- Clever Dog Lab, Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna, University of ViennaVienna, Austria
- Wolf Science CenterErnstbrunn, Austria
- Department of Cognitive Biology, University of ViennaVienna, Austria
| | - Zsófia Virányi
- Clever Dog Lab, Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna, University of ViennaVienna, Austria
- Wolf Science CenterErnstbrunn, Austria
| | - Borbála Turcsán
- Clever Dog Lab, Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna, University of ViennaVienna, Austria
- Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapest, Hungary
| | - Zsolt Rónai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis UniversityBudapest, Hungary
| | - Mária Sasvári-Székely
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis UniversityBudapest, Hungary
| | - Zsófia Bánlaki
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis UniversityBudapest, Hungary
| |
Collapse
|
50
|
Lee WS, McColl B, Maksimovic J, Vadolas J. Epigenetic interplay at the β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:393-404. [DOI: 10.1016/j.bbagrm.2017.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 02/02/2023]
|