1
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Geara P, Dilworth FJ. Epigenetic integration of signaling from the regenerative environment. Curr Top Dev Biol 2024; 158:341-374. [PMID: 38670712 DOI: 10.1016/bs.ctdb.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Skeletal muscle has an extraordinary capacity to regenerate itself after injury due to the presence of tissue-resident muscle stem cells. While these muscle stem cells are the primary contributor to the regenerated myofibers, the process occurs in a regenerative microenvironment where multiple different cell types act in a coordinated manner to clear the damaged myofibers and restore tissue homeostasis. In this regenerative environment, immune cells play a well-characterized role in initiating repair by establishing an inflammatory state that permits the removal of dead cells and necrotic muscle tissue at the injury site. More recently, it has come to be appreciated that the immune cells also play a crucial role in communicating with the stem cells within the regenerative environment to help coordinate the timing of repair events through the secretion of cytokines, chemokines, and growth factors. Evidence also suggests that stem cells can help modulate the extent of the inflammatory response by signaling to the immune cells, demonstrating a cross-talk between the different cells in the regenerative environment. Here, we review the current knowledge on the innate immune response to sterile muscle injury and provide insight into the epigenetic mechanisms used by the cells in the regenerative niche to integrate the cellular cross-talk required for efficient muscle repair.
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Affiliation(s)
- Perla Geara
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, United States
| | - F Jeffrey Dilworth
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, United States.
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2
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Arogundade TT, Gbadamosi I, Enaibe BU. Maternal diet supplemented with African walnuts enhances cortico-hippocampal gene expression and histomorphology in rat offspring. Nutr Neurosci 2024; 27:159-171. [PMID: 36635992 DOI: 10.1080/1028415x.2023.2166804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND The brain is built up during pregnancy. How it functions afterwards depends on how the expectant mother's diet nourishes it. Walnuts contain significant quantities of polyunsaturated fatty acids (PUFAs) and bioactive phytochemicals, which enhance brain health and function even with advancing age. This study examined the effects of a walnut-enriched diet (WED) on corticohippocampal histoarchitecture and gene expression in rat offspring. MATERIALS AND METHODS Twenty-eight female adult Wistar rats (n= 7) averaging about 185 g in weight were used for this study. After mating, pregnant dams were split randomly into four groups: A (standard rat chow/control), B (WED from GD 0 - PND 21), C (WED from GD 0 - PND 1), D (WED from PND 1 - PND 21). Offspring of dams were sacrificed at adolescence (PND 35), with brain tissues of interest harvested for subsequent analyses. RESULTS We observed no significant correlates in litter size, body, and brain weights across the experimental groups. Histomorphology revealed no distortion in cellular layering and delineation of cells in the PFC and dentate gyrus of both control and WED groups. Nissl staining intensity was enhanced in the offspring of dams exposed to WED versus the control, indicating improved proteostasis. Upregulated mRNA expression of DNMT3a, H2Ax, OPA1, and BDNF was observed in cortical and hippocampal tissues of WEDexposed offspring compared with the control group. CONCLUSION A diet enriched with African walnuts during early development induced changes predictive of cognitive improvements and enhanced stress-response signalling, plasticity, and neural resilience in rat offspring.
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Affiliation(s)
- Tolulope T Arogundade
- Division of Neurobiology, Department of Anatomy, Faculty of Basic Medical Sciences, University of Ilorin, Ilorin, Nigeria
- Department of Anatomy, Faculty of Basic Medical Sciences, Redeemer's University, Ede, Nigeria
| | - Ismail Gbadamosi
- Laboratory for Translational Research in Neuropsychiatric Disorders (TREND), BRAINCITY - Center of Excellence for Neural Plasticity and Brain Disorders, Institute of Experimental Biology Marceli Nencki, Polish Academy of Sciences, Warsaw, Poland
| | - Bernard U Enaibe
- Division of Neurobiology, Department of Anatomy, Faculty of Basic Medical Sciences, University of Ilorin, Ilorin, Nigeria
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3
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Yin J, Gu T, Chaudhry N, Davidson NE, Huang Y. Epigenetic modulation of antitumor immunity and immunotherapy response in breast cancer: biological mechanisms and clinical implications. Front Immunol 2024; 14:1325615. [PMID: 38268926 PMCID: PMC10806158 DOI: 10.3389/fimmu.2023.1325615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024] Open
Abstract
Breast cancer (BC) is the most common non-skin cancer and the second leading cause of cancer death in American women. The initiation and progression of BC can proceed through the accumulation of genetic and epigenetic changes that allow transformed cells to escape the normal cell cycle checkpoint control. Unlike nucleotide mutations, epigenetic changes such as DNA methylation, histone posttranslational modifications (PTMs), nucleosome remodeling and non-coding RNAs are generally reversible and therefore potentially responsive to pharmacological intervention. Epigenetic dysregulations are critical mechanisms for impaired antitumor immunity, evasion of immune surveillance, and resistance to immunotherapy. Compared to highly immunogenic tumor types, such as melanoma or lung cancer, breast cancer has been viewed as an immunologically quiescent tumor which displays a relatively low population of tumor-infiltrating lymphocytes (TIL), low tumor mutational burden (TMB) and modest response rates to immune checkpoint inhibitors (ICI). Emerging evidence suggests that agents targeting aberrant epigenetic modifiers may augment host antitumor immunity in BC via several interrelated mechanisms such as enhancing tumor antigen presentation, activation of cytotoxic T cells, inhibition of immunosuppressive cells, boosting response to ICI, and induction of immunogenic cell death (ICD). These discoveries have established a highly promising basis for using combinatorial approaches of epigenetic drugs with immunotherapy as an innovative paradigm to improve outcomes of BC patients. In this review, we summarize the current understanding of how epigenetic processes regulate immune cell function and antitumor immunogenicity in the context of the breast tumor microenvironment. Moreover, we discuss the therapeutic potential and latest clinical trials of the combination of immune checkpoint blockers with epigenetic agents in breast cancer.
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Affiliation(s)
- Jun Yin
- The University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Tiezheng Gu
- The University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Norin Chaudhry
- Department of Internal Medicine, Division of Hematology, Oncology, and Blood and Marrow Transplantation, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Nancy E. Davidson
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA, United States
| | - Yi Huang
- Department of Internal Medicine, Division of Hematology, Oncology, and Blood and Marrow Transplantation, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
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4
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Flynn LT, Gao WJ. DNA methylation and the opposing NMDAR dysfunction in schizophrenia and major depression disorders: a converging model for the therapeutic effects of psychedelic compounds in the treatment of psychiatric illness. Mol Psychiatry 2023; 28:4553-4567. [PMID: 37679470 PMCID: PMC11034997 DOI: 10.1038/s41380-023-02235-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Psychedelic compounds are being increasingly explored as a potential therapeutic option for treating several psychiatric conditions, despite relatively little being known about their mechanism of action. One such possible mechanism, DNA methylation, is a process of epigenetic regulation that changes gene expression via chemical modification of nitrogenous bases. DNA methylation has been implicated in the pathophysiology of several psychiatric conditions, including schizophrenia (SZ) and major depressive disorder (MDD). In this review, we propose alterations to DNA methylation as a converging model for the therapeutic effects of psychedelic compounds, highlighting the N-methyl D-aspartate receptor (NMDAR), a crucial mediator of synaptic plasticity with known dysfunction in both diseases, as an example and anchoring point. We review the established evidence relating aberrant DNA methylation to NMDAR dysfunction in SZ and MDD and provide a model asserting that psychedelic substances may act through an epigenetic mechanism to provide therapeutic effects in the context of these disorders.
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Affiliation(s)
- L Taylor Flynn
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
- MD/PhD program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Wen-Jun Gao
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA.
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5
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García-Ortiz MV, Cano-Ramírez P, Toledano-Fonseca M, Aranda E, Rodríguez-Ariza A. Diagnosing and monitoring pancreatic cancer through cell-free DNA methylation: progress and prospects. Biomark Res 2023; 11:88. [PMID: 37798621 PMCID: PMC10552233 DOI: 10.1186/s40364-023-00528-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Pancreatic cancer is one of the most challenging cancers due to its high mortality rates. Considering the late diagnosis and the limited survival benefit with current treatment options, it becomes imperative to optimize early detection, prognosis and prediction of treatment response. To address these challenges, significant research efforts have been undertaken in recent years to develop liquid-biopsy-based biomarkers for pancreatic cancer. In particular, an increasing number of studies point to cell-free DNA (cfDNA) methylation analysis as a promising non-invasive approach for the discovery and validation of epigenetic biomarkers with diagnostic or prognostic potential. In this review we provide an update on recent advancements in the field of cfDNA methylation analysis in pancreatic cancer. We discuss the relevance of DNA methylation in the context of pancreatic cancer, recent cfDNA methylation research, its clinical utility, and future directions for integrating cfDNA methylation analysis into routine clinical practice.
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Affiliation(s)
- María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain.
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain.
| | - Pablo Cano-Ramírez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
| | - Marta Toledano-Fonseca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
| | - Enrique Aranda
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
- Department of Medicine, Faculty of Medicine, University of Córdoba, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
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6
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Sahinyan K, Lazure F, Blackburn DM, Soleimani VD. Decline of regenerative potential of old muscle stem cells: contribution to muscle aging. FEBS J 2023; 290:1267-1289. [PMID: 35029021 DOI: 10.1111/febs.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 01/01/2023]
Abstract
Muscle stem cells (MuSCs) are required for life-long muscle regeneration. In general, aging has been linked to a decline in the numbers and the regenerative potential of MuSCs. Muscle regeneration depends on the proper functioning of MuSCs, which is itself dependent on intricate interactions with its niche components. Aging is associated with both cell-intrinsic and niche-mediated changes, which can be the result of transcriptional, posttranscriptional, or posttranslational alterations in MuSCs or in the components of their niche. The interplay between cell intrinsic alterations in MuSCs and changes in the stem cell niche environment during aging and its impact on the number and the function of MuSCs is an important emerging area of research. In this review, we discuss whether the decline in the regenerative potential of MuSCs with age is the cause or the consequence of aging skeletal muscle. Understanding the effect of aging on MuSCs and the individual components of their niche is critical to develop effective therapeutic approaches to diminish or reverse the age-related defects in muscle regeneration.
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Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
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7
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Pathania AS, Prathipati P, Pandey MK, Byrareddy SN, Coulter DW, Gupta SC, Challagundla KB. The emerging role of non-coding RNAs in the epigenetic regulation of pediatric cancers. Semin Cancer Biol 2022; 83:227-241. [PMID: 33910063 DOI: 10.1016/j.semcancer.2021.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/09/2023]
Abstract
Epigenetics is a process that involves the regulation of gene expression without altering the sequence of DNA. Numerous studies have documented that epigenetic mechanisms play a critical role in cell growth, differentiation, and cancer over the past decade. The well-known epigenetic modifications are either on DNA or at the histone proteins. Although several studies have focused on regulating gene expression by non-coding RNAs, the current understanding of their biological functions in various human diseases, particularly in cancers, is inadequate. Only about two percent of DNA is involved in coding the protein-coding genes, and leaving the rest 98 percent is non-coding and the scientific community regarded as junk or noise with no known purpose. Most non-coding RNAs are derived from such junk DNA and are known to be involved in various signaling pathways involving cancer initiation, progression, and the development of therapy resistance in many human cancer types. Recent studies have suggested that non-coding RNAs, especially microRNAs, piwi-interactingRNAs, and long non-coding RNAs, play a significant role in controlling epigenetic mechanism(s), indicating the potential effect of epigenetic modulation of non-coding RNAs on cancer progression. In this review article, we briefly presented epigenetic marks' characteristics, crosstalk between epigenetic modifications and microRNAs, piwi-interactingRNAs, and long non-coding RNAs to uncover the effect on the phenotype of pediatric cancers. Further, current knowledge on understanding the RNA epigenetics will help design novel therapeutics that target epigenetic regulatory networks to benefit cancer patients in the clinic.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Philip Prathipati
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Manoj K Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Siddappa N Byrareddy
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Don W Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Subash C Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; The Children's Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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8
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Liu YN, Qin Y, Wu B, Peng H, Li M, Luo H, Liu LL. DNA Methylation in Polycystic Ovary Syndrome:Emerging Evidence and Challenges. Reprod Toxicol 2022; 111:11-19. [PMID: 35562068 DOI: 10.1016/j.reprotox.2022.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 12/09/2022]
Abstract
Polycystic ovary syndrome (PCOS) is a disease related to reproductive endocrine abnormalities in women of reproductive age, often accompanied by metabolic diseases such as hyperandrogenemia, insulin resistance and dyslipidemia. However, the etiology and mechanism of PCOS are still unclear. In recent years, more and more studies have found that epigenetic factors play an important role in PCOS. DNA methylation is the most widely studied epigenetic modification. At present, changes of DNA methylation have been found in serum, ovarian, hypothalamus, skeletal muscle, adipose tissue of PCOS patients, and these changes are closely related to insulin resistance, lipid metabolism and follicular development of PCOS. Although the current research on DNA methylation in PCOS is not in-depth, it indicated up a good direction for future research on the etiology and mechanism of PCOS. This review discussed the relationship between DNA methylation and PCOS. It is expected to help accelerate the application of DNA methylation in the diagnosis and treatment of PCOS.
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Affiliation(s)
- Yan-Nan Liu
- Nursing School, Hunan University of Medicine, Huaihua 418000, Hunan, China
| | - Yi Qin
- Faculty of Nursing, Guangxi University of Chinese Medicine, Nanning,530200, Guangxi, China
| | - Bin Wu
- Nursing School, Hunan University of Medicine, Huaihua 418000, Hunan, China
| | - Hui Peng
- Nursing School, Hunan University of Medicine, Huaihua 418000, Hunan, China
| | - Ming Li
- School of Medicine, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine,Hunan University of Medicine, Huaihua 418000, Hunan, China
| | - Hai Luo
- School of Medicine, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine,Hunan University of Medicine, Huaihua 418000, Hunan, China.
| | - Lin-Lin Liu
- Faculty of Nursing, Guangxi University of Chinese Medicine, Nanning,530200, Guangxi, China.
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Miyajima Y, Noguchi S, Tanaka Y, Li JR, Nishimura H, Kishima M, Lim J, Furuhata E, Suzuki T, Kasukawa T, Suzuki H. Prediction of transcription factors associated with DNA demethylation during human cellular development. Chromosome Res 2022; 30:109-121. [PMID: 35142952 PMCID: PMC8942926 DOI: 10.1007/s10577-022-09685-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/19/2022]
Abstract
DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. Recently, it has been shown that a small subgroup of transcription factors (TFs) might promote DNA demethylation at their binding sites. We developed a bioinformatics pipeline to predict from genome-wide DNA methylation data TFs that promote DNA demethylation at their binding site. We applied the pipeline to International Human Epigenome Consortium methylome data and selected 393 candidate transcription factor binding motifs and associated 383 TFs that are likely associated with DNA demethylation. Validation of a subset of the candidate TFs using an in vitro assay suggested that 28 of 49 TFs from various TF families had DNA-demethylation-promoting activity; TF families, such as bHLH and ETS, contained both TFs with and without the activity. The identified TFs showed large demethylated/methylated CpG ratios and their demethylated CpGs showed significant bias toward hypermethylation in original cells. Furthermore, the identified TFs promoted demethylation of distinct sets of CpGs, with slight overlap of the targeted CpGs among TF family members, which was consistent with the results of a gene ontology (GO) term analysis of the identified TFs. Gene expression analysis of the identified TFs revealed that multiple TFs from various families are specifically expressed in human cells and tissues. Together, our results suggest that a large number of TFs from various TF families are associated with cell-type-specific DNA demethylation during human cellular development.
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Affiliation(s)
- Yurina Miyajima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuki Tanaka
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan
| | - Jing-Ru Li
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hajime Nishimura
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Mami Kishima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Joanne Lim
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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10
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Wei X, Du P, Zhao Z. Impacts of DNA methylation on Tau protein related genes in the brains of patients with Alzheimer's disease. Neurosci Lett 2021; 763:136196. [PMID: 34437990 DOI: 10.1016/j.neulet.2021.136196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 08/09/2021] [Accepted: 08/20/2021] [Indexed: 01/01/2023]
Abstract
As the most common cause of dementia, Alzheimer's disease (AD) is progressively neurodegenerative disease. In the initial stage, Alzheimer's disease is related to the memory disorder, followed by a serious progressive decline in cognitive function, and finally died. Neurofibrillary tangles (NFTs) deposited in neurons form one of the histopathological features of AD. NFTs are composed of abnormally modified forms, such as hyperphosphorylation, of tau protein. DNA methylation on Tau protein related genes in the brains of AD patients plays an important role in AD pathogenesis. In this paper, the process and role of gene methylation in abnormal Tau modification and aggregation in the development of Alzheimer's disease were discussed. The effect of DNA methylation on tau protein in the brain of patients with Alzheimer's disease will help to find new targets in the development of drugs for treating Alzheimer's disease.
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Affiliation(s)
- Xieze Wei
- Institute of Anesthesia, Department of Anatomy, Baotou Medical College, Baotou, Inner Mongolia, China; Xinxiang Central Hospital, China
| | | | - Zhiying Zhao
- Institute of Anesthesia, Department of Anatomy, Baotou Medical College, Baotou, Inner Mongolia, China.
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11
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He J, He H, Qi Y, Yang J, Zhi L, Jia Y. Application of epigenetics in dermatological research and skin management. J Cosmet Dermatol 2021; 21:1920-1930. [PMID: 34357681 DOI: 10.1111/jocd.14355] [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: 03/23/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Epigenetics has recently evolved from a collection of diverse phenomena to a defined and far-reaching field of study. Epigenetic modifications of the genome, such as DNA methylation and histone modifications, have been reported to play a role in some skin diseases or cancer. AIMS The purpose of this article was to review the development of epigenetic in recent decades and their applications in dermatological research. METHODS An extensive literature search was conducted on epigenetic modifications since the first research on epigenetic. RESULTS This article summarizes the concept and development of epigenetics, as well as the process and principle of epigenetic modifications such as DNA methylation, histone modification, and non-coding RNA. Their application in some skin diseases and cosmetic research and development is also summarized. CONCLUSIONS This information will help to understand the mechanisms of epigenetics and some non-coding RNA, the discovery of the related drugs, and provide new insights for skin health management and cosmetic research and development.
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Affiliation(s)
- Jianbiao He
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,College of Chemistry and Materials Engineering, Key Laboratory of Cosmetic of China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Huaming He
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,College of Chemistry and Materials Engineering, Key Laboratory of Cosmetic of China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Yufeng Qi
- Shandong Huawutang Biological Technology Co, Ltd, Shandong, China
| | - Jie Yang
- Shandong Huawutang Biological Technology Co, Ltd, Shandong, China
| | - Leilei Zhi
- Shandong Huawutang Biological Technology Co, Ltd, Shandong, China
| | - Yan Jia
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,College of Chemistry and Materials Engineering, Key Laboratory of Cosmetic of China National Light Industry, Beijing Technology and Business University, Beijing, China
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12
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Exosomal DNMT1 mRNA transcript is elevated in acute lymphoblastic leukemia which might reprograms leukemia progression. Cancer Genet 2021; 260-261:57-64. [PMID: 34426211 DOI: 10.1016/j.cancergen.2021.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/09/2021] [Accepted: 07/29/2021] [Indexed: 02/06/2023]
Abstract
DNMT1 (DNA-methyltransferase 1) is an enzyme which contributes to the process of normal embryonic development, and aberrant expression of DNMT1 leads to tumor/leukemia progression by inducing significant changes in DNA methylation and epigenetics. We found that DNMT1 mRNA transcript is elevated in Exo-PALL compared to Exo-HD. We also confirmed and showed heightened levels of DNMT1 mRNA transcript in Exo-CM of leukemia cell lines. Co-culture of Exo-PALL with target cells (leukemia B cells) showed transfer of exosomal DNMT1 mRNA transcript into the target cells, which may reprogram the biological nature of normal healthy cells and leukemia cells.
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13
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Khan AA, Liu X, Yan X, Tahir M, Ali S, Huang H. An overview of genetic mutations and epigenetic signatures in the course of pancreatic cancer progression. Cancer Metastasis Rev 2021; 40:245-272. [PMID: 33423164 DOI: 10.1007/s10555-020-09952-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023]
Abstract
Pancreatic cancer (PC) is assumed to be an intimidating and deadly malignancy due to being the leading cause of cancer-led mortality, predominantly affecting males of older age. The overall (5 years) survival rate of PC is less than 9% and is anticipated to be aggravated in the future due to the lack of molecular acquaintance and diagnostic tools for its early detection. Multiple factors are involved in the course of PC development, including genetics, cigarette smoking, alcohol, family history, and aberrant epigenetic signatures of the epigenome. In this review, we will mainly focus on the genetic mutations and epigenetic signature of PC. Multiple tumor suppressor and oncogene mutations are involved in PC initiation, including K-RAS, p53, CDKN2A, and SMAD4. The mutational frequency of these genes ranges from 50 to 98% in PC. The nature of mutation diagnosis is mostly homozygous deletion, point mutation, and aberrant methylation. In addition to genetic modification, epigenetic alterations particularly aberrant hypermethylation and hypomethylation also predispose patients to PC. Hypermethylation is mostly involved in the downregulation of tumor suppressor genes and leads to PC, while multiple genes also represent a hypomethylation status in PC. Several renewable drugs and detection tools have been developed to cope with this aggressive malady, but all are futile, and surgical resection remains the only choice for prolonged survival if diagnosed before metastasis. However, the available therapeutic development is insufficient to cure PC. Therefore, novel approaches are a prerequisite to elucidating the genetic and epigenetic mechanisms underlying PC progression for healthier lifelong survival.
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Affiliation(s)
- Aamir Ali Khan
- College of Life Science and Bioengineering, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang, Beijing, 100124, China
| | - Xinhui Liu
- College of Life Science and Bioengineering, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang, Beijing, 100124, China
| | - Xinlong Yan
- College of Life Science and Bioengineering, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang, Beijing, 100124, China.
| | - Muhammad Tahir
- College of Life Science and Bioengineering, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang, Beijing, 100124, China
| | - Sakhawat Ali
- College of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
| | - Hua Huang
- College of Life Science and Bioengineering, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang, Beijing, 100124, China.
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14
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Peng F, Tang H, Du J, Chen J, Peng C. Isoliquiritigenin Suppresses EMT-Induced Metastasis in Triple-Negative Breast Cancer through miR-200c/C-JUN/[Formula: see text]-Catenin. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2021; 49:505-523. [PMID: 33641651 DOI: 10.1142/s0192415x21500233] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Triple-negative breast cancer (TNBC) is the subtype of breast cancer with more aggressive growth and metastasis and without efficient therapies. Hence, it is worthwhile to search for potential effective drug candidates. According to our previous study, isoliquiritigenin (ISL) exerted a potent anticancer effect on breast cancer proliferation. Its effect on TNBC growth, metastasis and mechanism deserves further investigation. In this study, PCR array screened a significant increase of miR-200c in BT-549 and MDA-MB-231 cells after ISL treatment, and ISH exerted that miR-200c was expressed at a low level in breast cancer tissue of patients. We also found that ISL could up-regulate miR-200c, resulting in the inhibition of epithelial-mesenchymal transition. Meanwhile, ISL could inhibit metastasis and tumor growth in nude mice models through the increase of miR-200c. Further study displayed that ISL decreased c-Jun expression through the increase of miR-200c. Interestingly, we also detected that ISL might increase miR-200c expression through the demethylation of miR-200c promoter region. These findings indicated that ISL could be potentially developed as a novel drug candidate for TNBC in microRNA-based cancer therapies.
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Affiliation(s)
- Fu Peng
- School of Chinese Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional, Chinese Medicine, Chengdu, P. R. China.,West China School of Pharmacy, Sichuan University, Chengdu, P. R. China
| | - Hailin Tang
- School of Chinese Medicine, The University of Hong Kong, Hong Kong.,Department of Breast Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Junrong Du
- West China School of Pharmacy, Sichuan University, Chengdu, P. R. China
| | - Jianping Chen
- School of Chinese Medicine, The University of Hong Kong, Hong Kong
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional, Chinese Medicine, Chengdu, P. R. China
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15
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Li Y, Rong J, Zhong H, Liang M, Zhu C, Chang F, Zhou R. Prenatal Stress Leads to the Altered Maturation of Corticostriatal Synaptic Plasticity and Related Behavioral Impairments Through Epigenetic Modifications of Dopamine D2 Receptor in Mice. Mol Neurobiol 2021; 58:317-328. [PMID: 32935231 DOI: 10.1007/s12035-020-02127-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/08/2020] [Indexed: 12/31/2022]
Abstract
Prenatal stress (PRS) had a long-term adverse effect on motor behaviors. Corticostriatal synaptic plasticity, a cellular basis for motor controlling, has been proven to participate in the pathogenesis of many behavior disorders. Based on the reports about the involvement of epigenetic DNA alterations in PRS-induced long-term effects, this research investigated the influence of PRS on the development and maturation of corticostriatal synaptic plasticity and related behaviors and explored the underlying epigenetic mechanism. Subjects were male offspring of dams that were exposed to stress three times per day from the 10th day of pregnancy until delivery. The development and maturation of plasticity at corticostriatal synapses, dopamine signaling, behavioral habituation, and DNA methylation were examined and analyzed. Control mice expressed long-term potentiation (LTP) at corticostriatal synapses during postnatal days (PD) 12-14 and produced long-term depression (LTD) during PD 20-60. However, PRS mice exhibited sustained LTP during PD 12-60. The treatment with dopamine 2 receptor (D2R) agonist quinpirole recovered striatal LTD and improved the impaired behavioral habituation in PD 45 adult PRS mice. Additionally, adult PRS mice showed reduced D2R, excess DNA methyltransferase 1 (DNMT1), increased binding of DNMT1 to D2R promoter, and hypermethylation at D2R promoter in the striatum. The DNMT1 inhibitor 5-aza-deoxycytidine restored striatal synaptic plasticity and improved behavioral habituation in adult PRS mice via D2R-mediated dopamine signaling. DNMT1-associated D2R hypermethylation is responsible for altering the maturation of plasticity at corticostriatal synapses and impairing the behavioral habituation in PRS mice.
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Affiliation(s)
- Yingchun Li
- Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, 211166, Jiangsu Province, China
| | - Jing Rong
- Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, 211166, Jiangsu Province, China
| | - Haiquan Zhong
- Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, 211166, Jiangsu Province, China
| | - Min Liang
- Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, 211166, Jiangsu Province, China
| | - Chunting Zhu
- Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, 211166, Jiangsu Province, China
| | - Fei Chang
- Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, 211166, Jiangsu Province, China
| | - Rong Zhou
- Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, 211166, Jiangsu Province, China.
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16
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Bi H, Hojo K, Watanabe M, Yee C, Maski K, Saba S, Graff-Radford J, Machulda MM, St Louis EK, Humes IS, Flanagan EP, Nicolau S, Jones DT, Patterson MC, Kotagal S, Raz Y, Niu Z, Li J, Klein CJ. Expanded genetic insight and clinical experience of DNMT1-complex disorder. NEUROLOGY-GENETICS 2020; 6:e456. [PMID: 32754641 PMCID: PMC7357420 DOI: 10.1212/nxg.0000000000000456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022]
Abstract
Objective To report novel causal mutations, expanded clinical phenotypes, and clinical management of DNA methyltransferase 1 (DNMT1)-complex disorder. Methods Neurophysiologic testing, imaging, and genetic findings were summarized in clinical context for 5 cases with DNMT1-complex disorder. Results We identified 2 novel DNMT1 mutations (p.E510K and p.P1546A) by whole-exome sequencing (WES). Case 1 (p.E510K) presented with childhood ataxia, treatment-refractory seizures, and rapid cognitive decline in his 50s. Case 2 also had childhood onset and presented with seizures, language regression, hearing loss, narcolepsy with cataplexy symptoms, optic atrophy, sensory neuropathy, and hypogammaglobulinemia requiring IV immunoglobulin. Case 2 (p.P1546A) was identified with a de novo and the first mutation residing outside the targeting sequence domain. Case 3 (p.A570V) had paralytic asymmetric onset attacks triggered by emotionality and lasting sometimes for weeks. Neuropsychological testing showed executive dysfunction localizing to frontosubcortical and frontoparietal structures. He gradually developed left predominant brain atrophy. MRI showed T2 hyperintense lesions that enhanced on T1 postgadolinium images, and brain PET showed hypometabolism in atrophied regions. Case 4 (p.T497P) underwent left cochlear implant, resulting in significant hearing improvements at all tested frequencies (250–6,000 Hz). Case 5 (p.Y511H) had profound gait ataxia with posterior column atrophy of the spinal cord and abnormal evoked potentials primarily affecting the fasciculus gracilis. Conclusions Broader application of WES further expands genotype-phenotype correlations of DNMT1-complex disorder. Two mutations are identified with early childhood onsets. The expanded new phenotypes include asymmetric brain hemiatrophy with parenchymal gadolinium enhancement, spinal cord atrophy, prolonged cataplectic spells, and hypogammaglobulinemia. Hearing loss treatment by cochlear implantation is helpful and should be considered.
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Affiliation(s)
- Hongyan Bi
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Kaori Hojo
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Masashi Watanabe
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Christina Yee
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Kiran Maski
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Sadaf Saba
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Jonathan Graff-Radford
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Mary M Machulda
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Erik K St Louis
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Ilona Spitsyna Humes
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Eoin P Flanagan
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Stefan Nicolau
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - David T Jones
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Marc C Patterson
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Suresh Kotagal
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Yael Raz
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Zhiyv Niu
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Jun Li
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Christopher J Klein
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
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17
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Zhong H, Rong J, Zhu C, Liang M, Li Y, Zhou R. Epigenetic Modifications of GABAergic Interneurons Contribute to Deficits in Adult Hippocampus Neurogenesis and Depression-Like Behavior in Prenatally Stressed Mice. Int J Neuropsychopharmacol 2020; 23:274-285. [PMID: 32211762 PMCID: PMC7177164 DOI: 10.1093/ijnp/pyaa020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Prenatal stress (PRS) is considered a risk factor for depressive disorder. Adult hippocampal neurogenesis is believed to play a role in the regulation of affective behaviors. GABAergic interneuron is a key modulator in adult hippocampal neurogenesis. Growing evidence indicates that PRS has adverse effects on adult hippocampal neurogenesis and DNA epigenetic modifications of the GABAergic system. The aim of this study was to investigate whether epigenetic GABAergic dysfunction participates in the negative impact of PRS on adult hippocampal neurogenesis and related emotional behaviors. METHODS Behavioral tests were used to explore PRS-induced depression-like behaviors of adult female mice. Immunohistochemistry staining, real-time reverse transcription-polymerase chain reaction, western blot, and chromatin immunoprecipitation were employed to detect adult neurogenesis and epigenetic changes of the GABAergic system in the hippocampus of PRS mice. RESULTS PRS mice developed a depression phenotype accompanied by the inhibited maturation of hippocampal newborn neurons. Compared with control mice, PRS mice showed decreased expression of glutamic acid decarboxylase 67 at the mRNA and protein levels. GABAA receptor agonist phenobarbital could rectify the decrease of 5-bromo-2-deoxyuridine/neuronal nuclei double-positive (BrdU+/NeuN+) cells in PRS mice. PRS mice also showed increased expression of DNA methyltransferase 1 and increased binding of DNA methyltransferase 1 to glutamic acid decarboxylase 67 promoter region. The treatment with DNA methyltransferase 1 inhibitor 5-aza-deoxycytidine restored the decrease of BrdU+/NeuN+ cells and depression-like behaviors in PRS mice via improving GABAergic system. CONCLUSIONS The present results indicate that epigenetic changes of the GABAergic system are responsible for adult hippocampus neurogenesis and depression-like behaviors in PRS mice.
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Affiliation(s)
- Haiquan Zhong
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Jing Rong
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Chunting Zhu
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Min Liang
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Yingchun Li
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Rong Zhou
- Department of Physiology, Nanjing Medical University, Jiangsu, China,Correspondence: Rong Zhou, PhD, Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, Jiangsu Province, China 211166 ()
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18
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Pre-Exposure to Nicotine with Nocturnal Abstinence Induces Epigenetic Changes that Potentiate Nicotine Preference. Mol Neurobiol 2019; 57:1828-1846. [DOI: 10.1007/s12035-019-01843-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022]
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19
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Kim DH, Kim HM, Huong PTT, Han HJ, Hwang J, Cha-Molstad H, Lee KH, Ryoo IJ, Kim KE, Huh YH, Ahn JS, Kwon YT, Soung NK, Kim BY. Enhanced anticancer effects of a methylation inhibitor by inhibiting a novel DNMT1 target, CEP 131, in cervical cancer. BMB Rep 2019. [PMID: 31068247 PMCID: PMC6549914 DOI: 10.5483/bmbrep.2019.52.5.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Methylation is a primary epigenetic mechanism regulating gene expression. 5-aza-2′-deoxycytidine is an FDA-approved drug prescribed for treatment of cancer by inhibiting DNA-Methyl-Transferase 1 (DNMT1). Results of this study suggest that prolonged treatment with 5-aza-2′-deoxycytidine could induce centrosome abnormalities in cancer cells and that CEP131, a centrosome protein, is regulated by DNMT1. Interestingly, cancer cell growth was attenuated in vitro and in vivo by inhibiting the expression of Cep131. Finally, Cep131-deficient cells were more sensitive to treatment with DNMT1 inhibitors. These findings suggest that Cep131 is a potential novel anti-cancer target. Agents that can inhibit this protein may be useful alone or in combination with DNMT1 inhibitors to treat cancer.
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Affiliation(s)
- Dong Hyun Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116; Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Hye-Min Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Korea
| | - Pham Thi Thu Huong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Korea
| | - Ho-Jin Han
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116; Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Joonsung Hwang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Korea
| | - Hyunjoo Cha-Molstad
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Korea
| | - Kyung Ho Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Korea
| | - In-Ja Ryoo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Korea
| | - Kyoon Eon Kim
- Department of Biochemistry, College of Natural Science, Chungnam National University, Daejeon 34134, Korea
| | - Yang Hoon Huh
- Center for Electron Microscopy Research, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116; Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center, Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Nak-Kyun Soung
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116; Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Bo Yeon Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116; Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
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20
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Lyu G, Zong L, Zhang C, Huang X, Xie W, Fang J, Guan Y, Zhang L, Ni T, Gu J, Tao W. Metastasis-related methyltransferase 1 (Merm1) represses the methyltransferase activity of Dnmt3a and facilitates RNA polymerase I transcriptional elongation. J Mol Cell Biol 2019; 11:78-90. [PMID: 30535232 DOI: 10.1093/jmcb/mjy023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/20/2018] [Indexed: 11/13/2022] Open
Abstract
Stimulatory regulators for DNA methyltransferase activity, such as Dnmt3L and some Dnmt3b isoforms, affect DNA methylation patterns, thereby maintaining gene body methylation and maternal methylation imprinting, as well as the methylation landscape of pluripotent cells. Here we show that metastasis-related methyltransferase 1 (Merm1), a protein deleted in individuals with Williams-Beuren syndrome, acts as a repressive regulator of Dnmt3a. Merm1 interacts with Dnmt3a and represses its methyltransferase activity with the requirement of the binding motif for S-adenosyl-L-methionine. Functional analysis of gene regulation revealed that Merm1 is capable of maintaining hypomethylated rRNA gene bodies and co-localizes with RNA polymerase I in the nucleolus. Dnmt3a recruits Merm1, and in return, Merm1 ensures the binding of Dnmt3a to hypomethylated gene bodies. Such interplay between Dnmt3a and Merm1 facilitates transcriptional elongation by RNA polymerase I. Our findings reveal a repressive factor for Dnmt3a and uncover a molecular mechanism underlying transcriptional elongation of rRNA genes.
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Affiliation(s)
- Guoliang Lyu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Le Zong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Chao Zhang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Xiaoke Huang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Wenbing Xie
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Junnan Fang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yiting Guan
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Lijun Zhang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Ting Ni
- State Key Laboratory of Genetics Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai0, China
| | - Jun Gu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Wei Tao
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
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Cañadas-Garre M, Anderson K, McGoldrick J, Maxwell AP, McKnight AJ. Genomic approaches in the search for molecular biomarkers in chronic kidney disease. J Transl Med 2018; 16:292. [PMID: 30359254 PMCID: PMC6203198 DOI: 10.1186/s12967-018-1664-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/14/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is recognised as a global public health problem, more prevalent in older persons and associated with multiple co-morbidities. Diabetes mellitus and hypertension are common aetiologies for CKD, but IgA glomerulonephritis, membranous glomerulonephritis, lupus nephritis and autosomal dominant polycystic kidney disease are also common causes of CKD. MAIN BODY Conventional biomarkers for CKD involving the use of estimated glomerular filtration rate (eGFR) derived from four variables (serum creatinine, age, gender and ethnicity) are recommended by clinical guidelines for the evaluation, classification, and stratification of CKD. However, these clinical biomarkers present some limitations, especially for early stages of CKD, elderly individuals, extreme body mass index values (serum creatinine), or are influenced by inflammation, steroid treatment and thyroid dysfunction (serum cystatin C). There is therefore a need to identify additional non-invasive biomarkers that are useful in clinical practice to help improve CKD diagnosis, inform prognosis and guide therapeutic management. CONCLUSION CKD is a multifactorial disease with associated genetic and environmental risk factors. Hence, many studies have employed genetic, epigenetic and transcriptomic approaches to identify biomarkers for kidney disease. In this review, we have summarised the most important studies in humans investigating genomic biomarkers for CKD in the last decade. Several genes, including UMOD, SHROOM3 and ELMO1 have been strongly associated with renal diseases, and some of their traits, such as eGFR and serum creatinine. The role of epigenetic and transcriptomic biomarkers in CKD and related diseases is still unclear. The combination of multiple biomarkers into classifiers, including genomic, and/or epigenomic, may give a more complete picture of kidney diseases.
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Affiliation(s)
- M. Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - K. Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - J. McGoldrick
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - A. P. Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, UK
| | - A. J. McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
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22
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A circular RNA circ-DNMT1 enhances breast cancer progression by activating autophagy. Oncogene 2018; 37:5829-5842. [PMID: 29973691 DOI: 10.1038/s41388-018-0369-y] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/29/2018] [Accepted: 05/26/2018] [Indexed: 11/08/2022]
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23
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Tsung AJ, Guda MR, Asuthkar S, Labak CM, Purvis IJ, Lu Y, Jain N, Bach SE, Prasad DVR, Velpula KK. Methylation regulates HEY1 expression in glioblastoma. Oncotarget 2018; 8:44398-44409. [PMID: 28574840 PMCID: PMC5546488 DOI: 10.18632/oncotarget.17897] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/01/2017] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GBM) remains one of the most lethal and difficult-to-treat cancers of the central nervous system. The poor prognosis in GBM patients is due in part to its resistance to available treatments, which calls for identifying novel molecular therapeutic targets. In this study, we identified a mediator of Notch signaling, HEY1, whose methylation status contributes to the pathogenesis of GBM. Datamining studies, immunohistochemistry and immunoblot analysis showed that HEY1 is highly expressed in GBM patient specimens. Since methylation status of HEY1 may control its expression, we conducted bisulphite sequencing on patient samples and found that the HEY1 promoter region was hypermethylated in normal brain when compared to GBM specimens. Treatment on 4910 and 5310 xenograft cell lines with sodium butyrate (NaB) significantly decreased HEY1 expression with a concomitant increase in DNMT1 expression, confirming that promoter methylation may regulate HEY1 expression in GBM. NaB treatment also induced apoptosis of GBM cells as measured by flow cytometric analysis. Further, silencing of HEY1 reduced invasion, migration and proliferation in 4910 and 5310 cells. Furthermore, immunoblot and q-PCR analysis showed the existence of a potential positive regulatory loop between HEY1 and p53. Additionally, transcription factor interaction array with HEY1 recombinant protein predicted a correlation with p53 and provided various bonafide targets of HEY1. Collectively, these studies suggest HEY1 may be an important predictive marker for GBM and potential target for future GBM therapy.
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Affiliation(s)
- Andrew J Tsung
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.,Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.,Illinois Neurological Institute, Peoria, IL, USA
| | - Maheedhara R Guda
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Swapna Asuthkar
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Collin M Labak
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Ian J Purvis
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Yining Lu
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Neha Jain
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | | | | | - Kiran K Velpula
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.,Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.,Department of Microbiology, Yogi Vemana University, Kadapa, India
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Dual Effect of IL-6 -174 G/C Polymorphism and Promoter Methylation in the Risk of Coronary Artery Disease Among South Indians. Indian J Clin Biochem 2018; 34:180-187. [PMID: 31092991 DOI: 10.1007/s12291-018-0740-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/08/2018] [Indexed: 02/07/2023]
Abstract
Inflammation plays an important role in the pathogenesis of atherosclerosis and coronary syndromes; moreover, various lines of evidence suggest that genetic factors do contribute to the risk of coronary artery disease (CAD). The proinflammatory cytokine IL-6 is a central mediator of inflammation associated with CAD. The present study is aimed to investigate the association of single nucleotide polymorphism in the promoter region of the IL-6 gene (-174 G > C) and methylation with the susceptibility of CAD. Genotyping of IL-6 -174 G/C polymorphism was performed by PCR-RFLP. Methylation-specific PCR method was used to study the IL-6 gene promoter methylation. Analysis of 470 subjects (265 CAD patients and 205 controls) showed association of the -174 G/C variant with the CAD risk in dominant model (OR 1.58, 95% CI, 1.024-2.23, P = 0.04). Further, the analysis of the distribution of genotypes and alleles of -174 G > C polymorphism according to clinical features of CAD, revealed significant association of genotype and allele (OR 1.86, 95% CI 1.18-2.84 P = 0.01, and OR 1.71, 95% CI 1.09-2.23 P = 0.02 respectively) with diabetes, and we found no association with hypertension (OR 0.95, 95% CI 0.57-1.59, P = 0.8). We also analyzed the methylation status of IL-6 promoter region between cases and controls showed significant hypo methylation in CAD subjects (OR 2.36, 95% CI 1.51-4.259, P = 0.006). Additionally, GC, CC genotypes and C allele carriers show hypomethylation in CAD cases compared to controls (54.58 vs. 76.85%, 29.83 vs. 40% respectively). In conclusion, the promoter polymorphism -174 G/C is associated with CAD risk and further carriers of 'C' allele at -174 locus showed significant hypo methylation which could contribute to increased risk of CAD. The present study highlights the association of allele and genotypes with differential DNA methylation of CpG islands in the IL-6 promoter region which may affect IL-6 gene regulation.
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Zhu C, Liang M, Li Y, Feng X, Hong J, Zhou R. Involvement of Epigenetic Modifications of GABAergic Interneurons in Basolateral Amygdala in Anxiety-like Phenotype of Prenatally Stressed Mice. Int J Neuropsychopharmacol 2018; 21:570-581. [PMID: 29471396 PMCID: PMC6007574 DOI: 10.1093/ijnp/pyy006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Prenatal stress is considered a risk factor for anxiety disorder. Downregulation in the expression of GABAergic gene, that is, glutamic acid decarboxylase 67, associated with DNA methyltransferase overexpression in GABAergic neurons has been regarded as a characteristic component of anxiety disorder. Prenatal stress has an adverse effect on the development of the basolateral amygdala, which is a key region in anxiety regulation. The aim of this study is to analyze the possibility of epigenetic alterations of GABAergic neurons in the basolateral amygdala participating in prenatal stress-induced anxiety. METHODS Behavioral tests were used to explore the prenatal stress-induced anxiety behaviors of female adult mice. Real-time RT-PCR, western blot, chromatin immunoprecipitation, and electrophysiological analysis were employed to detect epigenetic changes of GABAergic system in the basolateral amygdala. RESULTS Prenatal stress mice developed an anxiety-like phenotype accompanied by a significant increase of DNA methyltransferase 1 and a reduced expression of glutamic acid decarboxylase 67 in the basolateral amygdala. Prenatal stress mice also showed the increased binding of DNA methyltransferase 1 and methyl CpG binding protein 2 to glutamic acid decarboxylase 67 promoter region. The decrease of glutamic acid decarboxylase 67 transcript was paralleled by an enrichment of 5-methylcytosine in glutamic acid decarboxylase 67 promoter regions. Electrophysiological study revealed the increase of postsynaptic neuronal excitability in the cortical-basolateral amygdala synaptic transmission of prenatal stress mice. 5-Aza-deoxycytidine treatment restored the increased synaptic transmission and anxiety-like behaviors in prenatal stress mice via improving GABAergic system. CONCLUSION The above results suggest that DNA epigenetic modifications of GABAergic interneurons in the basolateral amygdala participate in the etiology of anxiety-like phenotype in prenatal stress mice.
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Affiliation(s)
- Chunting Zhu
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Min Liang
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Yingchun Li
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Xuejiao Feng
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Juan Hong
- Department of Physiology, Nanjing Medical University, Jiangsu, China
| | - Rong Zhou
- Department of Physiology, Nanjing Medical University, Jiangsu, China,Correspondence: Rong Zhou, PhD, Department of Physiology, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing City, Jiangsu Province, China 211166 ()
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Suzuki T, Maeda S, Furuhata E, Shimizu Y, Nishimura H, Kishima M, Suzuki H. A screening system to identify transcription factors that induce binding site-directed DNA demethylation. Epigenetics Chromatin 2017; 10:60. [PMID: 29221486 PMCID: PMC5723091 DOI: 10.1186/s13072-017-0169-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023] Open
Abstract
Background DNA methylation is a fundamental epigenetic modification that is involved in many biological systems such as differentiation and disease. We and others recently showed that some transcription factors (TFs) are involved in the site-specific determination of DNA demethylation in a binding site-directed manner, although the reports of such TFs are limited. Results Here, we develop a screening system to identify TFs that induce binding site-directed DNA methylation changes. The system involves the ectopic expression of target TFs in model cells followed by DNA methylome analysis and overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. It successfully identified binding site-directed demethylation of SPI1, which is known to promote DNA demethylation in a binding site-directed manner. We extended our screening system to 15 master TFs involved in cellular differentiation and identified eight novel binding site-directed DNA demethylation-inducing TFs (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA, and TBX5). Gene ontology and tissue enrichment analysis revealed that these TFs demethylate genomic regions associated with corresponding biological roles. We also describe the characteristics of binding site-directed DNA demethylation induced by these TFs, including the targeting of highly methylated CpGs, local DNA demethylation, and the overlap of demethylated regions between TFs of the same family. Conclusions Our results show the usefulness of the developed screening system for the identification of TFs that induce DNA demethylation in a site-directed manner. Electronic supplementary material The online version of this article (10.1186/s13072-017-0169-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takahiro Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Shiori Maeda
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yuri Shimizu
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Hajime Nishimura
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Mami Kishima
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
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Wu T, Qu L, He G, Tian L, Li L, Zhou H, Jin Q, Ren J, Wang Y, Wang J, Kan X, Liu M, Shen J, Guo M, Sun Y. Regulation of laryngeal squamous cell cancer progression by the lncRNA H19/miR-148a-3p/DNMT1 axis. Oncotarget 2017; 7:11553-66. [PMID: 26872375 PMCID: PMC4905493 DOI: 10.18632/oncotarget.7270] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/05/2015] [Indexed: 12/21/2022] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a highly aggressive malignant cancer. The regulation of LSCC progression by long non-coding RNA (lncRNA) was not well understood. In this study, we reported that the lncRNA H19 was upregulated in LSCC. The expression levels of H19 were inversely correlated with the survival rate of LSCC patients. Knockdown of H19 expression inhibited LSCC cell migration, invasion and proliferation. We identified microRNA miR-148a-3p as an inhibitory target for H19. Overexpression of miR-148a-3p reduced LSCC migration, invasion and proliferation cell, while inhibition of miR-148a-3p did the opposite. The inhibition of LSCC progression induced by H19 knockdown required the activity of miR-148a-3p. We also identified DNA methyltransferase enzyme DNMT1 as a target of miR-148a-3p. Cellular DNA methylation levels were inhibited by both miR-148a-3p overexpression and H19 knockdown. In summary, our study demonstrated that the lncRNA H19 promoted LSCC progression via miR-148a-3p and DNMT1.
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Affiliation(s)
- Tianyi Wu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lingmei Qu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Fifth Affiliated Hospital of Harbin Medical University, Daqing, China
| | - Guoqing He
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linli Tian
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Liang Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Han Zhou
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qian Jin
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingyuan Ren
- Department of Head and Neck Surgery, The Oncology Hospital of Jilin province, Changchun, China
| | - Yu Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingting Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuan Kan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ming Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jia Shen
- Department of Orthopaedic Surgery and The Orthopaedic Hospital Research Center, University of California, Los Angeles, California, USA
| | - Mian Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanan Sun
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Klungland A, Robertson AB. Oxidized C5-methyl cytosine bases in DNA: 5-Hydroxymethylcytosine; 5-formylcytosine; and 5-carboxycytosine. Free Radic Biol Med 2017; 107:62-68. [PMID: 27890639 DOI: 10.1016/j.freeradbiomed.2016.11.038] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 01/31/2023]
Abstract
Recent reports suggest that the Tet enzyme family catalytically oxidize 5-methylcytosine in mammalian cells. The oxidation of 5-methylcytosine can result in three chemically distinct species - 5-hydroxymethylcytsine, 5-formylcytosine, and 5-carboxycytosine. While the base excision repair machinery processes 5-formylcytosine and 5-carboxycytosine rapidly, 5-hydroxymethylcytosine is stable under physiological conditions. As a stable modification 5-hydroxymethylcytosine has a broad range of functions, from stem cell pluriopotency to tumorigenesis. The subsequent oxidation products, 5-formylcytosine and 5-carboxycytosine, are suggested to be involved in an active DNA demethylation pathway. This review provides an overview of the biochemistry and biology of 5-methylcytosine oxidation products.
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Affiliation(s)
- Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway; Institute of Basic Medical Sciences, University of Oslo, PO Box 1018 Blindern, N-0315 Oslo, Norway
| | - Adam B Robertson
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway.
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CpG and Non-CpG Methylation in Epigenetic Gene Regulation and Brain Function. Genes (Basel) 2017; 8:genes8060148. [PMID: 28545252 PMCID: PMC5485512 DOI: 10.3390/genes8060148] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/18/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells. Thus, accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Here, we provide an overview of CpG and non-CpG methylation and their roles in neurological diseases.
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Keating ST, Plutzky J, El-Osta A. Epigenetic Changes in Diabetes and Cardiovascular Risk. Circ Res 2017; 118:1706-22. [PMID: 27230637 DOI: 10.1161/circresaha.116.306819] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/30/2016] [Indexed: 01/03/2023]
Abstract
Cardiovascular complications remain the leading causes of morbidity and premature mortality in patients with diabetes mellitus. Studies in humans and preclinical models demonstrate lasting gene expression changes in the vasculopathies initiated by previous exposure to high glucose concentrations and the associated overproduction of reactive oxygen species. The molecular signatures of chromatin architectures that sensitize the genome to these and other cardiometabolic risk factors of the diabetic milieu are increasingly implicated in the biological memory underlying cardiovascular complications and now widely considered as promising therapeutic targets. Atherosclerosis is a complex heterocellular disease where the contributing cell types possess distinct epigenomes shaping diverse gene expression. Although the extent that pathological chromatin changes can be manipulated in human cardiovascular disease remains to be established, the clinical applicability of epigenetic interventions will be greatly advanced by a deeper understanding of the cell type-specific roles played by writers, erasers, and readers of chromatin modifications in the diabetic vasculature. This review details a current perspective of epigenetic mechanisms of macrovascular disease in diabetes mellitus and highlights recent key descriptions of chromatinized changes associated with persistent gene expression in endothelial, smooth muscle, and circulating immune cells relevant to atherosclerosis. Furthermore, we discuss the challenges associated with pharmacological targeting of epigenetic networks to correct abnormal or deregulated gene expression as a strategy to alleviate the clinical burden of diabetic cardiovascular disease.
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Affiliation(s)
- Samuel T Keating
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (A.E.-O.), Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.P.); Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Victoria, Australia (A.E.-O.)
| | - Jorge Plutzky
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (A.E.-O.), Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.P.); Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Victoria, Australia (A.E.-O.)
| | - Assam El-Osta
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (A.E.-O.), Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.P.); Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Victoria, Australia (A.E.-O.).
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31
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Eid A, Zawia N. Consequences of lead exposure, and it’s emerging role as an epigenetic modifier in the aging brain. Neurotoxicology 2016; 56:254-261. [DOI: 10.1016/j.neuro.2016.04.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/14/2022]
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32
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Joshi M, Rajpathak SN, Narwade SC, Deobagkar D. Ensemble-Based Virtual Screening and Experimental Validation of Inhibitors Targeting a Novel Site of Human DNMT1. Chem Biol Drug Des 2016; 88:5-16. [PMID: 26850820 DOI: 10.1111/cbdd.12741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/16/2016] [Accepted: 01/31/2016] [Indexed: 12/29/2022]
Abstract
Human DNA methyltransferase1 (hDNMT1) is responsible for preserving DNA methylation patterns that play important regulatory roles in differentiation and development. Misregulation of DNA methylation has thus been linked to many syndromes, life style diseases, and cancers. Developing specific inhibitors of hDNMT1 is an important challenge in the area since the currently targeted cofactor and substrate binding site share structural features with various proteins. In this work, we generated a structural model of the active form of hDNMT1 and identified that the 5-methylcytosine (5-mC) binding site of the hDNMT1 is structurally unique to the protein. This site has been previously demonstrated to be critical for methylation activity. We further performed multiple nanosecond time scale atomistic molecular dynamics simulations of the structural model followed by virtual screening of the Asinex database to identify inhibitors targeting the 5-mC site. Two compounds were discovered that inhibited hDNMT1 in vitro, one of which also showed inhibition in vivo corroborating the screening procedure. This study thus identifies and attempts to validate for the first time a unique site of hDNMT1 that could be harnessed for rationally designing highly selective and potent hypomethylating agents.
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Affiliation(s)
- Manali Joshi
- Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Shriram N Rajpathak
- Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Santosh C Narwade
- Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Deepti Deobagkar
- Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India.,Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
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33
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Earp MA, Cunningham JM. DNA methylation changes in epithelial ovarian cancer histotypes. Genomics 2015; 106:311-21. [PMID: 26363302 DOI: 10.1016/j.ygeno.2015.09.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 09/04/2015] [Accepted: 09/06/2015] [Indexed: 12/12/2022]
Abstract
Survival after a diagnosis of ovarian cancer has not improved, and despite histological differences, treatment is similar for all cases. Understanding the molecular basis for ovarian cancer risk and prognosis is fundamental, and to this end much has been gleaned about genetic changes contributing to risk, and to a lesser extent, survival. There's considerable evidence for genetic differences between the four pathologically defined histological subtypes; however, the contribution of epigenetics is less well documented. In this report, we review alterations in DNA methylation in ovarian cancer, focusing on histological subtypes, and studies examining the roles of methylation in determining therapy response. As epigenetics is making its way into clinical care, we review the application of cell free DNA methylation to ovarian cancer diagnosis and care. Finally, we comment on recurrent limitations in the DNA methylation literature for ovarian cancer, which can and should be addressed to mature this field.
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Affiliation(s)
- Madalene A Earp
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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34
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Vaissière T, Miller CA. DNA methylation: dynamic and stable regulation of memory. Biomol Concepts 2015; 2:459-67. [PMID: 25962048 DOI: 10.1515/bmc.2011.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 09/17/2011] [Indexed: 12/26/2022] Open
Abstract
Epigenetic mechanisms have emerged as a central process in learning and memory. Histone modifications and DNA methy-lation are epigenetic events that can mediate gene transcription. Interesting features of these epigenetic changes are their transient and long lasting potential. Recent advances in neuroscience suggest that DNA methylation is both dynamic and stable, mediating the formation and maintenance of memory. In this review, we will further illustrate the recent hypothesis that DNA methylation participates in the transcriptional regulation necessary for memory.
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35
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Fatima S, Wagstaff KM, Loveland KL, Jans DA. Interactome of the negative regulator of nuclear import BRCA1-binding protein 2. Sci Rep 2015; 5:9459. [PMID: 25820252 PMCID: PMC4377634 DOI: 10.1038/srep09459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/06/2015] [Indexed: 11/09/2022] Open
Abstract
Although the negative regulator of nuclear import (NRNI) BRCA1 binding protein 2 (BRAP2) is highly expressed in testis, its role is largely unknown. Here we address this question by documenting the BRAP2 interactome from human testis, using the yeast 2-hybrid system to identify BRAP2-interacting proteins with roles in diverse cellular processes, including regulation of the actin cytoskeleton, ubiquitinylation, cell cycle/apoptosis and transcription. Interaction with BRAP2 in adult mouse testis with three of these, PH domain and leucine rich repeat protein phosphatase 1 (PHLPP1), A-Kinase anchor protein (AKAP3) and DNA methyl transferase 1 (DNMT1), was confirmed by coimmunoprecipitation assays. BRAP2's ability to inhibit PHLPP1 and DNMT1 nuclear localisation was also confirmed by quantitative confocal microscopy. Importantly, the physiological relevance thereof was implied by the cytoplasmic localisation of PHLPP1, AKAP3 and DNMT1 in pachytene spermatocytes/round spermatids where BRAP2 is present at high levels, and nuclear localisation of PHLPP1 and DNMT1 in spermatogonia concomitant with lower levels of BRAP2. Interestingly, BRAP2 was also present in murine spermatozoa, in part colocalised with AKAP3. Together the results indicate for the first time that BRAP2 may play an important NRNI role in germ cells of the testis, with an additional, scaffold/structural role in mature spermatozoa.
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Affiliation(s)
- Shadma Fatima
- Department.of Biochemistry &Molecular Biology Monash University, Clayton, Victoria, Australia
| | - Kylie M Wagstaff
- Department.of Biochemistry &Molecular Biology Monash University, Clayton, Victoria, Australia
| | - Kate L Loveland
- Department.of Biochemistry &Molecular Biology Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - David A Jans
- Department.of Biochemistry &Molecular Biology Monash University, Clayton, Victoria, Australia
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36
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Liu X, Jia X, Yuan H, Ma K, Chen Y, Jin Y, Deng M, Pan W, Chen S, Chen Z, de The H, Zon LI, Zhou Y, Zhou J, Zhu J. DNA methyltransferase 1 functions through C/ebpa to maintain hematopoietic stem and progenitor cells in zebrafish. J Hematol Oncol 2015; 8:15. [PMID: 25886310 PMCID: PMC4372312 DOI: 10.1186/s13045-015-0115-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/24/2015] [Indexed: 12/13/2022] Open
Abstract
Background DNA methyltransferase 1 (Dnmt1) regulates expression of many critical genes through maintaining parental DNA methylation patterns on daughter DNA strands during mitosis. It is essential for embryonic development and diverse biological processes, including maintenance of hematopoietic stem and progenitor cells (HSPCs). However, the precise molecular mechanism of how Dnmt1 is involved in HSPC maintenance remains unexplored. Methods An N-ethyl-N-nitrosourea (ENU)-based genetic screening was performed to identify putative mutants with defects in definitive HSPCs during hematopoiesis in zebrafish. The expression of hematopoietic markers was analyzed via whole mount in situ hybridization assay (WISH). Positional cloning approach was carried out to identify the gene responsible for the defective definitive hematopoiesis in the mutants. Analyses of the mechanism were conducted by morpholino-mediated gene knockdown, mRNA injection rescue assays, anti-phosphorylated histone H3 (pH3) immunostaining and TUNEL assay, quantitative real-time PCR, and bisulfite sequencing analysis. Results A heritable mutant line with impaired HSPCs of definitive hematopoiesis was identified. Positional cloning demonstrated that a stop codon mutation was introduced in dnmt1 which resulted in a predicted truncated Dnmt1 lacking the DNA methylation catalytic domain. Molecular analysis revealed that expression of CCAAT/enhancer-binding protein alpha (C/ebpa) was upregulated, which correlated with hypomethylation of CpG islands in the regulation regions of cebpa gene in Dnmt1 deficient HSPCs. Overexpression of a transcriptional repressive SUMO-C/ebpa fusion protein could rescue hematological defects in the dnmt1 mutants. Finally, dnmt1 and cebpa double null embryos exhibited no obvious abnormal hematopoiesis indicated that the HSPC defects triggered by dnmt1 mutation were C/ebpa dependent. Conclusions Dnmt1 is required for HSPC maintenance via cebpa regulation during definitive hematopoiesis in zebrafish. Electronic supplementary material The online version of this article (doi:10.1186/s13045-015-0115-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaohui Liu
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xiaoe Jia
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Hao Yuan
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Ke Ma
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Yi Chen
- Laboratory of Development and Diseases, State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yi Jin
- Laboratory of Development and Diseases, State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Min Deng
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Weijun Pan
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Saijuan Chen
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Zhu Chen
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hugues de The
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Université de Paris 7/INSERM/CNRS UMR 944/7212, 75475, Paris, France.
| | - Leonard I Zon
- Stem Cell Program, Hematology/Oncology Program at Children's Hospital Boston, Harvard Medical School, Boston, MA, 02114, USA.
| | - Yi Zhou
- Stem Cell Program, Hematology/Oncology Program at Children's Hospital Boston, Harvard Medical School, Boston, MA, 02114, USA.
| | - Jun Zhou
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jun Zhu
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Université de Paris 7/INSERM/CNRS UMR 944/7212, 75475, Paris, France.
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Ge R, Wang Z, Bechis SK, Otsetov AG, Hua S, Wu S, Wu CL, Tabatabaei S, Olumi AF. DNA methyl transferase 1 reduces expression of SRD5A2 in the aging adult prostate. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:870-82. [PMID: 25700986 DOI: 10.1016/j.ajpath.2014.11.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/21/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023]
Abstract
5-α Reductase type 2 (SRD5A2) is a critical enzyme for prostatic development and growth. Inhibition of SRD5A2 by finasteride is used commonly for the management of urinary obstruction caused by benign prostatic hyperplasia. Contrary to common belief, we have found that expression of SRD5A2 is variable and absent in one third of benign adult prostates. In human samples, absent SRD5A2 expression is associated with hypermethylation of the SRD5A2 promoter, and in vitro SRD5A2 promoter activity is suppressed by methylation. We show that methylation of SRD5A2 is regulated by DNA methyltransferase 1, and inflammatory mediators such as tumor necrosis factor α, NF-κB, and IL-6 regulate DNA methyltransferase 1 expression and thereby affect SRD5A2 promoter methylation and gene expression. Furthermore, we show that increasing age in mice and humans is associated with increased methylation of the SRD5A2 promoter and concomitantly decreased protein expression. Artificial induction of inflammation in prostate primary epithelial cells leads to hypermethylation of the SRD5A2 promoter and silencing of SRD5A2, whereas inhibition with tumor necrosis factor α inhibitor reactivates SRD5A2 expression. Therefore, expression of SRD5A2 is not static and ubiquitous in benign adult prostate tissues. Methylation and expression of SRD5A2 may be used as a gene signature to tailor therapies for more effective treatment of prostatic diseases.
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Affiliation(s)
- Rongbin Ge
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Zongwei Wang
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Seth K Bechis
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alexander G Otsetov
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shengyu Hua
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shulin Wu
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shahin Tabatabaei
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aria F Olumi
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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38
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Downs B, Wang SM. Epigenetic changes in BRCA1-mutated familial breast cancer. Cancer Genet 2015; 208:237-40. [PMID: 25800897 DOI: 10.1016/j.cancergen.2015.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 01/08/2015] [Accepted: 02/04/2015] [Indexed: 12/13/2022]
Abstract
Familial breast cancer occurs in about 10% of breast cancer cases. Germline mutation in BRCA1 is the most penetrant predisposition for the disease. Mutated BRCA1 leads to disease by causing genome instability via multiple mechanisms including epigenetic changes. This review summarizes recent progress in studying the correlation between BRCA1 predisposition and epigenetic alterations in BRCA1-type familial breast cancer.
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Affiliation(s)
- Bradley Downs
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - San Ming Wang
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.
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Apostolou P, Toloudi M, Kourtidou E, Mimikakou G, Vlachou I, Chatziioannou M, Kipourou V, Papasotiriou I. Potential role for the Metnase transposase fusion gene in colon cancer through the regulation of key genes. PLoS One 2014; 9:e109741. [PMID: 25333365 PMCID: PMC4198141 DOI: 10.1371/journal.pone.0109741] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/08/2014] [Indexed: 01/06/2023] Open
Abstract
The Metnase fusion gene consists of a SET histone methyltransferase domain and a transposase domain from Mariner transposase. This transposable element is involved in chromosome decatenation, enhances DNA repair, promotes foreign DNA integration, and assists topoisomerase II function. This study investigates the role of Metnase in colon cancer homeostasis and maintenance of the stemness phenotype in colon cancer stem cells (CSCs). Silencing of Metnase was performed in human cancer cell lines before and after treatment with cisplatin, and in colon CSCs. Subsequent changes in the expression of genes involved in repair mechanisms, DNA synthesis, topoisomerase II function, and metastasis as well stemness transcription factors were studied with RT-qPCR experiments. Cellular viability and apoptosis were evaluated by flow cytometry. The results suggest that Metnase influences the expression of many genes involved in the above processes. Furthermore, Metnase levels appear to impact upon expression of NANOG, OCT3/4, and SOX2. Suppression of Metnase also led to an increase in apoptosis. Therefore, Metnase may possess an important role in DNA repair, topoisomerase II function, and the maintenance of stemness during colon cancer development.
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Affiliation(s)
| | - Maria Toloudi
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Eleni Kourtidou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Georgia Mimikakou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Ioanna Vlachou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | | | - Vasiliki Kipourou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Ioannis Papasotiriou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
- * E-mail:
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Characterisation of microbial communities in Chinese liquor fermentation starters Daqu using nested PCR-DGGE. World J Microbiol Biotechnol 2014; 30:3055-63. [PMID: 25193747 DOI: 10.1007/s11274-014-1732-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
In this study, characterises of the microbial community structures of three typical Chinese liquor Daqu, as well as different kinds of light flavour Daqu were investigated using nested PCR-denaturing gradient gel electrophoresis (DGGE). The results showed that microbial diversity was considerably different, and the microfloral compositions were highly variable among various Daqu. Lactic acid bacteria, which accounted for 30.95 % of all identified bacteria, were dominant in all Daqu samples, whereas Bacillus species were also predominant in the Luzhou (14.8 %) and Langjiu Daqu (18.2 %). Citrobacter and Burkholderia were first identified in light flavour Daqu. Aspergillus was the dominant moulds, and the non-Saccharomyces yeast species, Saccharomycopsis fibuligera, Wallemia sebi, Wallemia muriae, and Pichia subpelliculosa, were the dominant yeasts. Rasamsonia, Galactomyces, Geotrichum and Wallemia were first identified using nested PCR-DGGE. Cluster analysis indicated that the microbial community structures of different Daqu samples exhibited some differences. These may be ascribed to the different peak production temperatures, raw material constituents and microhabitats around the liquor enterprises. The current study provides insights into the microbial community structures of three typical Daqu samples, and may facilitate the development of starter cultures for manufacturing Chinese liquor.
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Torroglosa A, Enguix-Riego MV, Fernández RM, Román-Rodriguez FJ, Moya-Jiménez MJ, de Agustín JC, Antiñolo G, Borrego S. Involvement of DNMT3B in the pathogenesis of Hirschsprung disease and its possible role as a regulator of neurogenesis in the human enteric nervous system. Genet Med 2014; 16:703-10. [PMID: 24577265 DOI: 10.1038/gim.2014.17] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/28/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Hirschsprung disease (OMIM 142623) is a neurocristopathy attributed to a failure of cell proliferation or migration and/or failure of the enteric precursors along the gut to differentiate during embryonic development. Although some genes involved in this pathology are well characterized, many aspects remain poorly understood. In this study, we aimed to identify novel genes implicated in the pathogenesis of Hirschsprung disease. METHODS We compared the expression patterns of genes involved in human stem cell pluripotency between enteric precursors from controls and Hirschsprung disease patients. We further evaluated the role of DNMT3B in the context of Hirschsprung disease by inmunocytochemistry, global DNA methylation assays, and mutational screening. RESULTS Seven differentially expressed genes were identified. We focused on DNMT3B, which encodes a DNA methyltransferase that performs de novo DNA methylation during embryonic development. DNMT3B mutational analysis in our Hirschsprung disease series revealed the presence of potentially pathogenic mutations (p.Gly25Arg, p.Arg190Cys, and p.Gly198Trp). CONCLUSION DNMT3B may be regulating enteric nervous system development through DNA methylation in the neural crest cells, suggesting that aberrant methylation patterns could have a relevant role in Hirschsprung disease. Moreover, the synergistic effect of mutations in both DNMT3B and other Hirschsprung disease-related genes may be contributing to a more severe phenotype in our Hirschsprung disease patients.
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Affiliation(s)
- Ana Torroglosa
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - María Valle Enguix-Riego
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - Raquel María Fernández
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - Francisco José Román-Rodriguez
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | | | | | - Guillermo Antiñolo
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - Salud Borrego
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
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Abstract
DNA methylation is a significant regulator of gene expression, and its role in carcinogenesis recently has been a subject of remarkable interest. The aim of this review is to analyze the mechanism and cell regulatory effects of both hypo- and hyper-DNA methylation on cancer. In this review, we report new developments and their implications regarding the effects of DNA methylation on cancer development. Indeed, alteration of the pattern of DNA methylation has been a constant finding in cancer cells of the same type and differences in the pattern of DNA methylation not only occur in a variety of tumor types, but also in developmental processes Furthermore, the pattern of histone modification appears to be a predicator of the risk of recurrence of human cancers. It is well known that hypermethylation represses transcription of the promoter sections of tumor-suppressor genes leading to gene silencing. However, hypomethylation also has been identified as a cause of oncogenesis. Furthermore, experiments concerning the mechanism of methylation and its control have led to the discovery of many regulatory enzymes and proteins. This review reports on methods developed for the detection of 5-hydroxymethylcytosine methylation at the 5-methylcytosine of protein domains in the CpG context compared to non-methylated DNA, histone modification, and microRNA change.
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Regulation of MDA-MB-231 cell proliferation by GSK-3β involves epigenetic modifications under high glucose conditions. Exp Cell Res 2014; 324:75-83. [DOI: 10.1016/j.yexcr.2014.03.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/09/2014] [Accepted: 03/25/2014] [Indexed: 11/24/2022]
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Cho J, Kang S, Lee BC. Identification of abnormal gene expression in bovine transgenic somatic cell nuclear transfer embryos. J Vet Sci 2014; 15:225-31. [PMID: 24675837 PMCID: PMC4087224 DOI: 10.4142/jvs.2014.15.2.225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/28/2013] [Indexed: 12/03/2022] Open
Abstract
This study was conducted to investigate the expression of three genes related to early embryonic development in bovine transgenic cloned embryos. To accomplish this, development of bovine transgenic somatic cell nuclear transfer (SCNT) embryos was compared with non-transgenic embryos. Next, mRNA transcription of three specific genes (DNMT1, Hsp 70.1, and Mash2) related to early embryo development in transgenic SCNT embryos was compared between transgenic and non-transgenic SCNTs, parthenogenetic embryos, and in vitro fertilization (IVF) embryos. Transgenic SCNT embryos showed significantly lower rates of development to the blastocyst stage than non-transgenic ones. To investigate normal gene expression, RNA was extracted from ten blastocysts derived from parthenogenesis, IVF, non-transgenic, and transgenic SCNT embryos and reverse-transcribed to synthesize cDNA. The cDNA was then subjected to PCR amplification and semi-quantified. More DNMT1 mRNA was detected in the transgenic SCNT group than the other three groups. Hsp 70.1 mRNA was detected in the IVF embryos, while lower levels were found in SCNT and parthenogenetic embryos. Mash2 mRNA was present at the highest levels in transgenic SCNT embryos. In conclusion, the higher levels of methylation and lower protein synthesis after heat shock in the transgenic SCNT embryos expected based on our results may cause lower embryonic development.
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Affiliation(s)
- Jongki Cho
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Daejeon 305-764, Korea
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45
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Zou C, Mallampalli RK. Regulation of histone modifying enzymes by the ubiquitin-proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:694-702. [PMID: 24389248 DOI: 10.1016/j.bbamcr.2013.12.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/17/2013] [Accepted: 12/24/2013] [Indexed: 11/30/2022]
Abstract
Histone post-translational modification is a key step that may result in an epigenetic mark that regulates chromatin structure and gene transcriptional activity thereby impacting many fundamental aspects of human biology. Subtypes of post-translational modification such as acetylation and methylation are executed by a variety of distinct modification enzymes. The cytoplasmic and nuclear concentrations of these enzymes are dynamically and tightly controlled at the protein level to precisely fine-tune transcriptional activity in response to environmental clues and during pathophysiological states. Recent data have emerged demonstrating that the life span of these critical nuclear enzymes involved in histone modification that impact chromatin structure and gene expression are controlled at the level of protein turnover by ubiquitin-proteasomal processing. This review focuses on the recent progress on mechanisms for ubiquitin-proteasomal degradation of histone modification enzymes and the potential pathophysiological significance of this process.
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Affiliation(s)
- Chunbin Zou
- Department of Medicine, The Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Rama K Mallampalli
- Department of Medicine, The Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Cell Biology and Physiology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA 15240, USA.
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Zhou R, Chen F, Chang F, Bai Y, Chen L. Persistent overexpression of DNA methyltransferase 1 attenuating GABAergic inhibition in basolateral amygdala accounts for anxiety in rat offspring exposed perinatally to low-dose bisphenol A. J Psychiatr Res 2013; 47:1535-44. [PMID: 23791455 DOI: 10.1016/j.jpsychires.2013.05.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 05/03/2013] [Accepted: 05/15/2013] [Indexed: 12/18/2022]
Abstract
Substantial evidence indicates that predisposition to diseases can be acquired during early stages of development and interactions between environmental and genetic factors may be implicated in the onset of many pathological conditions. We have shown that perinatal exposure to bisphenol A (BPA) at environmental dose level causes long-term anxiety-like behaviors in rats. The aim of this study was to examine epigenetic reprogramming effect of BPA on anxiety-related neurobehavior in the rat offspring. The results of real-time RT-PCR displayed that the overexpression of DNA methyltransferase 1 (DNMT1) mRNA was accompanied by the reduction of glutamic acid decarboxylase 67 (GAD67) mRNA level in the basolateral amygdala (BLA) of postnatal day 45 BPA-exposed female rats. Chronic intro-BLA injection with 5-ada-CdR could rectify the GAD67 mRNA expression. Behavioral data showed that the anxiety-like behaviors in BPA-exposed rats were reversed by intro-BLA treatment with 5-ada-CdR which could be further blocked by PTX. Electrophysiological study revealed behavioral alterations were associated with the increase of postsynaptic neuronal excitability in the cortical-BLA pathway which appeared as multispike responses, paired-pulse facilitation instead of paired-pulse inhibition and long-term potentiation and 5-aza-CdR treatment restored the increased synaptic transmission in the BLA via improving GABAergic system. The above results suggest that the overexpression of DNMT1 in the BLA is responsible for the etiology of anxiety associated with BPA exposure via GABAergic disinhibition. In addition, we also find these long-term neurobehavioral effects of developmental BPA exposure are reversible in adolescent period.
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Affiliation(s)
- Rong Zhou
- Department of Physiology, Nanjing Medical University, Hanzhong Road 140, Nanjing, Jiangsu, China
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Adwan L, Zawia NH. Epigenetics: a novel therapeutic approach for the treatment of Alzheimer's disease. Pharmacol Ther 2013; 139:41-50. [PMID: 23562602 PMCID: PMC3693222 DOI: 10.1016/j.pharmthera.2013.03.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 03/19/2013] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is the most common type of dementia in the elderly. It is characterized by the deposition of two forms of aggregates within the brain, the amyloid β plaques and tau neurofibrillary tangles. Currently, no disease-modifying agent is approved for the treatment of AD. Approved pharmacotherapies target the peripheral symptoms but they do not prevent or slow down the progression of the disease. Although several disease-modifying immunotherapeutic agents are in clinical development, many have failed due to the lack of efficacy or serious adverse events. Epigenetic changes including DNA methylation and histone modifications are involved in learning and memory and have been recently highlighted for holding promise as potential targets for AD therapeutics. Dynamic and latent epigenetic alterations are incorporated in AD pathological pathways and present valuable reversible targets for AD and other neurological disorders. The approval of epigenetic drugs for cancer treatment has opened the door for the development of epigenetic drugs for other disorders including neurodegenerative diseases. In particular, methyl donors and histone deacetylase inhibitors are being investigated for possible therapeutic effects to rescue memory and cognitive decline found in such disorders. This review explores the area of epigenetics for potential AD interventions and presents the most recent findings in this field.
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Affiliation(s)
- Lina Adwan
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
| | - Nasser H. Zawia
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
- Interdisciplinary Neuroscience Program, University of Rhode Island, Kingston, RI, USA
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Kullmann K, Deryal M, Ong MF, Schmidt W, Mahlknecht U. DNMT1 genetic polymorphisms affect breast cancer risk in the central European Caucasian population. Clin Epigenetics 2013; 5:7. [PMID: 23638630 PMCID: PMC3646668 DOI: 10.1186/1868-7083-5-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 04/16/2013] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION DNA methylation of CpG islands within the promoter region of genes is an epigenetic modification with an important role in the development of cancer and it is typically mediated by DNA methyltransferases (DNMTs). In cancer cells, global hypomethylation of the genome as a whole and regional hypermethylation of CpG islands have been reported. Four groups of DNMTs have been identified: DNMT1, DNMT2 (TRDMT1), DNMT3A and DNMT3B. DNMT2 uses the catalytic mechanism of DNMTs, but does in fact methylate RNA. Little is known about the significance of these genes in human breast cancer. In the study presented herein, we analyzed five distinct DNMT single SNPs with regard to potential associations with breast cancer risk. CASE DESCRIPTION In this study, we genotyped 221 female Caucasian breast cancer patients and 221 female Caucasian healthy controls, and we used five allele-specific real-time polymerase chain reaction (qPCR) assays. We selected one locus within the DNMT1 gene and two loci within the DNMT3A and DNMT3B genes, respectively. Statistics were calculated using the chi-squared and Fisher's exact tests, and correlated with clinical parameters such as age, diagnosis, histology, TNM stage, hormonal receptor status, human epidermal growth factor receptor 2 (HER2) status, response to treatment and survival. Statistically significant results were obtained for correlations with the DNMT1 gene. DISCUSSION AND EVALUATION Five genomic loci within the DNMT1, DNMT3A and DNMT3B genes were assessed. Statistical significance (P = 0.030) was identified for DNMT1 SNP (A201G, rs2228612): six women within the control group were GG homozygous (variant), while this mutation was absent in the breast cancer group. CONCLUSIONS We conclude that women with the DNMT1 SNP (A201G, rs2228612) GG homozygous genotype (variant) have a lower risk of developing breast cancer compared to heterozygous or wildtype genotypes. To date, alterations within the DNMT1 gene have not been reported to be associated with cancer in the Caucasian population.
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Affiliation(s)
- Kathrin Kullmann
- Department of Internal Medicine, Division of Immunotherapy and Gene Therapy, José Carreras Research Center, Saarland University Medical Center, Homburg/Saar D-66421, Germany.
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Umehara Y, Hanaoka K, Watanabe D. Distinct functions of Dnmt3a and Dnmt3b de novo DNA methyltransferases in ES cell proliferation and differentiation. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/scd.2013.32017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology 2013; 38:23-38. [PMID: 22781841 PMCID: PMC3521964 DOI: 10.1038/npp.2012.112] [Citation(s) in RCA: 2318] [Impact Index Per Article: 210.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/07/2012] [Accepted: 05/08/2012] [Indexed: 02/06/2023]
Abstract
In the mammalian genome, DNA methylation is an epigenetic mechanism involving the transfer of a methyl group onto the C5 position of the cytosine to form 5-methylcytosine. DNA methylation regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA. During development, the pattern of DNA methylation in the genome changes as a result of a dynamic process involving both de novo DNA methylation and demethylation. As a consequence, differentiated cells develop a stable and unique DNA methylation pattern that regulates tissue-specific gene transcription. In this chapter, we will review the process of DNA methylation and demethylation in the nervous system. We will describe the DNA (de)methylation machinery and its association with other epigenetic mechanisms such as histone modifications and noncoding RNAs. Intriguingly, postmitotic neurons still express DNA methyltransferases and components involved in DNA demethylation. Moreover, neuronal activity can modulate their pattern of DNA methylation in response to physiological and environmental stimuli. The precise regulation of DNA methylation is essential for normal cognitive function. Indeed, when DNA methylation is altered as a result of developmental mutations or environmental risk factors, such as drug exposure and neural injury, mental impairment is a common side effect. The investigation into DNA methylation continues to show a rich and complex picture about epigenetic gene regulation in the central nervous system and provides possible therapeutic targets for the treatment of neuropsychiatric disorders.
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Affiliation(s)
- Lisa D Moore
- Interdepartmental Program in Neuroscience and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Thuc Le
- Interdepartmental Program in Neuroscience and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Guoping Fan
- Interdepartmental Program in Neuroscience and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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