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Shaikh M, Doshi G. Epigenetic aging in major depressive disorder: Clocks, mechanisms and therapeutic perspectives. Eur J Pharmacol 2024; 978:176757. [PMID: 38897440 DOI: 10.1016/j.ejphar.2024.176757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/09/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
Depression, a chronic mental disorder characterized by persistent sadness, loss of interest, and difficulty in daily tasks, impacts millions globally with varying treatment options. Antidepressants, despite their long half-life and minimal effectiveness, leave half of patients undertreated, highlighting the need for new therapies to enhance well-being. Epigenetics, which studies genetic changes in gene expression or cellular phenotype without altering the underlying Deoxyribonucleic Acid (DNA) sequence, is explored in this article. This article delves into the intricate relationship between epigenetic mechanisms and depression, shedding light on how environmental stressors, early-life adversity, and genetic predispositions shape gene expression patterns associated with depression. We have also discussed Histone Deacetylase (HDAC) inhibitors, which enhance cognitive function and mood regulation in depression. Non-coding RNAs, (ncRNAs) such as Long Non-Coding RNAs (lncRNAs) and micro RNA (miRNAs), are highlighted as potential biomarkers for detecting and monitoring major depressive disorder (MDD). This article also emphasizes the reversible nature of epigenetic modifications and their influence on neuronal growth processes, underscoring the dynamic interplay between genetics, environment, and epigenetics in depression development. It explores the therapeutic potential of targeting epigenetic pathways in treating clinical depression. Additionally, it examines clinical findings related to epigenetic clocks and their role in studying depression and biological aging.
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Affiliation(s)
- Muqtada Shaikh
- SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, 400 056, India
| | - Gaurav Doshi
- SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, 400 056, India.
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2
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Lanka G, Banerjee S, Adhikari N, Ghosh B. Fragment-based discovery of new potential DNMT1 inhibitors integrating multiple pharmacophore modeling, 3D-QSAR, virtual screening, molecular docking, ADME, and molecular dynamics simulation approaches. Mol Divers 2024:10.1007/s11030-024-10837-5. [PMID: 38637479 DOI: 10.1007/s11030-024-10837-5] [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: 11/29/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
DNA methyl transferases (DNMTs) are one of the crucial epigenetic modulators associated with a wide variety of cancer conditions. Among the DNMT isoforms, DNMT1 is correlated with bladder, pancreatic, and breast cancer, as well as acute myeloid leukemia and esophagus squamous cell carcinoma. Therefore, the inhibition of DNMT1 could be an attractive target for combating cancers and other metabolic disorders. The disadvantages of the existing nucleoside and non-nucleoside DNMT1 inhibitors are the main motive for the discovery of novel promising inhibitors. Here, pharmacophore modeling, 3D-QSAR, and e-pharmacophore modeling of DNMT1 inhibitors were performed for the large fragment database screening. The resulting fragments with high dock scores were combined into molecules. The current study revealed several constitutional pharmacophoric features that can be essential for selective DNMT1 inhibition. The fragment docking and virtual screening identified 10 final hit molecules that exhibited good binding affinities in terms of docking score, binding free energies, and acceptable ADME properties. Also, the modified lead molecules (GL1b and GL2b) designed in this study showed effective binding with DNMT1 confirmed by their docking scores, binding free energies, 3D-QSAR predicted activities and acceptable drug-like properties. The MD simulation studies also suggested that leads (GL1b and GL2b) formed stable complexes with DNMT1. Therefore, the findings of this study can provide effective information for the development/identification of novel DNMT1 inhibitors as effective anticancer agents.
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Affiliation(s)
- Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
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3
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Manzer HS, Brunetti T, Doran KS. Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization. mBio 2023; 14:e0230623. [PMID: 37905908 PMCID: PMC10746215 DOI: 10.1128/mbio.02306-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Group B Streptococcus (GBS) colonizes the female reproductive tract (FRT) in one-third of women, and carriage leads to numerous adverse pregnancy outcomes including the preterm premature rupture of membranes, chorioamnionitis, and stillbirth. The presence of GBS in the FRT during pregnancy is also the largest predisposing factor for the transmission of GBS and invasive neonatal diseases, including pneumonia, sepsis, and meningitis. The factors contributing to GBS colonization are still being elucidated. Here, we show for the first time that GBS transcription is regulated by an orphan DNA cytosine methyltransferase (Dcm). Many GBS factors are regulated by Dcm, especially those involved in carbohydrate transport and metabolism. We show that GBS persistence in the FRT is dependent on the catabolism of sugars found on the vaginal mucin MUC5B. Collectively, this work highlights the regulatory importance of a DNA methyltransferase and identifies both host and bacterial factors required for GBS colonization.
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Affiliation(s)
- Haider S. Manzer
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tonya Brunetti
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kelly S. Doran
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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4
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Qin H, Liu J, Fang C, Deng Y, Zhang Y. DNA methylation: The epigenetic mechanism of Alzheimer's disease. IBRAIN 2023; 9:463-472. [PMID: 38680511 PMCID: PMC11045197 DOI: 10.1002/ibra.12121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 05/01/2024]
Abstract
Nowadays, with the development of the social health care system, there is an increasing trend towards an aging society. The incidence of Alzheimer's disease (AD) is also on the rise. AD is a kind of neurodegenerative disease that can be found in any age group. For years, scientists have been committing to discovering the cause of AD. DNA methylation is one of the most common epigenetic mechanisms in mammals and plays a vital role in the pathogenesis of several diseases, including tumors. Studying chemical changes in the epigenome, or DNA methylation can help us understand the effects of our environment and life on diseases, such as smoking, depression, and menopause, which may affect people's chances of developing Alzheimer's or other diseases. Recent studies have identified some crucial genes like ANK1, RHBDF2, ABCA7, and BIN1, linking DNA methylation to AD. This review focuses on elucidating the relationship between DNA methylation and the pathogenesis of AD and provides an outlook on possible targeted therapeutic modalities.
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Affiliation(s)
- Hao‐Yue Qin
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Jiao‐Yan Liu
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Chang‐Le Fang
- Faculty of Health SciencesUniversity of AdelaideMelbourneVICAustralia
| | - Yan‐Ping Deng
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Ying Zhang
- State Key Laboratories for Quality Research in Chinese Medicines, Faculty of PharmacyMacau University of Science and TechnologyMacauChina
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5
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Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform. BMC Bioinformatics 2023; 24:33. [PMID: 36721080 PMCID: PMC9890740 DOI: 10.1186/s12859-023-05163-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing (NGS) platform, GenoLab M is a promising alternative platform. However, its comprehensive evaluation for WGBS has not been reported. We sequenced two bisulfite-converted mammal DNA in this research using our GenoLab M and NovaSeq 6000, respectively. Then, we systematically compared those data via four widely used WGBS tools (BSMAP, Bismark, BatMeth2, BS-Seeker2) and a new bisulfite-seq tool (BSBolt). We interrogated their computational time, genome depth and coverage, and evaluated their percentage of methylated Cs. RESULT Here, benchmarking a combination of pre- and post-processing methods, we found that trimming improved the performance of mapping efficiency in eight datasets. The data from two platforms uncovered ~ 80% of CpG sites genome-wide in the human cell line. Those data sequenced by GenoLab M achieved a far lower proportion of duplicates (~ 5.5%). Among pipelines, BSMAP provided an intriguing representation of 5-mC distribution at CpG sites with 5-mC levels > ~ 78% in datasets from human cell lines, especially in the GenoLab M. BSMAP performed more advantages in running time, uniquely mapped reads percentages, genomic coverage, and quantitative accuracy. Finally, compared with the previous methylation pattern of human cell line and mouse tissue, we confirmed that the data from GenoLab M performed similar consistency and accuracy in methylation levels of CpG sites with that from NovaSeq 6000. CONCLUSION Together we confirmed that GenoLab M was a qualified NGS platform for WGBS with high performance. Our results showed that BSMAP was the suitable pipeline that allowed for WGBS studies on the GenoLab M platform.
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Francés R, Mata-Garrido J, de la Fuente R, Carcelén M, Lafarga M, Berciano MT, García R, Hurlé MA, Tramullas M. Identification of Epigenetic Interactions between MicroRNA-30c-5p and DNA Methyltransferases in Neuropathic Pain. Int J Mol Sci 2022; 23:13994. [PMID: 36430472 PMCID: PMC9694031 DOI: 10.3390/ijms232213994] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Neuropathic pain is a prevalent and severe chronic syndrome, often refractory to treatment, whose development and maintenance may involve epigenetic mechanisms. We previously demonstrated a causal relationship between miR-30c-5p upregulation in nociception-related neural structures and neuropathic pain in rats subjected to sciatic nerve injury. Furthermore, a short course of an miR-30c-5p inhibitor administered into the cisterna magna exerts long-lasting antiallodynic effects via a TGF-β1-mediated mechanism. Herein, we show that miR-30c-5p inhibition leads to global DNA hyper-methylation of neurons in the lumbar dorsal root ganglia and spinal dorsal horn in rats subjected to sciatic nerve injury. Specifically, the inhibition of miR-30-5p significantly increased the expression of the novo DNA methyltransferases DNMT3a and DNMT3b in those structures. Furthermore, we identified the mechanism and found that miR-30c-5p targets the mRNAs of DNMT3a and DNMT3b. Quantitative methylation analysis revealed that the promoter region of the antiallodynic cytokine TGF-β1 was hypomethylated in the spinal dorsal horn of nerve-injured rats treated with the miR-30c-5p inhibitor, while the promoter of Nfyc, the host gene of miR-30c-5p, was hypermethylated. These results are consistent with long-term protection against neuropathic pain development after nerve injury. Altogether, our results highlight the key role of miR-30c-5p in the epigenetic mechanisms' underlying neuropathic pain and provide the basis for miR-30c-5p as a therapeutic target.
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Affiliation(s)
- Raquel Francés
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Jorge Mata-Garrido
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, 39011 Santander, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
| | - Roberto de la Fuente
- Servicio de Anestesiología, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain
| | - María Carcelén
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Miguel Lafarga
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, 39011 Santander, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
| | - María Teresa Berciano
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, 39011 Santander, Spain
| | - Raquel García
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | - María A. Hurlé
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Mónica Tramullas
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
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7
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Xu L, Zhou C, Liang Y, Fan T, Zhang F, Chen X, Yuan W. Epigenetic modifications in the accumulation and function of myeloid-derived suppressor cells. Front Immunol 2022; 13:1016870. [PMID: 36439186 PMCID: PMC9691837 DOI: 10.3389/fimmu.2022.1016870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/31/2022] [Indexed: 12/27/2023] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are key players under various pathologic conditions, such as cancer. Epigenetic modifications such as DNA methylation, RNA-mediated processes, and histone modification can alter gene transcription, and thus regulating pathological process. Studies have shown that epigenetic modification contributes to the accumulation and function of MDSCs. This review summarizes the crosstalk between the epigenetic alterations and MDSCs functions, and briefly introduces how the accumulation and function of MDSCs caused by epigenetic modification impact on the disease development, which represents as a promising therapeutic strategy for the related disorders.
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Affiliation(s)
| | | | | | | | | | | | - Wei Yuan
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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8
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Fernandes V, Sood A, Preeti K, Khatri DK, Singh SB. Neuroepigenetic alterations in the prefrontal cortex of type 2 diabetic mice through DNA hypermethylation. Mol Biol Rep 2022; 49:12017-12028. [DOI: 10.1007/s11033-022-08018-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022]
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9
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Agborbesong E, Li LX, Li L, Li X. Molecular Mechanisms of Epigenetic Regulation, Inflammation, and Cell Death in ADPKD. Front Mol Biosci 2022; 9:922428. [PMID: 35847973 PMCID: PMC9277309 DOI: 10.3389/fmolb.2022.922428] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder, which is caused by mutations in the PKD1 and PKD2 genes, characterizing by progressive growth of multiple cysts in the kidneys, eventually leading to end-stage kidney disease (ESKD) and requiring renal replacement therapy. In addition, studies indicate that disease progression is as a result of a combination of factors. Understanding the molecular mechanisms, therefore, should facilitate the development of precise therapeutic strategies for ADPKD treatment. The roles of epigenetic modulation, interstitial inflammation, and regulated cell death have recently become the focuses in ADPKD. Different epigenetic regulators, and the presence of inflammatory markers detectable even before cyst growth, have been linked to cyst progression. Moreover, the infiltration of inflammatory cells, such as macrophages and T cells, have been associated with cyst growth and deteriorating renal function in humans and PKD animal models. There is evidence supporting a direct role of the PKD gene mutations to the regulation of epigenetic mechanisms and inflammatory response in ADPKD. In addition, the role of regulated cell death, including apoptosis, autophagy and ferroptosis, have been investigated in ADPKD. However, there is no consensus whether cell death promotes or delays cyst growth in ADPKD. It is therefore necessary to develop an interactive picture between PKD gene mutations, the epigenome, inflammation, and cell death to understand why inherited PKD gene mutations in patients may result in the dysregulation of these processes that increase the progression of renal cyst formation.
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Affiliation(s)
- Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Linda Xiaoyan Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Lu Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
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10
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Jiang W, Tan XY, Li JM, Yu P, Dong M. DNA Methylation: A Target in Neuropathic Pain. Front Med (Lausanne) 2022; 9:879902. [PMID: 35872752 PMCID: PMC9301322 DOI: 10.3389/fmed.2022.879902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Neuropathic pain (NP), caused by an injury or a disease affecting the somatosensory nervous system of the central and peripheral nervous systems, has become a global health concern. Recent studies have demonstrated that epigenetic mechanisms are among those that underlie NP; thus, elucidating the molecular mechanism of DNA methylation is crucial to discovering new therapeutic methods for NP. In this review, we first briefly discuss DNA methylation, demethylation, and the associated key enzymes, such as methylases and demethylases. We then discuss the relationship between NP and DNA methylation, focusing on DNA methyltransferases including methyl-CpG-binding domain (MBD) family proteins and ten-eleven translocation (TET) enzymes. Based on experimental results of neuralgia in animal models, the mechanism of DNA methylation-related neuralgia is summarized, and useful targets for early drug intervention in NP are discussed.
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Affiliation(s)
- Wei Jiang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Xuan-Yu Tan
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Jia-Ming Li
- Department of Emergency, The First Hospital of Jilin University, Changchun, China
| | - Peng Yu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
- *Correspondence: Peng Yu
| | - Ming Dong
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
- Ming Dong
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11
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Sarkies P. Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions. Biochem Soc Trans 2022; 50:1179-1190. [PMID: 35521905 PMCID: PMC9246332 DOI: 10.1042/bst20210725] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/14/2022]
Abstract
DNA methylation is an epigenetic modification with a very long evolutionary history. However, DNA methylation evolves surprisingly rapidly across eukaryotes. The genome-wide distribution of methylation diversifies rapidly in different lineages, and DNA methylation is lost altogether surprisingly frequently. The growing availability of genomic and epigenomic sequencing across organisms highlights this diversity but also illuminates potential factors that could explain why both the DNA methylation machinery and its genome-wide distribution evolve so rapidly. Key to this are new discoveries about the fitness costs associated with DNA methylation, and new theories about how the fundamental biochemical mechanisms of DNA methylation introduction and maintenance could explain how new genome-wide patterns of methylation evolve.
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Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, U.K
- MRC London Institute of Molecular Biology, London, U.K
- Institute of Clinical Sciences, Imperial College London, London, U.K
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12
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DNA Methyltransferases and DNA Damage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:349-361. [DOI: 10.1007/978-3-031-11454-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Sarkies P. DNA methylation and sexual dimorphism: New insights from mealybugs. Mol Ecol 2021; 30:5621-5623. [PMID: 34687580 DOI: 10.1111/mec.16243] [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: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 01/09/2023]
Abstract
DNA methylation is an ancient epigenetic pathway found across eukaryotes. Nevertheless, the targets of DNA methylation within genomes evolve extremely rapidly. Arthropods display many such examples. The mealybug Planococcus citri has evolved methylation at promoter sequences, associated with gene silencing just as in mammals. In this issue of Molecular Ecology, Bain et al. (2021), thoroughly characterise mealybug methylation, exploring its potential functions in gene expression and the spectacular sexual dimorphism that is a characteristic of this species. Their results provide new insights into the complex relationship between DNA methylation and gene expression and highlight how rapidly different methylation systems can evolve.
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Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, UK.,Institute of Clinical Sciences, Imperial College London, London, UK
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14
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Hu C, Liu X, Zeng Y, Liu J, Wu F. DNA methyltransferase inhibitors combination therapy for the treatment of solid tumor: mechanism and clinical application. Clin Epigenetics 2021; 13:166. [PMID: 34452630 PMCID: PMC8394595 DOI: 10.1186/s13148-021-01154-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 08/16/2021] [Indexed: 12/15/2022] Open
Abstract
DNA methylation, an epigenetic modification, regulates gene transcription and maintains genome stability. DNA methyltransferase (DNMT) inhibitors can activate silenced genes at low doses and cause cytotoxicity at high doses. The ability of DNMT inhibitors to reverse epimutations is the basis of their use in novel strategies for cancer therapy. In this review, we examined the literature on DNA methyltransferase inhibitors. We summarized the mechanisms underlying combination therapy using DNMT inhibitors and clinical trials based on combining hypomethylation agents with other chemotherapeutic drugs. We also discussed the efficacy of such compounds as antitumor agents, the need to optimize treatment schedules and the regimens for maximal biologic effectiveness. Notably, the combination of DNMT inhibitors and chemotherapy and/or immune checkpoint inhibitors may provide helpful insights into the development of efficient therapeutic approaches.
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Affiliation(s)
- Chunhong Hu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, 410011, Hunan, China
| | - Xiaohan Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yue Zeng
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Junqi Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Fang Wu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, 410011, Hunan, China.
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15
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King DE, Sparling AC, Joglekar R, Meyer JN, Murphy SK. Direct comparisons of bisulfite pyrosequencing versus targeted bisulfite sequencing. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000444. [PMID: 34423283 PMCID: PMC8377520 DOI: 10.17912/micropub.biology.000444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022]
Abstract
DNA methylation is an important epigenetic mechanism involved in proper genome function. Bisulfite pyrosequencing (PSQ) is a commonly used technique to quantify DNA methylation. Although very accurate, bisulfite pyrosequencing can be expensive and time consuming for large-scale quantitative DNA methylation analysis at the single nucleotide level. High throughput DNA methylation sequencing has the potential to address these limitations, but its comparability to other methylation detection methods has not been well studied. We compared QIAseq Targeted Methyl Panel technologies (QMS) and PSQ by analyzing four CpG sites within four genes involved in neurodevelopment. QMS and PSQ had an average 5.6% difference in the detected level of DNA methylation for the same four CpG sites. However, we observed a strong correlation in the levels of methylation across all four CpG sites between the two technologies. These findings demonstrate the comparability of QMS relative to PSQ in the ability to accurately quantify DNA methylation at specific CpG sites.
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Affiliation(s)
- Dillon E. King
- Nicholas School of Environment, Duke University, Durham NC,
Department of Obstetrics and Gynecology, Duke University, Durham NC
| | | | | | - Joel N. Meyer
- Nicholas School of Environment, Duke University, Durham NC
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University, Durham NC,
Correspondence to: Susan K. Murphy ()
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Insights into S-adenosyl-l-methionine (SAM)-dependent methyltransferase related diseases and genetic polymorphisms. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108396. [PMID: 34893161 DOI: 10.1016/j.mrrev.2021.108396] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Enzymatic methylation catalyzed by methyltransferases has a significant impact on many human biochemical reactions. As the second most ubiquitous cofactor in humans, S-adenosyl-l-methionine (SAM or AdoMet) serves as a methyl donor for SAM-dependent methyltransferases (MTases), which transfer a methyl group to a nucleophilic acceptor such as O, As, N, S, or C as the byproduct. SAM-dependent methyltransferases can be grouped into different types based on the substrates. Here we systematically reviewed eight types of methyltransferases associated with human diseases. Catechol O-methyltransferase (COMT), As(III) S-adenosylmethionine methyltransferase (AS3MT), indolethylamine N-methyltransferase (INMT), phenylethanolamine N-methyltransferase (PNMT), histamine N-methyltransferase (HNMT), nicotinamide N-methyltransferase (NNMT), thiopurine S-methyltransferase (TPMT) and DNA methyltansferase (DNMT) are classic SAM-dependent MTases. Correlations between genotypes and disease susceptibility can be partially explained by genetic polymorphisms. The physiological function, substrate specificity, genetic variants and disease susceptibility associated with these eight SAM-dependent methyltransferases are discussed in this review.
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17
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Sehgal R, Kaur N, Ramakrishna G, Trehanpati N. Immune Surveillance by Myeloid-Derived Suppressor Cells in Liver Diseases. Dig Dis 2021; 40:301-312. [PMID: 34157708 DOI: 10.1159/000517459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/27/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Myeloid-derived suppressor cells (MDSCs) are immunosuppressive in nature, originate in the bone marrow, and are mainly found in the blood, spleen, and liver. In fact, liver acts as an important organ for induction and accumulation of MDSCs, especially during infection, inflammation, and cancer. In humans and rodents, models of liver diseases revealed that MDSCs promote regeneration and drive the inflammatory processes, leading to hepatitis, fibrogenesis, and cirrhosis, ultimately resulting in hepatocellular carcinoma. SUMMARY This brief review is focused on the in-depth understanding of the key molecules involved in the expansion and regulation of MDSCs and their underlying immunosuppressive mechanisms in liver diseases. KEY MESSAGE Modulated MDSCs can be used for therapeutic purposes in inflammation, cancer, and sepsis.
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Affiliation(s)
- Rashi Sehgal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India.,Amity Institute of Biotechnology (AIB), Amity University, Noida, India
| | - Navkiran Kaur
- Amity Institute of Biotechnology (AIB), Amity University, Noida, India
| | - Gayatri Ramakrishna
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Nirupma Trehanpati
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
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18
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Zheng BX, Malik A, Xiong M, Bekker A, Tao YX. Nerve trauma-caused downregulation of opioid receptors in primary afferent neurons: Molecular mechanisms and potential managements. Exp Neurol 2020; 337:113572. [PMID: 33340498 DOI: 10.1016/j.expneurol.2020.113572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/06/2020] [Accepted: 12/13/2020] [Indexed: 12/18/2022]
Abstract
Neuropathic pain is the most common clinical disorder destroying the quality of patient life and leading to a marked economic and social burden. Opioids are still last option for pharmacological treatment of this disorder, but their antinociceptive effects are limited in part due to the downregulation of opioid receptors in the primary afferent neurons after peripheral nerve trauma. How this downregulation occurs is not completely understood, but recent studies have demonstrated that peripheral nerve trauma drives the alterations in epigenetic modifications (including DNA methylation, histone methylation and mciroRNAs), expression of transcription factors, post-transcriptional modifications (e.g., RNA methylation) and protein translation initiation in the neurons of nerve trauma-related dorsal root ganglion (DRG) and that these alternations may be associated with nerve trauma-caused downregulation of DRG opioid receptors. This review presents how opioid receptors are downregulated in the DRG after peripheral nerve trauma, specifically focusing on distinct molecular mechanisms underlying transcriptional and translational processes. This review also discusses how this downregulation contributes to the induction and maintenance of neuropathic pain. A deeper understanding of these molecular mechanisms likely provides a novel avenue for prevention and/or treatment of neuropathic pain.
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Affiliation(s)
- Bi-Xin Zheng
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Ayma Malik
- Rutgers Graduate School of Biomedical Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Ming Xiong
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Alex Bekker
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Yuan-Xiang Tao
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA; Department of Physiology, Pharmacology & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA; Department of Cell Biology & Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA.
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19
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Zhou S, Feng S, Qin W, Wang X, Tang Y, Yuan S. Epigenetic Regulation of Spermatogonial Stem Cell Homeostasis: From DNA Methylation to Histone Modification. Stem Cell Rev Rep 2020; 17:562-580. [PMID: 32939648 DOI: 10.1007/s12015-020-10044-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
Spermatogonial stem cells(SSCs)are the ultimate germline stem cells with the potential of self-renewal and differentiation, and a dynamic balance of SSCs play an essential role in spermatogenesis. During the gene expression process, genomic DNA and nuclear protein, working together, contribute to SSC homeostasis. Recently, emerging studies have shown that epigenome-related molecules such as chromatin modifiers play an important role in SSC homeostasis through regulating target gene expression. Here, we focus on two types of epigenetic events, including DNA methylation and histone modification, and summarize their function in SSC homeostasis. Understanding the molecular mechanism during SSC homeostasis will promote the recognition of epigenetic biomarkers in male infertility, and bring light into therapies of infertile patients.Graphical Abstract.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, 510500, Guangzhou, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, 510500, Guangzhou, China.
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China. .,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, 518057, China.
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20
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Colwell M, Wanner NM, Drown C, Drown M, Dolinoy DC, Faulk C. Paradoxical whole genome DNA methylation dynamics of 5'aza-deoxycytidine in chronic low-dose exposure in mice. Epigenetics 2020; 16:209-227. [PMID: 32619143 DOI: 10.1080/15592294.2020.1790951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Decitabine (5-aza-2'deoxycytidine; DAC) is a DNA methyltransferase inhibitor used to hypomethylate the epigenome. Current dosing regimens of DAC for use in mice vary widely and their hypomethylating ability has not been robustly characterized, despite reliable results of hypomethylation of the epigenome with cell lines in vitro and tissue specificity in vivo. We investigated the effects on the DNA methylome and gene expression within mice exposed to chronic low doses of DAC ranging from 0 to 0.35 mg/kg over a period of 7 weeks without causing toxicity. Our dose paradigm resulted in no cytotoxic effects within target tissues, although testes weight and sperm concentration significantly reduced as dose increased (p-value <0.05). By whole genome bisulphite sequencing (WGBS), we identify tissue and dose-specific differentially methylated CpGs (DMCs) and regions (DMRs) in testes and liver. Testes methylation is more sensitive to DAC exposure when compared to liver, cortex, and hippocampus. Gene expression was dysregulated in testes and liver, targeting non-specific pathways as dose increases. Together our data suggest DNA methylation and gene expression are disrupted by in vivo DAC treatment in a non-uniform manner contrary to expectations, and that no dose level or regimen is sufficient to cause systemic hypomethylation in whole mice.
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Affiliation(s)
- Mathia Colwell
- Department of Animal Science, University of Minnesota College of Food, Agricultural and Natural Resource Scientists , St. Paul, MN, USA
| | - Nicole M Wanner
- Department of Veterinary and Biomedical Sciences, University of Minnesota College of Veterinary Medicine , St. Paul, MN, USA
| | - Chelsea Drown
- Department of Animal Science, University of Minnesota College of Food, Agricultural and Natural Resource Scientists , St. Paul, MN, USA
| | - Melissa Drown
- Department of Animal Science, University of Minnesota College of Food, Agricultural and Natural Resource Scientists , St. Paul, MN, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan , Ann Arbor, MI, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota College of Food, Agricultural and Natural Resource Scientists , St. Paul, MN, USA
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21
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Lewis SH, Ross L, Bain SA, Pahita E, Smith SA, Cordaux R, Miska EA, Lenhard B, Jiggins FM, Sarkies P. ------Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods. PLoS Genet 2020; 16:e1008864. [PMID: 32584820 PMCID: PMC7343188 DOI: 10.1371/journal.pgen.1008864] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/08/2020] [Accepted: 05/15/2020] [Indexed: 12/23/2022] Open
Abstract
Cytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters of genes. In insects, DNA methylation is generally restricted to a small subset of transcribed genes, with both intergenic regions and transposable elements (TEs) depleted of methylation. The evolutionary origin and the function of these methylation patterns are poorly understood. Here we characterise the evolution of DNA methylation across the arthropod phylum. While the common ancestor of the arthropods had low levels of TE methylation and did not methylate promoters, both of these functions have evolved independently in centipedes and mealybugs. In contrast, methylation of the exons of a subset of transcribed genes is ancestral and widely conserved across the phylum, but has been lost in specific lineages. A similar set of genes is methylated in all species that retained exon-enriched methylation. We show that these genes have characteristic patterns of expression correlating to broad transcription initiation sites and well-positioned nucleosomes, providing new insights into potential mechanisms driving methylation patterns over hundreds of millions of years.
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Affiliation(s)
- Samuel H. Lewis
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Laura Ross
- Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Stevie A. Bain
- Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Eleni Pahita
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Stephen A. Smith
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions Universite de Poitiers, France
| | - Eric A. Miska
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
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22
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Zubrzycka A, Zubrzycki M, Perdas E, Zubrzycka M. Genetic, Epigenetic, and Steroidogenic Modulation Mechanisms in Endometriosis. J Clin Med 2020; 9:E1309. [PMID: 32370117 PMCID: PMC7291215 DOI: 10.3390/jcm9051309] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
Endometriosis is a chronic gynecological disease, affecting up to 10% of reproductive-age women. The exact cause of the disease is unknown; however, it is a heritable condition affected by multiple genetic, epigenetic, and environmental factors. Previous studies reported variations in the epigenetic patterns of numerous genes known to be involved in the aberrant modulation of cell cycle steroidogenesis, abnormal hormonal, immune and inflammatory status in endometriosis, apoptosis, adhesion, angiogenesis, proliferation, immune and inflammatory processes, response to hypoxia, steroidogenic pathway and hormone signaling are involved in the pathogenesis of endometriosis. Accumulating evidence suggest that various epigenetic aberrations may contribute to the pathogenesis of endometriosis. Among them, DNA methyltransferases, histone deacetylators, and non-coding microRNAs demonstrate differential expression within endometriotic lesions and in the endometrium of patients with endometriosis. It has been indicated that the identification of epigenetic differences within the DNA or histone proteins may contribute to the discovery of a useful prognostic biomarker, which could aid in the future earlier detection, timely diagnosis, and initiation of a new approach to the treatment of endometriosis, as well as inform us about the effectiveness of treatment and the stage of the disease. As the etiology of endometriosis is highly complex and still far from being fully elucidated, the presented review focuses on different approaches to identify the genetic and epigenetic links of endometriosis and its pathogenesis.
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Affiliation(s)
- Anna Zubrzycka
- Department of Biomedicine and Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; Poland;
- Department of Operative and Conservative Gynecology, K. Jonscher Memorial Hospital, Milionowa 14, 93-113 Lodz, Poland
| | - Marek Zubrzycki
- Department of Cardiac Surgery and Transplantology, The Cardinal Stefan Wyszynski Institute of Cardiology, Alpejska 42, 04-628 Warsaw, Poland;
| | - Ewelina Perdas
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland;
| | - Maria Zubrzycka
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland;
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23
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Zal F, Yarahmadi A, Totonchi H, Barazesh M, Moradi Sarabi M. Nicotine attenuates global genomic DNA methylation by influencing DNMTs gene expression in human endometrial stromal cells. Genes Environ 2020; 42:6. [PMID: 32042366 PMCID: PMC7003317 DOI: 10.1186/s41021-020-0144-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND There is increasing evidence indicating an incidence of infertility and also the risk of endometrial cancers among smokers. However, the mechanism underlying nicotine adverse effect on female reproduction remains unclear. Growing evidence has suggested that environmental exposures such as nicotine could modulate the epigenome. No study has yet been published to evaluate the direct effect of nicotine on the epigenome profiling of human endometrial stromal cells (HESC). Herein, we decided to examine the direct effects of nicotine on global genomic DNA methylation status and DNA methyl- transferases (DNMTs) gene expression in HESC. HESC were treated with different doses of nicotine (0 or control, 10- 11, 10- 8 and 10- 6) M for 24 h and their genomic global DNA methylation and gene expression of DNMTs (DNMT1, DNMT3A, and DNMT3B) were investigated using ELISA and real-time PCR, respectively. RESULTS Nicotine treatments reduced the average level of DNMTs gene expression by 90, 79, and 73.4% in 10- 11, 10- 8 and 10- 6 M of nicotine treated cells as compared to control cells, respectively (p < 0.05). Also, 10- 8 and 10- 6 M of nicotine concentrations effectively reduced the amounts of 5-methylated cytosine (5-mC) by 1.09 and 1.87% compared to control cells, respectively (p < 0.05). The 5-mC percentages were positively correlated with the relative cellular DNMTs expression in HESC as verified by the Pearson correlation test. CONCLUSION An interesting possibility raised by the current study is that the reduced genomic global DNA methylation level in HESC may be partly due to the suppression of DNMTs gene expression caused by nicotine in these cells. GRAPHICAL ABSTRACT
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Affiliation(s)
- Fatemeh Zal
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Yarahmadi
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamidreza Totonchi
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahdi Barazesh
- Biotechnology Department, School of advanced medical sciences and technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Moradi Sarabi
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, 381251698 Iran
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
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24
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The effects of the DNA Demethylating reagent, 5-azacytidine on SMCHD1 genomic localization. BMC Genet 2020; 21:3. [PMID: 31941450 PMCID: PMC6964063 DOI: 10.1186/s12863-020-0809-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/06/2020] [Indexed: 12/03/2022] Open
Abstract
Background DNA methylation is an epigenetic modification that mainly repress expression of genes essential during embryogenesis and development. There are key ATPase-dependent enzymes that read or write DNA methylation to remodel chromatin and regulate gene expression. Structural maintenance of chromosome hinge domain containing 1 (SMCHD1) is an architectural protein that regulates expression of numerous genes, some of which are imprinted, that are sensitive to DNA methylation. In addition, SMCHD1 germline mutations lead to developmental diseases; facioscapulohumoral muscular dystrophy (FSHD), bosma arhinia and micropthalmia (BAMS). Current evidence suggests that SMCHD1 functions through maintenance or de novo DNA methylation required for chromatin compaction. However, it is unclear if DNA methylation is also essential for genomic recruitment of SMCHD1 and its role as an architectural protein. We previously isolated SMCHD1 using a methylated DNA region from mouse pituitary growth hormone (Gh1) promoter, suggesting that methylation is required for SMCHD1 DNA binding. The goal of this study was to further understand DNA methylation directed role of SMCHD1 in regulating gene expression. Therefore, we profiled SMCHD1 genome wide occupancy in human neuroblastoma SH-SY5Y cells and evaluated if DNA methylation is required for SMCHD1 genomic binding by treating cells with the DNA demethylating reagent, 5-azacytidine (5-azaC). Results Our data suggest that the majority of SMCHD1 binding occurs in intron and intergenic regions. Gene ontology analysis of genes associated with SMCHD1 genomic occupancy that is sensitive to 5-azaC treatment suggests SMCHD1 involvement in central nervous system development. The potassium voltage-gated channel subfamily Q member1 (KCNQ1) gene that associates with central nervous system is a known SMCHD1 target. We showed SMCHD1 binding to an intronic region of KCNQ1 that is lost following 5-azaC treatment suggesting DNA methylation facilitated binding of SMCHD1. Indeed, deletion of SMCHD1 by CRISPR- Cas9 increases KCNQ1 gene expression confirming its role in regulating KCNQ1 gene expression. Conclusion These findings provide novel insights on DNA methylation directed function of SMCHD1 in regulating expression of genes associated with central nervous system development that impact future drug development strategies.
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Functional Analysis of DNMT3A DNA Methyltransferase Mutations Reported in Patients with Acute Myeloid Leukemia. Biomolecules 2019; 10:biom10010008. [PMID: 31861499 PMCID: PMC7022712 DOI: 10.3390/biom10010008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/30/2022] Open
Abstract
In mammals, DNA methylation is necessary for the maintenance of genomic stability, gene expression regulation, and other processes. During malignant diseases progression, changes in both DNA methylation patterns and DNA methyltransferase (MTase) genes are observed. Human de novo MTase DNMT3A is most frequently mutated in acute myeloid leukemia (AML) with a striking prevalence of R882H mutation, which has been extensively studied. Here, we investigate the functional role of the missense mutations (S714C, R635W, R736H, R771L, P777R, and F752V) found in the catalytic domain of DNMT3A in AML patients. These were accordingly mutated in the murine Dnmt3a catalytic domain (S124C, R45W, R146H, R181L, P187R, and F162V) and in addition, one-site CpG-containing DNA substrates were used as a model system. The 3–15-fold decrease (S124C and P187R) or complete loss (F162V, R45W, and R146H) of Dnmt3a-CD methylation activity was observed. Remarkably, Pro 187 and Arg 146 are not located at or near the Dnmt3a functional motives. Regulatory protein Dnmt3L did not enhance the methylation activity of R45W, R146H, P187R, and F162V mutants. The key steps of the Dnmt3a-mediated methylation mechanism, including DNA binding and transient covalent intermediate formation, were examined. There was a complete loss of DNA-binding affinity for R45W located in the AdoMet binding region and for R146H. Dnmt3a mutants studied in vitro suggest functional impairment of DNMT3A during pathogenesis.
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26
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Sato K, Kumagai N, Suzuki N. Alteration of the DNA Methylation Signature of Renal Erythropoietin-Producing Cells Governs the Sensitivity to Drugs Targeting the Hypoxia-Response Pathway in Kidney Disease Progression. Front Genet 2019; 10:1134. [PMID: 31798631 PMCID: PMC6863978 DOI: 10.3389/fgene.2019.01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic kidney disease (CKD) affects more than 10% of the population worldwide and burdens citizens with heavy medical expenses in many countries. Because a vital erythroid growth factor, erythropoietin (EPO), is secreted from renal interstitial fibroblasts [renal EPO-producing (REP) cells], anemia arises as a major complication of CKD. We determined that hypoxia-inducible factor 2α (HIF2α), which is inactivated by HIF-prolyl hydroxylase domain-containing proteins (PHDs) in an oxygen-dependent manner, tightly regulates EPO production in REP cells at the gene transcription level to maintain oxygen homeostasis. HIF2α-mediated disassembly of the nucleosome in the EPO gene is also involved in hypoxia-inducible EPO production. In renal anemia patients, anemic and pathological hypoxia is ineffective toward EPO induction due to the inappropriate over-activation of PHDs in REP cells transformed into myofibroblasts (MF-REP cells) due to kidney damage. Accordingly, PHD inhibitory compounds are being developed for the treatment of renal anemia. However, our studies have demonstrated that the promoter regions of the genes encoding EPO and HIF2α are highly methylated in MF-REP cells, and the expression of these genes is epigenetically silenced with CKD progression. This finding notably indicates that the efficacy of PHD inhibitors depends on the CKD stage of each patient. In addition, a strategy for harvesting renal cells, including REP cells from the urine of patients, is proposed to identify plausible biomarkers for CKD and to develop personalized precision medicine against CKD by a non-invasive strategy.
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Affiliation(s)
- Koji Sato
- Division of Oxygen Biology, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naonori Kumagai
- Department of Pediatrics, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Norio Suzuki
- Division of Oxygen Biology, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
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Yu J, Zayas J, Qin B, Wang L. Targeting DNA methylation for treating triple-negative breast cancer. Pharmacogenomics 2019; 20:1151-1157. [PMID: 31755366 PMCID: PMC7026764 DOI: 10.2217/pgs-2019-0078] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for 15-20% of all invasive breast cancers and tends to have aggressive histological features and poor clinical outcomes. Unlike, estrogen receptor- or HER2-positive diseases, TNBC patients currently lack the US FDA-approved targeted therapies. DNA methylation is a critical mechanism of epigenetic modification. It is well known that aberrant DNA methylation contributes to the malignant transformation of cells by silencing critical tumor suppressor genes. DNA methyltransferase inhibitors reactivate silenced tumor suppressor genes and result in tumor growth arrest, with therapeutic effects observed in patients with hematologic malignancies. The antitumor effect of these DNA methyltransferase inhibitors has also been explored in solid tumors, especially in TNBC that currently lacks targeted therapies.
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Affiliation(s)
- Jia Yu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jacqueline Zayas
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic School of Medicine & The Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
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28
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An immortalized cell line derived from renal erythropoietin-producing (REP) cells demonstrates their potential to transform into myofibroblasts. Sci Rep 2019; 9:11254. [PMID: 31375751 PMCID: PMC6677766 DOI: 10.1038/s41598-019-47766-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 07/23/2019] [Indexed: 12/22/2022] Open
Abstract
The erythroid growth factor erythropoietin (Epo) is produced by renal interstitial fibroblasts, called REP (renal Epo-producing) cells, in a hypoxia-inducible manner. In chronic kidney disease (CKD), REP cells lose their Epo-production ability, leading to renal anaemia. Concurrently, REP cells are suggested to be transformed into myofibroblasts, which are the major player of renal fibrosis. Although establishment of cultured cell lines derived from REP cells has been a long-term challenge, we here successfully established a REP-cell-derived immortalized and cultivable cell line (Replic cells) by using a genetically modified mouse line. Replic cells exhibited myofibroblastic phenotypes and lost their Epo-production ability, reflecting the situation in renal fibrosis. Additionally, we found that cell-autonomous TGFβ signalling contributes to maintenance of the myofibroblastic features of Replic cells. Furthermore, the promoters of genes for Epo and HIF2α, a major activator of Epo gene expression, were highly methylated in Replic cells. Thus, these results strongly support our contention that REP cells are the origin of myofibroblasts in fibrotic kidneys and demonstrate that cell-autonomous TGFβ signalling and epigenetic silencing are involved in renal fibrosis and renal anaemia, respectively, in CKD. The Replic cell line is a useful tool to further investigate the molecular mechanisms underlying renal fibrosis.
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Zhu Y, Cao Z, Lu C. Microfluidic MeDIP-seq for low-input methylomic analysis of mammary tumorigenesis in mice. Analyst 2019; 144:1904-1915. [PMID: 30631869 DOI: 10.1039/c8an02271b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Studies of dynamic epigenomic changes during tumorigenesis using mice often require profiling epigenomes using a tiny quantity of tissue samples. Conventional epigenomic tests do not support such analysis due to the large amount of materials required by these assays. In this study, we developed an ultrasensitive microfluidics-based methylated DNA immunoprecipitation followed by next-generation sequencing (MeDIP-seq) technology for profiling methylomes using as little as 0.5 ng DNA (or ∼100 cells) with 1.5 h on-chip process for immunoprecipitation. This technology enabled us to examine genome-wide DNA methylation in a C3(1)/SV40 T-antigen transgenic mouse model during different stages of mammary cancer development. Using our data, we identified differentially methylated regions and their associated genes in different periods of cancer development. Our results showed that unique methylomic features were presented in various tumor developmental stages.
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Affiliation(s)
- Yan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
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Contribution of DNMT1 to Neuropathic Pain Genesis Partially through Epigenetically Repressing Kcna2 in Primary Afferent Neurons. J Neurosci 2019; 39:6595-6607. [PMID: 31182635 DOI: 10.1523/jneurosci.0695-19.2019] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 02/08/2023] Open
Abstract
Expressional changes of pain-associated genes in primary sensory neurons of DRG are critical for neuropathic pain genesis. DNA methyltransferase (DNMT)-triggered DNA methylation silences gene expression. We show here that DNMT1, a canonical maintenance methyltransferase, acts as the de novo DNMT and is required for neuropathic pain genesis likely through repressing at least DRG Kcna2 gene expression in male mice. Peripheral nerve injury upregulated DNMT1 expression in the injured DRG through the transcription factor cAMP response element binding protein-triggered transcriptional activation of Dnmt1 gene. Blocking this upregulation prevented nerve injury-induced DNA methylation within the promoter and 5'-untranslated region of Kcna2 gene, rescued Kcna2 expression and total Kv current, attenuated hyperexcitability in the injured DRG neurons, and alleviated nerve injury-induced pain hypersensitivities. Given that Kcna2 is a key player in neuropathic pain, our findings suggest that DRG DNMT1 may be a potential target for neuropathic pain management.SIGNIFICANCE STATEMENT In the present study, we reported that DNMT1, a canonical DNA maintenance methyltransferase, is upregulated via the activation of the transcription factor CREB in the injured DRG after peripheral nerve injury. This upregulation was responsible for nerve injury-induced de novo DNA methylation within the promoter and 5'-untranslated region of the Kcna2 gene, reductions in Kcna2 expression and Kv current and increases in neuronal excitability in the injured DRG. Since pharmacological inhibition or genetic knockdown of DRG DNMT1 alleviated nerve injury-induced pain hypersensitivities, DRG DNMT1 contributes to neuropathic pain genesis partially through repression of DRG Kcna2 gene expression.
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Li SY, Park J, Guan Y, Chung K, Shrestha R, Palmer MB, Susztak K. DNMT1 in Six2 Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development. J Am Soc Nephrol 2019; 30:594-609. [PMID: 30850438 PMCID: PMC6442333 DOI: 10.1681/asn.2018070687] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/03/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cytosine methylation of regulatory regions, such as promoters and enhancers, plays a key role in regulating gene expression, however, its role in kidney development has not been analyzed. METHODS To identify functionally important epigenome-modifying enzymes and genome regions where methylation modifications are functionally important for kidney development, we performed genome-wide methylation analysis, expression profiling, and systematic genetic targeting of DNA methyltransferases (Dnmt1, Dnmt3a, and Dnmt3b) and Ten-eleven translocation methylcytosine hydroxylases (Tet2) in nephron progenitor cells (Six2Cre) in mice. RESULTS Genome-wide methylome analysis indicated dynamic changes on promoters and enhancers during development. Six2CreDnmt3af/f, Six2CreDnmt3bf/f, and Six2CreTet2f/f mice showed no significant structural or functional renal abnormalities. In contrast, Six2CreDnmt1f/f mice died within 24 hours of birth, from a severe kidney developmental defect. Genome-wide methylation analysis indicated a marked loss of methylation of transposable elements. RNA sequencing detected endogenous retroviral transcripts. Expression of intracellular viral sensing pathways (RIG-I), early embryonic, nonrenal lineage genes and increased cell death contributed to the phenotype development. In podocytes, loss of Dnmt1, Dnmt3a, Dnmt3b, or Tet2 did not lead to functional or structural differences at baseline or after toxic injury. CONCLUSIONS Genome-wide cytosine methylation and gene expression profiling showed that by silencing embryonic, nonrenal lineage genes and transposable elements, DNMT1-mediated cytosine methylation is essential for kidney development.
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Affiliation(s)
- Szu-Yuan Li
- Renal-Electrolyte and Hypertension Division, Department of Medicine
- Department of Genetics, and
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; and
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jihwan Park
- Renal-Electrolyte and Hypertension Division, Department of Medicine
- Department of Genetics, and
| | - Yuting Guan
- Renal-Electrolyte and Hypertension Division, Department of Medicine
- Department of Genetics, and
| | - Kiwung Chung
- Renal-Electrolyte and Hypertension Division, Department of Medicine
- Department of Genetics, and
| | - Rojesh Shrestha
- Renal-Electrolyte and Hypertension Division, Department of Medicine
- Department of Genetics, and
| | - Matthew B Palmer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Katalin Susztak
- Renal-Electrolyte and Hypertension Division, Department of Medicine,
- Department of Genetics, and
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32
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Wang L, Zhao J, Li Y, Wang Z, Kang S. Genome-wide analysis of DNA methylation in endometriosis using Illumina Human Methylation 450 K BeadChips. Mol Reprod Dev 2019; 86:491-501. [PMID: 30740831 DOI: 10.1002/mrd.23127] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 12/13/2022]
Abstract
Endometriosis is a common chronic gynecologic disorder characterized by the presence and growth of endometrial-like tissue outside of the uterine cavity. Although the exact etiology remains unclear, epigenetic modifications, such as DNA methylation, are thought to contribute to the pathogenesis of endometriosis. Here, we used the Illumina Human Methylation 450 K BeadChip Array to analyze the genome-wide DNA methylation profiles of six endometriotic lesions and six eutopic endometria from patients with ovarian endometriosis and six endometria of women without endometriosis. Compared with the eutopic endometria of women with endometriosis, 12,159 differentially methylated CpG sites and 375 differentially methylated promoter regions were identified in endometriotic lesions. GO analyses showed that these putative differentially methylated genes were primarily associated with immune response, inflammatory response, response to steroid hormone stimulus, cell adhesion, negative regulation of apoptosis, and activation of the MAPK activity. In addition, the expression levels of DNMT1, DNMT3A, DNMT3B, and MBD2 in endometriotic lesions and eutopic endometria were significantly decreased compared with control endometria. Our findings suggest that aberrant DNA methylation status in endometriotic lesions may play a significant role in the pathogenesis and progression of endometriosis.
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Affiliation(s)
- Lixian Wang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jian Zhao
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yan Li
- Department of Molecular Biology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zihe Wang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shan Kang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
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MBD1 Contributes to the Genesis of Acute Pain and Neuropathic Pain by Epigenetic Silencing of Oprm1 and Kcna2 Genes in Primary Sensory Neurons. J Neurosci 2018; 38:9883-9899. [PMID: 30266739 DOI: 10.1523/jneurosci.0880-18.2018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 02/06/2023] Open
Abstract
The transmission of normal sensory and/or acute noxious information requires intact expression of pain-associated genes within the pain pathways of nervous system. Expressional changes of these genes after peripheral nerve injury are also critical for neuropathic pain induction and maintenance. Methyl-CpG-binding domain protein 1 (MBD1), an epigenetic repressor, regulates gene transcriptional activity. We report here that MBD1 in the primary sensory neurons of DRG is critical for the genesis of acute pain and neuropathic pain as DRG MBD1-deficient mice exhibit the reduced responses to acute mechanical, heat, cold, and capsaicin stimuli and the blunted nerve injury-induced pain hypersensitivities. Furthermore, DRG overexpression of MBD1 leads to spontaneous pain and evoked pain hypersensitivities in the WT mice and restores acute pain sensitivities in the MBD1-deficient mice. Mechanistically, MDB1 represses Oprm1 and Kcna2 gene expression by recruiting DNA methyltransferase DNMT3a into these two gene promoters in the DRG neurons. DRG MBD1 is likely a key player under the conditions of acute pain and neuropathic pain.SIGNIFICANCE STATEMENT In the present study, we revealed that the mice with deficiency of methyl-CpG-binding domain protein 1 (MBD1), an epigenetic repressor, in the DRG displayed the reduced responses to acute noxious stimuli and the blunted neuropathic pain. We also showed that DRG overexpression of MBD1 produced the hypersensitivities to noxious stimuli in the WT mice and rescued acute pain sensitivities in the MBD1-deficient mice. We have also provided the evidence that MDB1 represses Oprm1 and Kcna2 gene expression by recruiting DNA methyltransferase DNMT3a into these two gene promoters in the DRG neurons. DRG MBD1 may participate in the genesis of acute pain and neuropathic pain likely through regulating DNMT3a-controlled Oprm1 and Kcna2 gene expression in the DRG neurons.
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34
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Miao XR, Fan LC, Wu S, Mao Q, Li Z, Lutz B, Xu JT, Lu Z, Tao YX. DNMT3a contributes to the development and maintenance of bone cancer pain by silencing Kv1.2 expression in spinal cord dorsal horn. Mol Pain 2018; 13:1744806917740681. [PMID: 29056068 PMCID: PMC5676500 DOI: 10.1177/1744806917740681] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Metastatic bone tumor-induced changes in gene transcription and translation in pain-related regions of the nervous system may participate in the development and maintenance of bone cancer pain. Epigenetic modifications including DNA methylation regulate gene transcription. Here, we report that intrathecal injection of decitabine, a DNA methyltransferase (DNMT) inhibitor, dose dependently attenuated the development and maintenance of bone cancer pain induced by injecting prostate cancer cells into the tibia. The level of the de novo DNMT3a, but not DNMT3b, time dependently increased in the ipsilateral L4/5 dorsal horn (not L4/5 dorsal root ganglion) after prostate cancer cells injection. Blocking this increase through microinjection of recombinant adeno-associated virus 5 (AAV5) expressing Dnmt3a shRNA into dorsal horn rescued prostate cancer cells-induced downregulation of dorsal horn Kv1.2 expression and impaired prostate cancer cells-induced pain hypersensitivity. In turn, mimicking this increase through microinjection of AAV5 expressing full-length Dnmt3a into dorsal horn reduced dorsal horn Kv1.2 expression and produced pain hypersensitivity in the absence of prostate cancer cells injection. Administration of neither decitabine nor virus affected locomotor function and acute responses to mechanical, thermal, or cold stimuli. Given that Dnmt3a mRNA is co-expressed with Kcna2 mRNA (encoding Kv1.2) in individual dorsal horn neurons, our findings suggest that increased dorsal horn DNMT3a contributes to bone cancer pain through silencing dorsal horn Kv1.2 expression. DNMT3a may represent a potential new target for cancer pain management.
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Affiliation(s)
| | | | | | - Qingxiang Mao
- Xinqiao Hospital, The Third Military Medical University
| | | | | | | | - Zhijie Lu
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University
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35
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Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Res 2018; 28:1364-1371. [PMID: 30093547 PMCID: PMC6120621 DOI: 10.1101/gr.232587.117] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopulations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples. We have optimized a new transposase-based library preparation assay for the Illumina HiSeq X platform suitable for limited amounts of DNA and providing a major cost reduction for WGBS. By incorporating methylated cytosines during fragment end repair, we reveal an end-repair artifact affecting 1%-2% of reads that we can remove analytically. We show that the use of a high (G + C) content spike-in performs better than PhiX in terms of bisulfite sequencing quality. As expected, the loci with transposase-accessible chromatin are DNA hypomethylated and enriched in flanking regions by post-translational modifications of histones usually associated with positive effects on gene expression. Using these transposase-accessible loci to represent the cis-regulatory loci in the genome, we compared the representation of these loci between WGBS and other genome-wide DNA methylation assays, showing WGBS to outperform substantially all of the alternatives. We conclude that it is now technologically and financially feasible to perform WGBS in larger numbers of samples with greater accuracy than previously possible.
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Affiliation(s)
- Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Will Liao
- New York Genome Center, New York, New York 10013, USA
| | - Frank Wos
- New York Genome Center, New York, New York 10013, USA
| | - Andrew D Johnston
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | - Toby Bloom
- New York Genome Center, New York, New York 10013, USA
| | | | - Soren Germer
- New York Genome Center, New York, New York 10013, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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36
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Dong X, Zhang J, Yang F, Wu J, Cai R, Wang T, Zhang J. Effect of luteolin on the methylation status of the OPCML gene and cell growth in breast cancer cells. Exp Ther Med 2018; 16:3186-3194. [PMID: 30214542 DOI: 10.3892/etm.2018.6526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/24/2018] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to investigate the effect of luteolin on the methylation of opioid binding protein/cell adhesion molecule (OPCML) in breast cancer cells, as well as its underlying mechanism of action. Human breast cancer cell lines BT474 and MCF-7 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum. The cells were treated with 0-30 µmol/l luteolin prior to investigation. Reverse transcription-quantitative polymerase chain reaction and western blot analysis were used to determine the mRNA and protein expression, respectively. High performance liquid chromatography and electrosprary ionization-mass spectrometry was used to analyze the methylation of the OPCML promoter region and whole genome. The methylation activity in the cell nucleus was determined using a DNA methyltransferase catalytic test. ELISA analysis was used to detect changes in the activity of transcription factors Sp1 and nuclear factor (NF)-κB. An MTT assay was performed to determine cell proliferation, while flow cytometry was used to detect cell cycle stage and apoptosis. Luteolin effectively upregulated the expression of OPCML in breast cancer cells. Luteolin activated OPCML by reducing intracellular methylation levels. Luteolin downregulated intracellular methylation levels by decreasing Sp1 and NF-κB activities. Luteolin affected the expression of DNMT1 and OPCML by downregulating Sp1 activity. Luteolin inhibited the proliferation and induced the apoptosis of BT474 and MCF-7 cells. The results of the present study suggest that luteolin inhibits the growth of breast cancer cells by decreasing the methylation and upregulating the expression of the OPCML gene.
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Affiliation(s)
- Xinmin Dong
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China.,Department of Oncology, The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 010010, P.R. China
| | - Jian Zhang
- Department of Radiotherapy, The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 010017, P.R. China
| | - Fan Yang
- Department of Basic Medicine, Xiangnan University, Chenzhou, Hunan 423000, P.R. China
| | - Jing Wu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Rui Cai
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Tian Wang
- Department of Hematology and Oncology, Yan'an People's Hospital, Yan'an, Shaanxi 716000, P.R. China
| | - Jiren Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
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37
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Zhang Y, Zhang M, Li L, Wei B, He A, Lu L, Li X, Zhang L, Xu Z, Sun M. Methylation-reprogrammed Wnt/β-catenin signalling mediated prenatal hypoxia-induced brain injury in foetal and offspring rats. J Cell Mol Med 2018; 22:3866-3874. [PMID: 29808608 PMCID: PMC6050486 DOI: 10.1111/jcmm.13660] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Prenatal hypoxia (PH) is a common pregnancy complication, harmful to brain development. This study investigated whether and how PH affected Wnt pathway in the brain. Pregnant rats were exposed to hypoxia (10.5% O2) or normoxia (21% O2; Control). Foetal brain weight and body weight were decreased in the PH group, the ratio of brain weight to body weight was increased significantly. Prenatal hypoxia increased mRNA expression of Wnt3a, Wnt7a, Wnt7b and Fzd4, but not Lrp6. Activated β‐catenin protein and Fosl1 expression were also significantly up‐regulated. Increased Hif1a expression was found in the PH group associated with the higher Wnt signalling. Among 5 members of the Sfrp family, Sfrp4 was down‐regulated. In the methylation‐regulating genes, higher mRNA expressions of Dnmt1 and Dnmt3b were found in the PH group. Sodium bisulphite and sequencing revealed hyper‐methylation in the promoter region of Sfrp4 gene in the foetal brain, accounting for its decreased expression and contributing to the activation of the Wnt‐Catenin signalling. The study of PC12 cells treated with 5‐aza further approved that decreased methylation could result in the higher Sfrp4 expression. In the offspring hippocampus, protein levels of Hif1a and mRNA expression of Sfrp4 were unchanged, whereas Wnt signal pathway was inhibited. The data demonstrated that PH activated the Wnt pathway in the foetal brain, related to the hyper‐methylation of Sfrp4 as well as Hif1a signalling. Activated Wnt signalling might play acute protective roles to the foetal brain in response to hypoxia, also would result in disadvantageous influence on the offspring in long‐term.
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Affiliation(s)
- Yingying Zhang
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Mengshu Zhang
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Lingjun Li
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Bin Wei
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Axin He
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Likui Lu
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Xiang Li
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Lubo Zhang
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China.,Center for Perinatal Biology, Loma Linda University, Loma Linda, CA, USA
| | - Zhice Xu
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China.,Center for Perinatal Biology, Loma Linda University, Loma Linda, CA, USA
| | - Miao Sun
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
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Yu J, Qin B, Moyer AM, Nowsheen S, Liu T, Qin S, Zhuang Y, Liu D, Lu SW, Kalari KR, Visscher DW, Copland JA, McLaughlin SA, Moreno-Aspitia A, Northfelt DW, Gray RJ, Lou Z, Suman VJ, Weinshilboum R, Boughey JC, Goetz MP, Wang L. DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine. J Clin Invest 2018; 128:2376-2388. [PMID: 29708513 DOI: 10.1172/jci97924] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/13/2018] [Indexed: 01/22/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with poor prognosis that lacks targeted therapies, especially in patients with chemotherapy-resistant disease. Since DNA methylation-induced silencing of tumor suppressors is common in cancer, reversal of promoter DNA hypermethylation by 5-aza-2'-deoxycytidine (decitabine), an FDA-approved DNA methyltransferase (DNMT) inhibitor, has proven effective in treating hematological neoplasms. However, its antitumor effect varies in solid tumors, stressing the importance of identifying biomarkers predictive of therapeutic response. Here, we focused on the identification of biomarkers to select decitabine-sensitive TNBC through increasing our understanding of the mechanism of decitabine action. We showed that protein levels of DNMTs correlated with response to decitabine in patient-derived xenograft (PDX) organoids originating from chemotherapy-sensitive and -resistant TNBCs, suggesting DNMT levels as potential biomarkers of response. Furthermore, all 3 methytransferases, DNMT1, DNMT3A, and DNMT3B, were degraded following low-concentration, long-term decitabine treatment both in vitro and in vivo. The DNMT proteins could be ubiquitinated by the E3 ligase, TNF receptor-associated factor 6 (TRAF6), leading to lysosome-dependent protein degradation. Depletion of TRAF6 blocked decitabine-induced DNMT degradation, conferring resistance to decitabine. Our study suggests a potential mechanism of regulating DNMT protein degradation and DNMT levels as response biomarkers for DNMT inhibitors in TNBCs.
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Affiliation(s)
- Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Bo Qin
- Department of Molecular Pharmacology and Experimental Therapeutics.,Department of Oncology, and
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Somaira Nowsheen
- Department of Oncology, and.,Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic School of Medicine and the Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota, USA
| | - Tongzheng Liu
- Department of Oncology, and.,Jinan University Institute of Tumor Pharmacology, Guangzhou, China
| | - Sisi Qin
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Yongxian Zhuang
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Duan Liu
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Shijia W Lu
- Department of Molecular Pharmacology and Experimental Therapeutics.,Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel W Visscher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | | - Richard J Gray
- Department of Surgery, Mayo Clinic, Scottsdale, Arizona, USA
| | | | - Vera J Suman
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics.,Department of Oncology, and
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics
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Wang C, Wang F, Li Z, Cao Q, Huang L, Chen S. MeCP2-mediated epigenetic regulation in senescent endothelial progenitor cells. Stem Cell Res Ther 2018; 9:87. [PMID: 29615114 PMCID: PMC5883541 DOI: 10.1186/s13287-018-0828-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/25/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cellular aging may be associated with epigenetics. Methyl-CpG-binding protein 2 (MeCP2) and sirtuin 1 (SIRT1) are two important epigenetic factors. Our former work demonstrated that MeCP2 expression increased and SIRT1 expression decreased in senescent endothelial progenitor cells (EPCs). This article aims to reveal the epigenetic regulation caused by MeCP2 in EPCs and discuss its mechanism. METHODS Tube formation assay and cell apoptosis detection were used to evaluate the function of senescent EPCs induced by MeCP2 overexpression. Western blot analysis was used to testify the relative protein expression changed by MeCP2. Bisulfite sequencing methylation assay and chromatin immunoprecipitation assay were used to assess the degree of methylation and the relation of MeCP2 and SIRT1. RESULTS MeCP2 reduced angiogenesis of senescent EPCs, promoted apoptosis, and caused senescent EPC dysfunction through SIRT1 promoter hypermethylation and histone modification. CONCLUSIONS MeCP2 mediated senescent EPC dysfunction through epigenetic regulation.
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Affiliation(s)
- Chunli Wang
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Wang
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Li
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Cao
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liya Huang
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuyan Chen
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Ziller MJ, Ortega JA, Quinlan KA, Santos DP, Gu H, Martin EJ, Galonska C, Pop R, Maidl S, Di Pardo A, Huang M, Meltzer HY, Gnirke A, Heckman CJ, Meissner A, Kiskinis E. Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. Cell Stem Cell 2018; 22:559-574.e9. [PMID: 29551301 DOI: 10.1016/j.stem.2018.02.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 12/18/2017] [Accepted: 02/23/2018] [Indexed: 01/10/2023]
Abstract
The somatic DNA methylation (DNAme) landscape is established early in development but remains highly dynamic within focal regions that overlap with gene regulatory elements. The significance of these dynamic changes, particularly in the central nervous system, remains unresolved. Here, we utilize a powerful human embryonic stem cell differentiation model for the generation of motor neurons (MNs) in combination with genetic mutations in the de novo DNAme machinery. We quantitatively dissect the role of DNAme in directing somatic cell fate with high-resolution genome-wide bisulfite-, bulk-, and single-cell-RNA sequencing. We find defects in neuralization and MN differentiation in DNMT3A knockouts (KO) that can be rescued by the targeting of DNAme to key developmental loci using catalytically inactive dCas9. We also find decreased dendritic arborization and altered electrophysiological properties in DNMT3A KO MNs. Our work provides a list of DNMT3A-regulated targets and a mechanistic link between de novo DNAme, cellular differentiation, and human MN function.
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Affiliation(s)
- Michael J Ziller
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Juan A Ortega
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Katharina A Quinlan
- Department of Biomedical and Pharmaceutical Sciences, George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA
| | - David P Santos
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric J Martin
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Christina Galonska
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Ramona Pop
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Susanne Maidl
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Alba Di Pardo
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mei Huang
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Herbert Y Meltzer
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - C J Heckman
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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41
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Wang Z, Olumi AF. Metformin: an antiproliferative agent and methylation regulator in treating prostatic disease? Am J Physiol Renal Physiol 2018; 314:F407-F411. [PMID: 29117997 PMCID: PMC5899225 DOI: 10.1152/ajprenal.00443.2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Existing drugs that have been used in clinical practice for other purposes can prove useful for reutilization, since much of the safety profile and pharmacokinetics have been completed. Therefore, the drugs can enter clinical practice for a variety of causes with less regulatory burden. Metformin may prove to be such a drug; it may have a role in other diseases, besides the management of diabetes. In this perspective, we provide our findings and understanding of metformin as an alternative way to treat urological abnormal proliferation. We propose the potential mechanisms into two hallmarks: direct antiproliferative function via insulin-like growth factor (IGF) signaling pathway and epigenetic modulating via adjusting DNA methylation. These specific hallmarks may ultimately contribute to a better understanding of metformin in treating prostatic diseases.
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Affiliation(s)
- Zongwei Wang
- 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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42
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Zhang C, Wang S, Liu Y, Yang C. Epigenetics in myeloid derived suppressor cells: a sheathed sword towards cancer. Oncotarget 2018; 7:57452-57463. [PMID: 27458169 PMCID: PMC5303001 DOI: 10.18632/oncotarget.10767] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/10/2016] [Indexed: 12/16/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs), a heterogeneous population of cells composed of progenitors and precursors to myeloid cells, are deemed to participate in the development of tumor-favoring immunosuppressive microenvironment. Thus, the regulatory strategies targeting MDSCs' expansion, differentiation, accumulation and function could possibly be effective “weapons” in anti-tumor immunotherapies. Epigenetic mechanisms, which involve DNA modification, covalent histone modification and RNA interference, result in the heritable down-regulation or silencing of gene expression without a change in DNA sequences. Epigenetic modification of MDSC's functional plasticity leads to the remodeling of its characteristics, therefore reframing the microenvironment towards countering tumor growth and metastasis. This review summarized the pertinent findings on the DNA methylation, covalent histone modification, microRNAs and small interfering RNAs targeting MDSC in cancer genesis, progression and metastasis. The potentials as well as possible obstacles in translating into anti-cancer therapeutics were also discussed.
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Affiliation(s)
- Chao Zhang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Shuo Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Yufeng Liu
- General Surgery, Department of Nursing, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
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43
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Ginder GD, Williams DC. Readers of DNA methylation, the MBD family as potential therapeutic targets. Pharmacol Ther 2017; 184:98-111. [PMID: 29128342 DOI: 10.1016/j.pharmthera.2017.11.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA methylation represents a fundamental epigenetic modification that regulates chromatin architecture and gene transcription. Many diseases, including cancer, show aberrant methylation patterns that contribute to the disease phenotype. DNA methylation inhibitors have been used to block methylation dependent gene silencing to treat hematopoietic neoplasms and to restore expression of developmentally silenced genes. However, these inhibitors disrupt methylation globally and show significant off-target toxicities. As an alternative approach, we have been studying readers of DNA methylation, the 5-methylcytosine binding domain family of proteins, as potential therapeutic targets to restore expression of aberrantly and developmentally methylated and silenced genes. In this review, we discuss the role of DNA methylation in gene regulation and cancer development, the structure and function of the 5-methylcytosine binding domain family of proteins, and the possibility of targeting the complexes these proteins form to treat human disease.
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Affiliation(s)
- Gordon D Ginder
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, United States; Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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44
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Wei H, Jiang S, Chen L, He C, Wu S, Peng H. Characterization of Cytosine Methylation and the DNA Methyltransferases of Toxoplasma gondii. Int J Biol Sci 2017; 13:458-470. [PMID: 28529454 PMCID: PMC5436566 DOI: 10.7150/ijbs.18644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/22/2017] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a key epigenetic modification which confers phenotypic plasticity and adaptation. Cyst-forming strains of Toxoplasma gondii undergo tachyzoite to bradyzoite conversion after initial acute infection of a host, and the reverse conversion may occur in immune-suppressed hosts. The formation of m5C is catalyzed by DNA methyltransferase (DNMT). We identified two functional DNA methyltransferases, TgDNMTa and TgDNMTb, in T. gondii that may mediate DNA methylation. The recombinant proteins showed intrinsic methyltransferase activity; both have higher transcription levels in bradyzoites than that in tachyzoites. We performed genome-wide analysis of DNA methylation in tachyzoites and bradyzoites. The results showed more methylation sites in bradyzoites than that in tachyzoites. The most significantly enriched GO-terms of genes with DNA methylation were associated with basal cellular processes such as energy metabolism and parasite resistance to host immunity. Tachyzoite proliferation in parasitophorous vacuoles (PV) can be inhibited by the DNA methyltransferase inhibitor 5-azacytidine, a chemical analogue of the nucleotide cytosine that can inactivate DNA methyltransferases. These findings provide the first confirmation of DNA methylation in T. gondii.
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Affiliation(s)
- Haixia Wei
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Shichen Jiang
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Longfei Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Cheng He
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Shuizhen Wu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Hongjuan Peng
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
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45
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DNA methyltransferase DNMT3a contributes to neuropathic pain by repressing Kcna2 in primary afferent neurons. Nat Commun 2017; 8:14712. [PMID: 28270689 PMCID: PMC5344974 DOI: 10.1038/ncomms14712] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/20/2017] [Indexed: 12/26/2022] Open
Abstract
Nerve injury induces changes in gene transcription in dorsal root ganglion (DRG) neurons, which may contribute to nerve injury-induced neuropathic pain. DNA methylation represses gene expression. Here, we report that peripheral nerve injury increases expression of the DNA methyltransferase DNMT3a in the injured DRG neurons via the activation of the transcription factor octamer transcription factor 1. Blocking this increase prevents nerve injury-induced methylation of the voltage-dependent potassium (Kv) channel subunit Kcna2 promoter region and rescues Kcna2 expression in the injured DRG and attenuates neuropathic pain. Conversely, in the absence of nerve injury, mimicking this increase reduces the Kcna2 promoter activity, diminishes Kcna2 expression, decreases Kv current, increases excitability in DRG neurons and leads to spinal cord central sensitization and neuropathic pain symptoms. These findings suggest that DNMT3a may contribute to neuropathic pain by repressing Kcna2 expression in the DRG.
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46
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Francelle L, Lotz C, Outeiro T, Brouillet E, Merienne K. Contribution of Neuroepigenetics to Huntington's Disease. Front Hum Neurosci 2017; 11:17. [PMID: 28194101 PMCID: PMC5276857 DOI: 10.3389/fnhum.2017.00017] [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: 11/07/2016] [Accepted: 01/10/2017] [Indexed: 12/29/2022] Open
Abstract
Unbalanced epigenetic regulation is thought to contribute to the progression of several neurodegenerative diseases, including Huntington’s disease (HD), a genetic disorder considered as a paradigm of epigenetic dysregulation. In this review, we attempt to address open questions regarding the role of epigenetic changes in HD, in the light of recent advances in neuroepigenetics. We particularly discuss studies using genome-wide scale approaches that provide insights into the relationship between epigenetic regulations, gene expression and neuronal activity in normal and diseased neurons, including HD neurons. We propose that cell-type specific techniques and 3D-based methods will advance knowledge of epigenome in the context of brain region vulnerability in neurodegenerative diseases. A better understanding of the mechanisms underlying epigenetic changes and of their consequences in neurodegenerative diseases is required to design therapeutic strategies more effective than current strategies based on histone deacetylase (HDAC) inhibitors. Researches in HD may play a driving role in this process.
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Affiliation(s)
- Laetitia Francelle
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Caroline Lotz
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
| | - Tiago Outeiro
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Emmanuel Brouillet
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de Recherche Fondamentale, Institut d'Imagerie Biomédicale, Molecular Imaging Center, Neurodegenerative diseases Laboratory, UMR 9199, CNRS Université Paris-Sud, Université Paris-Saclay Fontenay-aux-Roses, France
| | - Karine Merienne
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
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47
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Jeltsch A, Ehrenhofer-Murray A, Jurkowski TP, Lyko F, Reuter G, Ankri S, Nellen W, Schaefer M, Helm M. Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation. RNA Biol 2016; 14:1108-1123. [PMID: 27232191 PMCID: PMC5699548 DOI: 10.1080/15476286.2016.1191737] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A group of homologous nucleic acid modification enzymes called Dnmt2, Trdmt1, Pmt1, DnmA, and Ehmet in different model organisms catalyze the transfer of a methyl group from the cofactor S-adenosyl-methionine (SAM) to the carbon-5 of cytosine residues. Originally considered as DNA MTases, these enzymes were shown to be tRNA methyltransferases about a decade ago. Between the presumed involvement in DNA modification-related epigenetics, and the recent foray into the RNA modification field, significant progress has characterized Dnmt2-related research. Here, we review this progress in its diverse facets including molecular evolution, structural biology, biochemistry, chemical biology, cell biology and epigenetics.
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Affiliation(s)
- Albert Jeltsch
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | | | - Tomasz P Jurkowski
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | - Frank Lyko
- c Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center , Heidelberg , Germany
| | - Gunter Reuter
- d Institute of Biology, Developmental Genetics, Martin Luther University Halle , Halle , Germany
| | - Serge Ankri
- e Department of Molecular Microbiology , The Bruce Rappaport Faculty of Medicine , Technion , Haifa , Israel
| | - Wolfgang Nellen
- f Abteilung für Genetik, Universität Kassel , Kassel , Germany
| | - Matthias Schaefer
- g Medical University of Vienna, Center for Anatomy & Cell Biology , Vienna , Austria
| | - Mark Helm
- h Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Mainz , Germany
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48
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KOUKOURA OURANIA, SIFAKIS STAVROS, SPANDIDOS DEMETRIOSA. DNA methylation in endometriosis (Review). Mol Med Rep 2016; 13:2939-48. [PMID: 26934855 PMCID: PMC4805102 DOI: 10.3892/mmr.2016.4925] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 12/01/2022] Open
Abstract
Endometriosis is defined by the presence and growth of functional endometrial tissue, outside the uterine cavity, primarily in the ovaries, pelvic peritoneum and rectovaginal septum. Although it is a benign disease, it presents with malignant characteristics, such as invasion to surrounding tissues, metastasis to distant locations and recurrence following treatment. Accumulating evidence suggests that various epigenetic aberrations may play an essential role in the pathogenesis of endometriosis. Aberrant DNA methylation represents a possible mechanism repsonsible for this disease, linking gene expression alterations observed in endometriosis with hormonal and environmental factors. Several lines of evidence indicate that endometriosis may partially be due to selective epigenetic deregulations influenced by extrinsic factors. Previous studies have shed light into the epigenetic component of endometriosis, reporting variations in the epigenetic patterns of genes known to be involved in the aberrant hormonal, immunologic and inflammatory status of endometriosis. Although recent studies, utilizing advanced molecular techniques, have allowed us to further elucidate the possible association of DNA methylation with altered gene expression, whether these molecular changes represent the cause or merely the consequence of the disease is a question which remains to be answered. This review provides an overview of the current literature on the role of DNA methylation in the pathophysiology and malignant evolution of endometriosis. We also provide insight into the mechanisms through which DNA methylation-modifying agents may be the next step in the research of the pharmaceutical treatment of endometriosis.
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Affiliation(s)
- OURANIA KOUKOURA
- Department of Obstetrics and Gynecology, University Hospital of Larissa, Larissa 41500, Greece
| | - STAVROS SIFAKIS
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, Heraklion 71003, Greece
| | - DEMETRIOS A. SPANDIDOS
- Laboratory of Clinical Virology, University of Crete Medical School, Heraklion 71409, Greece
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Lukashevich OV, Cherepanova NA, Jurkovska RZ, Jeltsch A, Gromova ES. Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity. BMC BIOCHEMISTRY 2016; 17:7. [PMID: 27001594 PMCID: PMC4802922 DOI: 10.1186/s12858-016-0064-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/02/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood. RESULTS Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified. Their methylation activity, DNA binding affinity, ability to flip the target cytosine out of the DNA double helix and covalent complex formation with DNA have been examined. Substitutions of N167 lead to reduced catalytic activity and reduced base flipping. Catalytic activity, base flipping, and covalent conjugate formation were almost completely abolished for the mutant enzymes with substitutions of R200 or R202. CONCLUSIONS We conclude that R202 plays a similar role in catalysis in Dnmt3a-CD as R232 in M.SssI and R165 in M.HhaI, which could be positioning of the cytosine for nucleophilic attack by a conserved Cys. R200 of Dnmt3a-CD is important in both catalysis and cytosine flipping. Both conserved R200 and R202 are involved in creating and stabilizing of the transient covalent intermediate of the methylation reaction. N167 might contribute to the positioning of the residues from the motif VI, but does not play a direct role in catalysis.
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Affiliation(s)
- Olga V Lukashevich
- Department of Chemistry, Moscow State University, 119991, Moscow, Russia
| | | | - Renata Z Jurkovska
- BioMedX Innovation Center, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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50
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Abstract
The purpose of this review is to provide an overview of the complexity of the epigenetic target space. Chemical modifications of histones and nucleic acids constitute a key epigenetic mechanism. Whereas modifications such as methylation and acetylation are well-known, there are many additional, less explored modifications described here. The writers, readers and erasers of such diverse modifications, which constitute a major portion of the potential epigenetic target space, are discussed, in addition to the various other protein families that do not fall under these three categories. Finally, disease relevance and druggability of epigenetic targets are discussed with concluding remarks about the richness and diversity they will provide for future targeted therapies.
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Affiliation(s)
- Vineet Pande
- Discovery Sciences, Janssen-Pharmaceutical Companies of Johnson & Johnson , Turnhoutseweg 30, Beerse 2340, Belgium
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