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Mesci P, LaRock CN, Jeziorski JJ, Nakashima H, Chermont N, Ferrasa A, Herai RH, Ozaki T, Saleh A, Snethlage CE, Sanchez S, Goldberg G, Trujillo CA, Nakashima K, Nizet V, Muotri AR. Human microglial cells as a therapeutic target in a neurodevelopmental disease model. Stem Cell Reports 2024; 19:1074-1091. [PMID: 39059378 PMCID: PMC11368698 DOI: 10.1016/j.stemcr.2024.06.013] [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: 07/04/2023] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Although microglia are macrophages of the central nervous system, their involvement is not limited to immune functions. The roles of microglia during development in humans remain poorly understood due to limited access to fetal tissue. To understand how microglia can impact human neurodevelopment, the methyl-CpG binding protein 2 (MECP2) gene was knocked out in human microglia-like cells (MGLs). Disruption of the MECP2 in MGLs led to transcriptional and functional perturbations, including impaired phagocytosis. The co-culture of healthy MGLs with MECP2-knockout (KO) neurons rescued synaptogenesis defects, suggesting a microglial role in synapse formation. A targeted drug screening identified ADH-503, a CD11b agonist, restored phagocytosis and synapse formation in spheroid-MGL co-cultures, significantly improved disease progression, and increased survival in MeCP2-null mice. These results unveil a MECP2-specific regulation of human microglial phagocytosis and identify a novel therapeutic treatment for MECP2-related conditions.
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Affiliation(s)
- Pinar Mesci
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA.
| | - Christopher N LaRock
- Department of Pediatrics, University of California San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92037, USA; Department of Microbiology and Immunology, Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Jacob J Jeziorski
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Hideyuki Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Natalia Chermont
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Adriano Ferrasa
- Experimental Multiuser Laboratory (LEM), Graduate Program in Health Sciences (PPGCS), School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná 80215-901, Brazil; Department of Informatics (DEINFO), Universidade Estadual de Ponta Grossa (UEPG), Ponta Grossa, Paraná 84030-900, Brazil
| | - Roberto H Herai
- Experimental Multiuser Laboratory (LEM), Graduate Program in Health Sciences (PPGCS), School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná 80215-901, Brazil; Research Department, Lico Kaesemodel Institute (ILK), Curitiba, Paraná, Brazil
| | - Tomoka Ozaki
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Aurian Saleh
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Cedric E Snethlage
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Sandra Sanchez
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Gabriela Goldberg
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Cleber A Trujillo
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Victor Nizet
- Department of Pediatrics, University of California San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92037, USA
| | - Alysson R Muotri
- University of California, San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, La Jolla, CA 92037, USA; University of California, San Diego, Kavli Institute for Brain and Mind, Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA 92093, USA.
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2
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Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Kalani L, Jorge-Torres OC, Esteller M, Ausio J, Abian O, Velazquez-Campoy A. Extending MeCP2 interactome: canonical nucleosomal histones interact with MeCP2. Nucleic Acids Res 2024; 52:3636-3653. [PMID: 38321951 DOI: 10.1093/nar/gkae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/08/2024] Open
Abstract
MeCP2 is a general regulator of transcription involved in the repression/activation of genes depending on the local epigenetic context. It acts as a chromatin regulator and binds with exquisite specificity to gene promoters. The set of epigenetic marks recognized by MeCP2 has been already established (mainly, cytosine modifications in CpG and CpA), as well as many of the constituents of its interactome. We unveil a new set of interactions for MeCP2 with the four canonical nucleosomal histones. MeCP2 interacts with high affinity with H2A, H2B, H3 and H4. In addition, Rett syndrome associated mutations in MeCP2 and histone epigenetic marks modulate these interactions. Given the abundance and the structural/functional relevance of histones and their involvement in epigenetic regulation, this new set of interactions and its modulating elements provide a new addition to the 'alphabet' for this epigenetic reader.
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Affiliation(s)
- David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | | | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Olga C Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907 l'Hospitalet de Llobregat, Barcelona, Spain
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
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3
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Ralvenius WT, Mungenast AE, Woolf H, Huston MM, Gillingham TZ, Godin SK, Penney J, Cam HP, Gao F, Fernandez CG, Czako B, Lightfoot Y, Ray WJ, Beckmann A, Goate AM, Marcora E, Romero-Molina C, Ayata P, Schaefer A, Gjoneska E, Tsai LH. A novel molecular class that recruits HDAC/MECP2 complexes to PU.1 motifs reduces neuroinflammation. J Exp Med 2023; 220:e20222105. [PMID: 37642942 PMCID: PMC10465325 DOI: 10.1084/jem.20222105] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/26/2023] [Accepted: 07/27/2023] [Indexed: 08/31/2023] Open
Abstract
Pervasive neuroinflammation occurs in many neurodegenerative diseases, including Alzheimer's disease (AD). SPI1/PU.1 is a transcription factor located at a genome-wide significant AD-risk locus and its reduced expression is associated with delayed onset of AD. We analyzed single-cell transcriptomic datasets from microglia of human AD patients and found an enrichment of PU.1-binding motifs in the differentially expressed genes. In hippocampal tissues from transgenic mice with neurodegeneration, we found vastly increased genomic PU.1 binding. We then screened for PU.1 inhibitors using a PU.1 reporter cell line and discovered A11, a molecule with anti-inflammatory efficacy and nanomolar potency. A11 regulated genes putatively by recruiting a repressive complex containing MECP2, HDAC1, SIN3A, and DNMT3A to PU.1 motifs, thus representing a novel mechanism and class of molecules. In mouse models of AD, A11 ameliorated neuroinflammation, loss of neuronal integrity, AD pathology, and improved cognitive performance. This study uncovers a novel class of anti-inflammatory molecules with therapeutic potential for neurodegenerative disorders.
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Affiliation(s)
- William T. Ralvenius
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison E. Mungenast
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah Woolf
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret M. Huston
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Z. Gillingham
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephen K. Godin
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jay Penney
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hugh P. Cam
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fan Gao
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Celia G. Fernandez
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Czako
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yaima Lightfoot
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William J. Ray
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adrian Beckmann
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alison M. Goate
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Romero-Molina
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pinar Ayata
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Advanced Science Research Center at the Graduate Center, Neuroscience Initiative, City University of New York, New York, NY, USA
| | - Anne Schaefer
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Elizabeta Gjoneska
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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4
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Vong P, Ouled-Haddou H, Garçon L. Histone Deacetylases Function in the Control of Early Hematopoiesis and Erythropoiesis. Int J Mol Sci 2022; 23:9790. [PMID: 36077192 PMCID: PMC9456231 DOI: 10.3390/ijms23179790] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Numerous studies have highlighted the role of post-translational modifications in the regulation of cell proliferation, differentiation and death. Among these modifications, acetylation modifies the physicochemical properties of proteins and modulates their activity, stability, localization and affinity for partner proteins. Through the deacetylation of a wide variety of functional and structural, nuclear and cytoplasmic proteins, histone deacetylases (HDACs) modulate important cellular processes, including hematopoiesis, during which different HDACs, by controlling gene expression or by regulating non-histone protein functions, act sequentially to provide a fine regulation of the differentiation process both in early hematopoietic stem cells and in more mature progenitors. Considering that HDAC inhibitors represent promising targets in cancer treatment, it is necessary to decipher the role of HDACs during hematopoiesis which could be impacted by these therapies. This review will highlight the main mechanisms by which HDACs control the hematopoietic stem cell fate, particularly in the erythroid lineage.
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Affiliation(s)
- Pascal Vong
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
| | | | - Loïc Garçon
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
- Service d’Hématologie Biologique, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
- Laboratoire de Génétique Constitutionnelle, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
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5
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Chang KJ, Wu HY, Yarmishyn AA, Li CY, Hsiao YJ, Chi YC, Lo TC, Dai HJ, Yang YC, Liu DH, Hwang DK, Chen SJ, Hsu CC, Kao CL. Genetics behind Cerebral Disease with Ocular Comorbidity: Finding Parallels between the Brain and Eye Molecular Pathology. Int J Mol Sci 2022; 23:9707. [PMID: 36077104 PMCID: PMC9456058 DOI: 10.3390/ijms23179707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Cerebral visual impairments (CVIs) is an umbrella term that categorizes miscellaneous visual defects with parallel genetic brain disorders. While the manifestations of CVIs are diverse and ambiguous, molecular diagnostics stand out as a powerful approach for understanding pathomechanisms in CVIs. Nevertheless, the characterization of CVI disease cohorts has been fragmented and lacks integration. By revisiting the genome-wide and phenome-wide association studies (GWAS and PheWAS), we clustered a handful of renowned CVIs into five ontology groups, namely ciliopathies (Joubert syndrome, Bardet-Biedl syndrome, Alstrom syndrome), demyelination diseases (multiple sclerosis, Alexander disease, Pelizaeus-Merzbacher disease), transcriptional deregulation diseases (Mowat-Wilson disease, Pitt-Hopkins disease, Rett syndrome, Cockayne syndrome, X-linked alpha-thalassaemia mental retardation), compromised peroxisome disorders (Zellweger spectrum disorder, Refsum disease), and channelopathies (neuromyelitis optica spectrum disorder), and reviewed several mutation hotspots currently found to be associated with the CVIs. Moreover, we discussed the common manifestations in the brain and the eye, and collated animal study findings to discuss plausible gene editing strategies for future CVI correction.
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Affiliation(s)
- Kao-Jung Chang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Hsin-Yu Wu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | | | - Cheng-Yi Li
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yu-Jer Hsiao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chun Chi
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Tzu-Chen Lo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - He-Jhen Dai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chiang Yang
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ding-Hao Liu
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - De-Kuang Hwang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chih-Chien Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chung-Lan Kao
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Department of Physical Medicine and Rehabilitation, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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6
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Mou Y, Wu G, Wang Q, Pan T, Zhang L, Xu Y, Xiong W, Zhou Q, Wang Y. Macrophage‐targeted delivery of
siRNA
to silence
Mecp2
gene expression attenuates pulmonary fibrosis. Bioeng Transl Med 2022; 7:e10280. [PMID: 35600643 PMCID: PMC9115697 DOI: 10.1002/btm2.10280] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease characterized by the infiltration of macrophages in the fibrotic region. Currently, no therapeutic strategies effectively control disease progression, and the 5‐year mortality of patients after diagnosis is unacceptably high. Thus, developing an effective and safe treatment for IPF is urgently needed. The present study illustrated that methyl‐CpG‐binding protein 2 (MECP2), a protein responsible for the interpretation of DNA methylome‐encoded information, was abnormally expressed in lung and bronchoalveolar lavage fluid samples of IPF patients and mice with onset of pulmonary fibrosis. And further studies verified that the overexpression of MECP2 occurred mainly in macrophages. Inhibition of Mecp2 expression in macrophages robustly abrogated alternatively activated macrophage (M2) polarization by regulating interferon regulatory factor 4 expression. Accordingly, cationic liposomes loading Mecp2 small interfering RNA (siRNA) were raised for the treatment of pulmonary fibrosis. It was noted that the liposomes accumulated in the fibrotic region after intratracheal injection, especially in macrophages. In addition, intratracheal administration of Mecp2 siRNA‐loaded liposomes significantly reversed the established pulmonary fibrosis with few side‐effects and high safety coefficients. Collectively, these results are essential not only for further understanding the DNA methylation in pathogenesis of IPF but also for providing a potent therapeutic strategy for IPF treatment in the clinic practice.
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Affiliation(s)
- Yong Mou
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Key Site of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Guo‐Rao Wu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Key Site of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qi Wang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Key Site of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ting Pan
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Key Site of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Lei Zhang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Key Site of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yongjian Xu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Key Site of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Weining Xiong
- Department of Respiratory and Critical Care Medicine, Shanghai Key Laboratory of Tissue Engineering, Shanghai Ninth People's Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qing Zhou
- The Center for Biomedical Research, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yi Wang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Key Site of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
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7
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Castro-Piedras I, Vartak D, Sharma M, Pandey S, Casas L, Molehin D, Rasha F, Fokar M, Nichols J, Almodovar S, Rahman RL, Pruitt K. Identification of Novel MeCP2 Cancer-Associated Target Genes and Post-Translational Modifications. Front Oncol 2020; 10:576362. [PMID: 33363010 PMCID: PMC7758440 DOI: 10.3389/fonc.2020.576362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
Abnormal regulation of DNA methylation and its readers has been associated with a wide range of cellular dysfunction. Disruption of the normal function of DNA methylation readers contributes to cancer progression, neurodevelopmental disorders, autoimmune disease and other pathologies. One reader of DNA methylation known to be especially important is MeCP2. It acts a bridge and connects DNA methylation with histone modifications and regulates many gene targets contributing to various diseases; however, much remains unknown about how it contributes to cancer malignancy. We and others previously described novel MeCP2 post-translational regulation. We set out to test the hypothesis that MeCP2 would regulate novel genes linked with tumorigenesis and that MeCP2 is subject to additional post-translational regulation not previously identified. Herein we report novel genes bound and regulated by MeCP2 through MeCP2 ChIP-seq and RNA-seq analyses in two breast cancer cell lines representing different breast cancer subtypes. Through genomics analyses, we localize MeCP2 to novel gene targets and further define the full range of gene targets within breast cancer cell lines. We also further examine the scope of clinical and pre-clinical lysine deacetylase inhibitors (KDACi) that regulate MeCP2 post-translationally. Through proteomics analyses, we identify many additional novel acetylation sites, nine of which are mutated in Rett Syndrome. Our study provides important new insight into downstream targets of MeCP2 and provide the first comprehensive map of novel sites of acetylation associated with both pre-clinical and FDA-approved KDACi used in the clinic. This report examines a critical reader of DNA methylation and has important implications for understanding MeCP2 regulation in cancer models and identifying novel molecular targets associated with epigenetic therapies.
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Affiliation(s)
- Isabel Castro-Piedras
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - David Vartak
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Monica Sharma
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Somnath Pandey
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Laura Casas
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Deborah Molehin
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Fahmida Rasha
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Mohamed Fokar
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, United States
| | - Jacob Nichols
- Department of Internal Medicine, Texas Tech University, Lubbock, TX, United States
| | - Sharilyn Almodovar
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | | | - Kevin Pruitt
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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8
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Regulating the Regulators: The Role of Histone Deacetylase 1 (HDAC1) in Erythropoiesis. Int J Mol Sci 2020; 21:ijms21228460. [PMID: 33187090 PMCID: PMC7696854 DOI: 10.3390/ijms21228460] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in transcriptional regulation in eukaryotic cells. Class I deacetylase HDAC1/2 often associates with repressor complexes, such as Sin3 (Switch Independent 3), NuRD (Nucleosome remodeling and deacetylase) and CoREST (Corepressor of RE1 silencing transcription factor) complexes. It has been shown that HDAC1 interacts with and modulates all essential transcription factors for erythropoiesis. During erythropoiesis, histone deacetylase activity is dramatically reduced. Consistently, inhibition of HDAC activity promotes erythroid differentiation. The reduction of HDAC activity not only results in the activation of transcription activators such as GATA-1 (GATA-binding factor 1), TAL1 (TAL BHLH Transcription Factor 1) and KLF1 (Krüpple-like factor 1), but also represses transcription repressors such as PU.1 (Putative oncogene Spi-1). The reduction of histone deacetylase activity is mainly through HDAC1 acetylation that attenuates HDAC1 activity and trans-repress HDAC2 activity through dimerization with HDAC1. Therefore, the acetylation of HDAC1 can convert the corepressor complex to an activator complex for gene activation. HDAC1 also can deacetylate non-histone proteins that play a role on erythropoiesis, therefore adds another layer of gene regulation through HDAC1. Clinically, it has been shown HDACi can reactivate fetal globin in adult erythroid cells. This review will cover the up to date research on the role of HDAC1 in modulating key transcription factors for erythropoiesis and its clinical relevance.
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9
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MeCP2 and Chromatin Compartmentalization. Cells 2020; 9:cells9040878. [PMID: 32260176 PMCID: PMC7226738 DOI: 10.3390/cells9040878] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/24/2022] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked to Rett syndrome in humans. Here, we focus on its isoforms and functional domains, interactions, modifications and mutations found in Rett patients. Finally, we address how these properties regulate and mediate the ability of MeCP2 to orchestrate chromatin compartmentalization and higher order genome architecture.
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10
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Tillotson R, Bird A. The Molecular Basis of MeCP2 Function in the Brain. J Mol Biol 2020; 432:1602-1623. [PMID: 31629770 DOI: 10.1016/j.jmb.2019.10.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/14/2022]
Abstract
MeCP2 is a reader of the DNA methylome that occupies a large proportion of the genome due to its high abundance and the frequency of its target sites. It has been the subject of extensive study because of its link with 'MECP2-related disorders', of which Rett syndrome is the most prevalent. This review integrates evidence from patient mutation data with results of experimental studies using mouse models, cell lines and in vitro systems to critically evaluate our understanding of MeCP2 protein function. Recent evidence challenges the idea that MeCP2 is a multifunctional hub that integrates diverse processes to underpin neuronal function, suggesting instead that its primary role is to recruit the NCoR1/2 co-repressor complex to methylated sites in the genome, leading to dampening of gene expression.
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Affiliation(s)
- Rebekah Tillotson
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| | - Adrian Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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11
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Wang P, Wang Z, Liu J. Role of HDACs in normal and malignant hematopoiesis. Mol Cancer 2020; 19:5. [PMID: 31910827 PMCID: PMC6945581 DOI: 10.1186/s12943-019-1127-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/26/2019] [Indexed: 01/09/2023] Open
Abstract
Normal hematopoiesis requires the accurate orchestration of lineage-specific patterns of gene expression at each stage of development, and epigenetic regulators play a vital role. Disordered epigenetic regulation has emerged as a key mechanism contributing to hematological malignancies. Histone deacetylases (HDACs) are a series of key transcriptional cofactors that regulate gene expression by deacetylation of lysine residues on histone and nonhistone proteins. In normal hematopoiesis, HDACs are widely involved in the development of various lineages. Their functions involve stemness maintenance, lineage commitment determination, cell differentiation and proliferation, etc. Deregulation of HDACs by abnormal expression or activity and oncogenic HDAC-containing transcriptional complexes are involved in hematological malignancies. Currently, HDAC family members are attractive targets for drug design, and a variety of HDAC-based combination strategies have been developed for the treatment of hematological malignancies. Drug resistance and limited therapeutic efficacy are key issues that hinder the clinical applications of HDAC inhibitors (HDACis). In this review, we summarize the current knowledge of how HDACs and HDAC-containing complexes function in normal hematopoiesis and highlight the etiology of HDACs in hematological malignancies. Moreover, the implication and drug resistance of HDACis are also discussed. This review presents an overview of the physiology and pathology of HDACs in the blood system.
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Affiliation(s)
- Pan Wang
- The Xiangya Hospital, Central South University, Changsha, 410005, Hunan, China.,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- The Xiangya Hospital, Central South University, Changsha, 410005, Hunan, China. .,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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12
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Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits. G3-GENES GENOMES GENETICS 2019; 9:2521-2533. [PMID: 31186305 PMCID: PMC6686932 DOI: 10.1534/g3.119.400294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Identifying the regulatory mechanisms of genome-wide association study (GWAS) loci affecting adipose tissue has been restricted due to limited characterization of adipose transcriptional regulatory elements. We profiled chromatin accessibility in three frozen human subcutaneous adipose tissue needle biopsies and preadipocytes and adipocytes from the Simpson Golabi-Behmel Syndrome (SGBS) cell strain using an assay for transposase-accessible chromatin (ATAC-seq). We identified 68,571 representative accessible chromatin regions (peaks) across adipose tissue samples (FDR < 5%). GWAS loci for eight cardiometabolic traits were enriched in these peaks (P < 0.005), with the strongest enrichment for waist-hip ratio. Of 110 recently described cardiometabolic GWAS loci colocalized with adipose tissue eQTLs, 59 loci had one or more variants overlapping an adipose tissue peak. Annotated variants at the SNX10 waist-hip ratio locus and the ATP2A1-SH2B1 body mass index locus showed allelic differences in regulatory assays. These adipose tissue accessible chromatin regions elucidate genetic variants that may alter adipose tissue function to impact cardiometabolic traits.
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13
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Dahl R. Old dog PU.1 reveals new tricks. Nat Immunol 2019; 20:520-522. [PMID: 30962594 DOI: 10.1038/s41590-019-0380-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Richard Dahl
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA.
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14
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Fischer J, Walter C, Tönges A, Aleth H, Jordão MJC, Leddin M, Gröning V, Erdmann T, Lenz G, Roth J, Vogl T, Prinz M, Dugas M, Jacobsen ID, Rosenbauer F. Safeguard function of PU.1 shapes the inflammatory epigenome of neutrophils. Nat Immunol 2019; 20:546-558. [DOI: 10.1038/s41590-019-0343-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 02/08/2019] [Indexed: 12/16/2022]
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15
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Sun L, Telles E, Karl M, Cheng F, Luetteke N, Sotomayor EM, Miller RH, Seto E. Loss of HDAC11 ameliorates clinical symptoms in a multiple sclerosis mouse model. Life Sci Alliance 2018; 1:e201800039. [PMID: 30456376 PMCID: PMC6238389 DOI: 10.26508/lsa.201800039] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 01/12/2023] Open
Abstract
In an animal model for multiple sclerosis, the absence of HDAC11 reduces clinical severity, spinal cord demyelination, and immune cell infiltration, suggesting that HDAC11 is a promising target for MS treatment. Multiple sclerosis (MS) is a chronic, immune-mediated, demyelinating disease of the central nervous system (CNS). There is no known cure for MS, and currently available drugs for managing this disease are only effective early on and have many adverse side effects. Results from recent studies suggest that histone deacetylase (HDAC) inhibitors may be useful for the treatment of autoimmune and inflammatory diseases such as MS. However, the underlying mechanisms by which HDACs influence immune-mediated diseases such as MS are unclear. More importantly, the question of which specific HDAC(s) are suitable drug targets for the potential treatment of MS remains unanswered. Here, we investigate the functional role of HDAC11 in experimental autoimmune encephalomyelitis, a mouse model for MS. Our results indicate that the loss of HDAC11 in KO mice significantly reduces clinical severity and demyelination of the spinal cord in the post-acute phase of experimental autoimmune encephalomyelitis. The absence of HDAC11 leads to reduced immune cell infiltration into the CNS and decreased monocytes and myeloid DCs in the chronic progressive phase of the disease. Mechanistically, HDAC11 controls the expression of the pro-inflammatory chemokine C–C motif ligand 2 (CCL2) gene by enabling the binding of PU.1 transcription factor to the CCL2 promoter. Our results reveal a novel pathophysiological function for HDAC11 in CNS demyelinating diseases, and warrant further investigations into the potential use of HDAC11-specific inhibitors for the treatment of chronic progressive MS.
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Affiliation(s)
- Lei Sun
- George Washington University Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Elphine Telles
- George Washington University Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Molly Karl
- Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Fengdong Cheng
- George Washington University Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Noreen Luetteke
- George Washington University Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Eduardo M Sotomayor
- George Washington University Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Robert H Miller
- Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Edward Seto
- George Washington University Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
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16
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PM20D1 is a quantitative trait locus associated with Alzheimer's disease. Nat Med 2018; 24:598-603. [PMID: 29736028 DOI: 10.1038/s41591-018-0013-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 02/12/2018] [Indexed: 11/09/2022]
Abstract
The chances to develop Alzheimer's disease (AD) result from a combination of genetic and non-genetic risk factors 1 , the latter likely being mediated by epigenetic mechanisms 2 . In the past, genome-wide association studies (GWAS) have identified an important number of risk loci associated with AD pathology 3 , but a causal relationship remains difficult to establish. In contrast, locus-specific or epigenome-wide association studies (EWAS) have revealed site-specific epigenetic alterations, which provide mechanistic insights for a particular risk gene but often lack the statistical power of GWAS 4 . Here, combining both approaches, we report a previously unidentified association of the peptidase M20-domain-containing protein 1 (PM20D1) with AD. We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. Furthermore, PM20D1 is increased following AD-related neurotoxic insults at symptomatic stages in the APP/PS1 mouse model of AD and in human patients with AD who are carriers of the non-risk haplotype. In line, genetically increasing or decreasing the expression of PM20D1 reduces and aggravates AD-related pathologies, respectively. These findings suggest that in a particular genetic background, PM20D1 contributes to neuroprotection against AD.
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17
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Pandey S, Pruitt K. Functional assessment of MeCP2 in Rett syndrome and cancers of breast, colon, and prostate. Biochem Cell Biol 2017; 95:368-378. [DOI: 10.1139/bcb-2016-0154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Ever since the first report that mutations in methyl-CpG-binding protein 2 (MeCP2) causes Rett syndrome (RTT), a severe neurological disorder in females world-wide, there has been a keen interest to gain a comprehensive understanding of this protein. While the classical model associated with MeCP2 function suggests its role in gene suppression via recruitment of co-repressor complexes and histone deacetylases to methylated CpG-sites, recent discoveries have brought to light its role in transcription activation, modulation of RNA splicing, and chromatin compaction. Various post-translational modifications (PTMs) of MeCP2 further increase its functional versatility. Involvement of MeCP2 in pathologies other than RTT, such as tumorigenesis however, remains poorly explored and understood. This review provides a survey of the literature implicating MeCP2 in breast, colon and prostate cancer.
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Affiliation(s)
- Somnath Pandey
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
| | - Kevin Pruitt
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
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18
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Seuter S, Neme A, Carlberg C. Epigenomic PU.1-VDR crosstalk modulates vitamin D signaling. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:405-415. [PMID: 28232093 DOI: 10.1016/j.bbagrm.2017.02.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/07/2017] [Accepted: 02/12/2017] [Indexed: 01/15/2023]
Abstract
The ETS-domain transcription factor PU.1 acts as a pioneer factor for other transcription factors including nuclear receptors. In this study, we report that in THP-1 human monocytes the PU.1 cistrome comprises 122,319 genomic sites. Interestingly, at 6498 (5.3%) of these loci PU.1 binding was significantly modulated by the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). In most cases 1,25(OH)2D3 increased PU.1 association, which correlated strongly with VDR co-location and overlap ratios for canonical DR3-type VDR binding sites. Genome-wide 6488 sites associating both with PU.1 and VDR as well as 5649 non-VDR overlapping, 1,25(OH)2D3-sensitive PU.1 loci represent the PU.1-VDR crosstalk and can be described by four gene regulatory scenarios, each. Chromatin accessibility was the major discriminator between these models. The location of the PU.1 binding loci in open chromatin coincided with a significantly smaller mean distance to the closest 1,25(OH)2D3 target gene. PU.1 knockdown indicated that the pioneer factor is relevant for the transcriptional activation of 1,25(OH)2D3 target genes but its impact differed in magnitude and orientation. In conclusion, PU.1 is an important modulator of VDR signaling in monocytes, including but also exceeding its role as a pioneer factor, but we found no evidence for a direct interaction of both proteins.
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Affiliation(s)
- Sabine Seuter
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Antonio Neme
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
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19
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Sanchez-Mut JV, Gräff J. Epigenetic Alterations in Alzheimer's Disease. Front Behav Neurosci 2015; 9:347. [PMID: 26734709 PMCID: PMC4681781 DOI: 10.3389/fnbeh.2015.00347] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/25/2015] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is the major cause of dementia in Western societies. It progresses asymptomatically during decades before being belatedly diagnosed when therapeutic strategies have become unviable. Although several genetic alterations have been associated with AD, the vast majority of AD cases do not show strong genetic underpinnings and are thus considered a consequence of non-genetic factors. Epigenetic mechanisms allow for the integration of long-lasting non-genetic inputs on specific genetic backgrounds, and recently, a growing number of epigenetic alterations in AD have been described. For instance, an accumulation of dysregulated epigenetic mechanisms in aging, the predominant risk factor of AD, might facilitate the onset of the disease. Likewise, mutations in several enzymes of the epigenetic machinery have been associated with neurodegenerative processes that are altered in AD such as impaired learning and memory formation. Genome-wide and locus-specific epigenetic alterations have also been reported, and several epigenetically dysregulated genes validated by independent groups. From these studies, a picture emerges of AD as being associated with DNA hypermethylation and histone deacetylation, suggesting a general repressed chromatin state and epigenetically reduced plasticity in AD. Here we review these recent findings and discuss several technical and methodological considerations that are imperative for their correct interpretation. We also pay particular focus on potential implementations and theoretical frameworks that we expect will help to better direct future studies aimed to unravel the epigenetic participation in AD.
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Affiliation(s)
- Jose V Sanchez-Mut
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Johannes Gräff
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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20
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PU.1 Suppresses Th2 Cytokine Expression via Silencing of GATA3 Transcription in Dendritic Cells. PLoS One 2015; 10:e0137699. [PMID: 26361334 PMCID: PMC4567381 DOI: 10.1371/journal.pone.0137699] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 08/19/2015] [Indexed: 01/04/2023] Open
Abstract
The transcription factor PU.1 is predominantly expressed in dendritic cells (DCs) and is essential for DC differentiation. Although there are several reports that PU.1 positively regulates the expression of DC-specific genes, whether PU.1 also has a suppressive effect on DCs is largely unknown. Here we demonstrate that PU.1 suppresses the expression of Th2 cytokines including IL-13 and IL-5 in bone marrow-derived DCs (BMDCs), through repression of the expression of GATA3, which is a master regulator of Th2 differentiations. When PU.1 siRNA was introduced into BMDCs, LPS-induced expression of IL-13 and IL-5 was increased along with upregulation of the constitutive expression of GATA2 and GATA3. The additional introduction of GATA3 siRNA but not of GATA2 siRNA abrogated PU.1 siRNA-mediated upregulation of IL-13 and IL-5. A chromatin immunoprecipitation assay showed that PU.1 bound to Gata3 proximal promoter region, which is more dominant than the distal promoter in driving GATA3 transcription in DCs. The degree of histone acetylation at the Gata3 promoter was decreased in PU.1 siRNA-introduced DCs, suggesting the involvement of PU.1 in chromatin modification of the Gata3 promoter. Treatment with a histone deacetylase (HDAC) inhibitor, trichostatin A, increased the degree of histone H3 acetylation at the Gata3 promoter and induced the subsequent expression of GATA3. Experiments using HDAC inhibitors and siRNAs showed that HDAC3 suppressed GATA3 expression. The recruitment of HDAC3 to the Gata3 promoter was decreased by PU.1 knockdown. LPS-induced IL-13 expression was dramatically reduced in BMDCs generated from mice lacking the conserved GATA3 response element, termed CGRE, which is an essential site for the binding of GATA3 on the Il-13 promoter. The degree of H3K4me3 at CGRE was significantly increased in PU.1 siRNA-transfected stimulated DCs. Our results indicate that PU.1 plays pivotal roles in DC development and function, serving not only as a transcriptional activator but also as a repressor.
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21
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Abstract
DNA methylation and histone modification are epigenetic mechanisms that result in altered gene expression and cellular phenotype. The exact role of methylation in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) remains unclear. However, aberrations (e.g. loss-/gain-of-function or up-/down-regulation) in components of epigenetic transcriptional regulation in general, and of the methylation machinery in particular, have been implicated in the pathogenesis of these diseases. In addition, many of these components have been identified as therapeutic targets for patients with MDS/AML, and are also being assessed as potential biomarkers of response or resistance to hypomethylating agents (HMAs). The HMAs 5-azacitidine (AZA) and 2'-deoxy-5-azacitidine (decitabine, DAC) inhibit DNA methylation and have shown significant clinical benefits in patients with myeloid malignancies. Despite being viewed as mechanistically similar drugs, AZA and DAC have differing mechanisms of action. DAC is incorporated 100% into DNA, whereas AZA is incorporated into RNA (80-90%) as well as DNA (10-20%). As such, both drugs inhibit DNA methyltransferases (DNMTs; dependently or independently of DNA replication) resulting in the re-expression of tumor-suppressor genes; however, AZA also has an impact on mRNA and protein metabolism via its inhibition of ribonucleotide reductase, resulting in apoptosis. Herein, we first give an overview of transcriptional regulation, including DNA methylation, post-translational histone-tail modifications, the role of micro-RNA and long-range epigenetic gene silencing. We place special emphasis on epigenetic transcriptional regulation and discuss the implication of various components in the pathogenesis of MDS/AML, their potential as therapeutic targets, and their therapeutic modulation by HMAs and other substances (if known). The main focus of this review is laid on dissecting the rapidly evolving knowledge of AZA and DAC with a special focus on their differing mechanisms of action, and the effect of HMAs on transcriptional regulation.
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Affiliation(s)
- Lisa Pleyer
- 3rd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Laboratory for Immunological and Molecular Cancer Research, Oncologic Center, Paracelsus Medical University Hospital Salzburg, Center for Clinical Cancer and Immunology Trials at Salzburg Cancer Research Institute , Salzburg , Austria
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22
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Seguín-Estévez Q, Dunand-Sauthier I, Lemeille S, Iseli C, Ibberson M, Ioannidis V, Schmid CD, Rousseau P, Barras E, Geinoz A, Xenarios I, Acha-Orbea H, Reith W. Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing. Nucleic Acids Res 2014; 42:9641-55. [PMID: 25104025 PMCID: PMC4150779 DOI: 10.1093/nar/gku674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The activation, or maturation, of dendritic cells (DCs) is crucial for the initiation of adaptive T-cell mediated immune responses. Research on the molecular mechanisms implicated in DC maturation has focused primarily on inducible gene-expression events promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC function by inducing widespread gene-silencing remain poorly understood. Yet the termination of key functions is known to be critical for the function of activated DCs. Genome-wide analysis of activation-induced histone deacetylation, combined with genome-wide quantification of activation-induced silencing of nascent transcription, led us to identify a novel inducible transcriptional-repression pathway that makes major contributions to the DC-maturation process. This silencing response is a rapid primary event distinct from repression mechanisms known to operate at later stages of DC maturation. The repressed genes function in pivotal processes--including antigen-presentation, extracellular signal detection, intracellular signal transduction and lipid-mediator biosynthesis--underscoring the central contribution of the silencing mechanism to rapid reshaping of DC function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this lineage-specific transcription factor in marking genes poised for inducible repression.
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Affiliation(s)
- Queralt Seguín-Estévez
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Isabelle Dunand-Sauthier
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Christian Iseli
- Vital-IT, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Mark Ibberson
- Vital-IT, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | | | - Christoph D Schmid
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland University of Basel, CH-4051 Basel, Switzerland
| | - Philippe Rousseau
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Antoine Geinoz
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ioannis Xenarios
- Vital-IT, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Hans Acha-Orbea
- Department of Biochemistry, Faculty of Biology and Medicine, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
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23
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Weigel C, Schmezer P, Plass C, Popanda O. Epigenetics in radiation-induced fibrosis. Oncogene 2014; 34:2145-55. [PMID: 24909163 DOI: 10.1038/onc.2014.145] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/17/2014] [Accepted: 04/23/2014] [Indexed: 02/06/2023]
Abstract
Radiotherapy is a major cancer treatment option but dose-limiting side effects such as late-onset fibrosis in the irradiated tissue severely impair quality of life in cancer survivors. Efforts to explain radiation-induced fibrosis, for example, by genetic variation remained largely inconclusive. Recently published molecular analyses on radiation response and fibrogenesis showed a prominent role of epigenetic gene regulation. This review summarizes the current knowledge on epigenetic modifications in fibrotic disease and radiation response, and it points out the important role for epigenetic mechanisms such as DNA methylation, microRNAs and histone modifications in the development of this disease. The synopsis illustrates the complexity of radiation-induced fibrosis and reveals the need for investigations to further unravel its molecular mechanisms. Importantly, epigenetic changes are long-term determinants of gene expression and can therefore support those mechanisms that induce and perpetuate fibrogenesis even in the absence of the initial damaging stimulus. Future work must comprise the interconnection of acute radiation response and long-lasting epigenetic effects in order to assess their role in late-onset radiation fibrosis. An improved understanding of the underlying biology is fundamental to better comprehend the origin of this disease and to improve both preventive and therapeutic strategies.
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Affiliation(s)
- C Weigel
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Schmezer
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - C Plass
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - O Popanda
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Bedogni F, Rossi RL, Galli F, Cobolli Gigli C, Gandaglia A, Kilstrup-Nielsen C, Landsberger N. Rett syndrome and the urge of novel approaches to study MeCP2 functions and mechanisms of action. Neurosci Biobehav Rev 2014; 46 Pt 2:187-201. [PMID: 24594195 DOI: 10.1016/j.neubiorev.2014.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/25/2013] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
Abstract
Rett syndrome (RTT) is a devastating genetic disorder that worldwide represents the most common genetic cause of severe intellectual disability in females. Most cases are caused by mutations in the X-linked MECP2 gene. Several recent studies have demonstrated that RTT mimicking animal models do not develop an irreversible condition and phenotypic rescue is possible. However, no cure for RTT has been identified so far, and patients are only given symptomatic and supportive treatments. The development of clinical applications imposes a more comprehensive knowledge of MeCP2 functional role(s) and their relevance for RTT pathobiology. Herein, we thoroughly survey the knowledge about MeCP2 structure and functions, highlighting the necessity of identifying more functional domains and the value of molecular genetics. Given that, in our opinion, RTT ultimately is generated by perturbations in gene transcription and so far no genes/pathways have been consistently linked to a dysfunctional MeCP2, we have used higher-level bioinformatic analyses to identify commonly deregulated mechanisms in MeCP2-defective samples. In this review we present our results and discuss the possible value of the utilized approach.
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Affiliation(s)
- Francesco Bedogni
- San Raffaele Rett Research Center, Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy; Laboratory of Genetic and Epigenetic Control of Gene Expression, Department of Theoretical and Applied Sciences, Division of Biomedical Research, University of Insubria, Busto Arsizio 21052, Italy
| | - Riccardo L Rossi
- Fondazione Istituto Nazionale Genetica Molecolare, Milan 20122, Italy
| | - Francesco Galli
- San Raffaele Rett Research Center, Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Clementina Cobolli Gigli
- San Raffaele Rett Research Center, Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy; Laboratory of Genetic and Epigenetic Control of Gene Expression, Department of Theoretical and Applied Sciences, Division of Biomedical Research, University of Insubria, Busto Arsizio 21052, Italy
| | - Anna Gandaglia
- San Raffaele Rett Research Center, Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy; Laboratory of Genetic and Epigenetic Control of Gene Expression, Department of Theoretical and Applied Sciences, Division of Biomedical Research, University of Insubria, Busto Arsizio 21052, Italy
| | - Charlotte Kilstrup-Nielsen
- Laboratory of Genetic and Epigenetic Control of Gene Expression, Department of Theoretical and Applied Sciences, Division of Biomedical Research, University of Insubria, Busto Arsizio 21052, Italy
| | - Nicoletta Landsberger
- San Raffaele Rett Research Center, Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy; Laboratory of Genetic and Epigenetic Control of Gene Expression, Department of Theoretical and Applied Sciences, Division of Biomedical Research, University of Insubria, Busto Arsizio 21052, Italy.
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25
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Cycon KA, Mulvaney K, Rimsza LM, Persky D, Murphy SP. Histone deacetylase inhibitors activate CIITA and MHC class II antigen expression in diffuse large B-cell lymphoma. Immunology 2013; 140:259-72. [PMID: 23789844 DOI: 10.1111/imm.12136] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 12/29/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL), the most common form of non-Hodgkin's lymphoma (NHL) diagnosed in the USA, consists of at least two distinct subtypes: germinal centre B (GCB) and activated B-cell (ABC). Decreased MHC class II (MHCII) expression on the tumours in both DLBCL subtypes directly correlates with significant decreases in patient survival. One common mechanism accounting for MHCII down-regulation in DLBCL is reduced expression of the MHC class II transactivator (CIITA), the master regulator of MHCII transcription. Furthermore, reduced CIITA expression in ABC DLBCL correlates with the presence of the transcriptional repressor positive regulatory domain-I-binding factor-1 (PRDI-BF1). However, the mechanisms underlying down-regulation of CIITA in GCB DLBCL are currently unclear. In this study, we demonstrate that neither PRDI-BF1 nor CpG hypermethylation at the CIITA promoters are responsible for decreased CIITA in GCB DLBCL. In contrast, histone modifications associated with an open chromatin conformation and active transcription were significantly lower at the CIITA promoters in CIITA(-) GCB cells compared with CIITA(+) B cells, which suggests that epigenetic mechanisms contribute to repression of CIITA transcription. Treatment of CIITA(-) or CIITA(low) GCB cells with several different histone deacetylase inhibitors (HDACi) activated modest CIITA and MHCII expression. However, CIITA and MHCII levels were significantly higher in these cells after exposure to the HDAC-1-specific inhibitor MS-275. These results suggest that CIITA transcription is repressed in GCB DLBCL cells through epigenetic mechanisms involving HDACs, and that HDACi treatment can alleviate repression. These observations may have important implications for patient therapy.
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Epigenetic silencing of Bim transcription by Spi-1/PU.1 promotes apoptosis resistance in leukaemia. Cell Death Differ 2013; 20:1268-78. [PMID: 23852375 DOI: 10.1038/cdd.2013.88] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/14/2013] [Accepted: 06/07/2013] [Indexed: 12/17/2022] Open
Abstract
Deregulation of transcriptional networks contributes to haematopoietic malignancies. The transcription factor Spi-1/PU.1 is a master regulator of haematopoiesis and its alteration leads to leukaemia. Spi-1 overexpression inhibits differentiation and promotes resistance to apoptosis in erythroleukaemia. Here, we show that Spi-1 inhibits mitochondrial apoptosis in vitro and in vivo through the transcriptional repression of Bim, a proapoptotic factor. BIM interacts with MCL-1 that behaves as a major player in the survival of the preleukaemic cells. The repression of BIM expression reduces the amount of BIM-MCL-1 complexes, thus increasing the fraction of potentially active antiapoptotic MCL-1. We then demonstrate that Spi-1 represses Bim transcription by binding to the Bim promoter and by promoting the trimethylation of histone 3 on lysine 27 (H3K27me3, a repressive histone mark) on the Bim promoter. The PRC2 repressive complex of Polycomb is directly responsible for the deposit of H3K27me3 mark at the Bim promoter. SUZ12 and the histone methyltransferase EZH2, two PRC2 subunits bind to the Bim promoter at the same location than H3K27me3, distinct of the Spi-1 DNA binding site. As Spi-1 interacts with SUZ12 and EZH2, these results indicate that Spi-1 modulates the activity of PRC2 without directly recruiting the complex to the site of its activity on the chromatin. Our results identify a new mechanism whereby Spi-1 represses transcription and provide mechanistic insights on the antiapoptotic function of a transcription factor mediated by the epigenetic control of gene expression.
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Bian EB, Huang C, Wang H, Chen XX, Tao H, Zhang L, Lv XW, Li J. The role of methyl-CpG binding protein 2 in liver fibrosis. Toxicology 2013; 309:9-14. [PMID: 23619607 DOI: 10.1016/j.tox.2013.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/15/2013] [Accepted: 04/15/2013] [Indexed: 01/07/2023]
Abstract
Liver injury is induced by various insults such as alcohol abuse, if insults persist, may result in the formation of liver fibrosis. Hepatic stellate cell (HSC) activation and transdifferentiation into hepatic myofibroblast, accompanied with potent pro-inflammatory and pro-fibrogenic activities and the down-regulation of anti-inflammatory anti-fibrogenic in gene expression in coordination with epigenetic modifications at the level of the chromatin structure, are pivotal events in liver fibrogenesis. In this review we focus on the role of the methyl-CpG binding protein 2 (MeCP2) transcriptional regulation of different target genes and the interaction MeCP2 with microRNAs (miRNAs) during liver fibrosis. In addition, we address different signaling pathways interacted with MeCP2 regulated HSC activation. Such approaches provide valuable insights into the potential targets of liver fibrosis, and are useful pointers for the development of future therapeutic strategies.
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Affiliation(s)
- Er-Bao Bian
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
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28
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Suzuki S, Nakano H, Takahashi S. Epigenetic regulation of the metallothionein-1A promoter by PU.1 during differentiation of THP-1 cells. Biochem Biophys Res Commun 2013; 433:349-53. [PMID: 23501100 DOI: 10.1016/j.bbrc.2013.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 01/30/2023]
Abstract
We recently demonstrated that metallothionein (MT)-1 A is a direct target gene negatively regulated by PU.1. In this study, we revealed that the expression of PU.1 was increased and accompanied by downregulation of MT-1A expression during TPA-induced THP-1 monocyte differentiation. Chromatin immunoprecipitation (ChIP) analysis demonstrated that PU.1 and the methyl CpG binding protein (MeCP) 2 bound to the same -887 to -602 region in the MT-1A promoter, and the binding of these proteins to this promoter was enhanced during differentiation. Consistently, bisulfite sequencing analyses around this region revealed that the proportion of methylated CpG sites was obivously increased during differentiation. In addition, ChIP analysis demonstrated that acetylated histone H4 around this region tended to be reduced and this may also play a role in the reduction of MT-1A expression during differentiation. Taken together, these findings suggest that MT-1A is epigenetically regulated by PU.1 during monocytic differentiation.
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Affiliation(s)
- Sawami Suzuki
- Division of Molecular Hematology, Kitasato University Graduate School of Medical Sciences, Miniami-ku, Sagamihara, Kanagawa, Japan
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29
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Abstract
Although the term 'epigenetics' was coined nearly seventy years ago, its critical function in memory processing by the adult CNS has only recently been appreciated. The hypothesis that epigenetic mechanisms regulate memory and behavior was motivated by the need for stable molecular processes that evade turnover of the neuronal proteome. In this article, we discuss evidence that supports a role for neural epigenetic modifications in the formation, consolidation and storage of memory. In addition, we will review the evidence that epigenetic mechanisms regulate synaptic plasticity, a cellular correlate of memory. We will also examine how the concerted action of multiple epigenetic mechanisms with varying spatiotemporal profiles influence selective gene expression in response to behavioral experience. Finally, we will suggest key areas for future research that will help elucidate the complex, vital and still mysterious, role of epigenetic mechanisms in neural function and behavior.
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Affiliation(s)
- Faraz A Sultan
- Department of Neurobiology, University of Alabama at Birmingham, Evelyn F McKnight Brain Institute, 1007 Shelby Building, 1825 University Boulevard Birmingham, AL 35294-2182, USA
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30
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Hite KC, Kalashnikova AA, Hansen JC. Coil-to-helix transitions in intrinsically disordered methyl CpG binding protein 2 and its isolated domains. Protein Sci 2012; 21:531-8. [PMID: 22294343 DOI: 10.1002/pro.2037] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 12/25/2011] [Accepted: 12/27/2011] [Indexed: 11/08/2022]
Abstract
Methyl CpG binding protein 2 (MeCP2) is a canonical intrinsically disordered protein (IDP), that is, it lacks stable secondary structure throughout its entire polypeptide chain. Because IDPs often have the propensity to become locally ordered, we tested whether full-length MeCP2 and its constituent domains would gain secondary structure in 2,2,2-trifluoroethanol (TFE), a cosolvent that stabilizes intramolecular hydrogen bonding in proteins. The α-helix, β-strand/turn, and unstructured content were determined as a function of TFE concentration by deconvolution of circular dichroism data. Results indicate that approximately two-thirds of the unstructured residues present in full-length MeCP2 were converted to α-helix in 70% TFE without a change in β-strand/turn. Thus, much of the MeCP2 polypeptide chain undergoes coil-to-helix transitions under conditions that favor intrachain hydrogen bond formation. The unstructured residues of the N-terminal (NTD) and C-terminal (CTD) domains were partially converted to α-helix in 70% TFE. In contrast, the central transcription regulation domain (TRD) became almost completely α-helical in 70% TFE. Unlike the NTD, CTD, and TRD, the unstructured content of the methyl DNA binding domain and the intervening domain did not change with increasing TFE concentration. These results indicate that the coil-to-helix transitions that occur in full-length MeCP2 are localized to the NTD, CTD, and TRD, with the TRD showing the greatest tendency for helix formation. The potential relationships between intrinsic disorder, coil-to-helix transitions, and MeCP2 structure and function are discussed.
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Affiliation(s)
- Kristopher C Hite
- Department of Biochemistry and Molecular Biology, Campus Delivery 1870, Colorado State University, Fort Collins, Colorado 80523, USA
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31
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Sanchez-Mut J, Huertas D, Esteller M. Aberrant epigenetic landscape in intellectual disability. PROGRESS IN BRAIN RESEARCH 2012; 197:53-71. [DOI: 10.1016/b978-0-444-54299-1.00004-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Nakazaki E, Tsolmon S, Han J, Isoda H. Proteomic study of granulocytic differentiation induced by apigenin 7-glucoside in human promyelocytic leukemia HL-60 cells. Eur J Nutr 2011; 52:25-35. [PMID: 22113421 DOI: 10.1007/s00394-011-0282-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 11/14/2011] [Indexed: 02/03/2023]
Abstract
BACKGROUND Nutritional factors is one of the most important regulators in the progression of cancer. Some dietary elements promote the growth of cancer but others, such as plant-derived compounds, may reverse this process. PURPOSE We tried to investigate yet another approach of cancer prevention through cancer cell differentiation, using a common non-mutagenic flavonoid apigenin 7-glucoside. METHODS HL-60 cells were treated with or without apigenin 7-glucoside. Cell proliferation was measured by MTT assay, and the cell cycle distribution was estimated by propidium iodide staining of DNA. To determine cellular differentiation, cell surface differentiation markers CD11b and CD14 were used. Two-dimensional gel electrophoresis was then performed to identify proteins that may be important in HL-60 cell differentiation following apigenin 7-glucoside treatment. RESULTS Apigenin 7-glucoside inhibited HL-60 cell growth, dose- and time-dependently, but did not cause apoptosis. The distribution of cells at different stages in the cell cycle indicated an accumulation of treated cells in G(2)/M phase. Moreover, apigenin 7-glucoside induced granulocytic differentiation of HL-60 cells. Ten proteins that might play essential role in granulocytic differentiation were identified by proteomics. CONCLUSIONS A complete understanding of the preventive effects of plant-based diet on cancer depends on the mechanisms of action of different plant components on processes. We hope these findings may contribute to the understandings of the different approaches for chemoprevention of cancer.
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Affiliation(s)
- Eri Nakazaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
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Hansen JC, Wexler BB, Rogers DJ, Hite KC, Panchenko T, Ajith S, Black BE. DNA binding restricts the intrinsic conformational flexibility of methyl CpG binding protein 2 (MeCP2). J Biol Chem 2011; 286:18938-48. [PMID: 21467044 PMCID: PMC3099709 DOI: 10.1074/jbc.m111.234609] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 03/29/2011] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry-based hydrogen/deuterium exchange (H/DX) has been used to define the polypeptide backbone dynamics of full-length methyl CpG binding protein 2 (MeCP2) when free in solution and when bound to unmethylated and methylated DNA. Essentially the entire MeCP2 polypeptide chain underwent H/DX at rates faster than could be measured (i.e. complete exchange in ≤10 s), with the exception of the methyl DNA binding domain (MBD). Even the H/DX of the MBD was rapid compared with that of a typical globular protein. Thus, there is no single tertiary structure of MeCP2. Rather, the full-length protein rapidly samples many different conformations when free in solution. When MeCP2 binds to unmethylated DNA, H/DX is slowed several orders of magnitude throughout the MBD. Binding of MeCP2 to methylated DNA led to additional minor H/DX protection, and only locally within the N-terminal portion of the MBD. H/DX also was used to examine the structural dynamics of the isolated MBD carrying three frequent mutations associated with Rett syndrome. The effects of the mutations ranged from very little (R106W) to a substantial increase in conformational sampling (F155S). Our H/DX results have yielded fine resolution mapping of the structure of full-length MeCP2 in the absence and presence of DNA, provided a biochemical basis for understanding MeCP2 function in normal cells, and predicted potential approaches for the treatment of a subset of RTT cases caused by point mutations that destabilize the MBD.
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Affiliation(s)
- Jeffrey C. Hansen
- From the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | | | | | - Kristopher C. Hite
- From the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | - Tanya Panchenko
- the Department of Biochemistry and Biophysics
- Graduate Group in Cell and Molecular Biology, and
| | - Sandya Ajith
- the Department of Biochemistry and Biophysics
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059
| | - Ben E. Black
- the Department of Biochemistry and Biophysics
- Graduate Group in Cell and Molecular Biology, and
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059
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Abstract
The transcription factor (TF) RUNX1 cooperates with lineage-specifying TFs (eg, PU.1/SPI1) to activate myeloid differentiation genes, such as macrophage and granulocyte macrophage colony-stimulating factor receptors (MCSFR and GMCSFR). Disruption of cooperative gene activation could contribute to aberrant repression of differentiation genes and leukemogenesis initiated by mutations and translocations of RUNX1. To investigate the mechanisms underlying cooperative gene activation, the effects of Runx1 deficiency were examined in an in vitro model of Pu.1-driven macrophage differentiation and in primary cells. Runx1 deficiency decreased Pu.1-mediated activation of Mcsfr and Gmcsfr, accompanied by decreased histone acetylation at the Mcsfr and Gmcsfr promoters, and increased endogenous corepressor (Eto2, Sin3A, and Hdac2) coimmunoprecipitation with Pu.1. In cotransfection experiments, corepressors were excluded from a multiprotein complex containing full-length RUNX1 and PU.1. However, corepressors interacted with PU.1 if wild-type RUNX1 was replaced with truncated variants associated with leukemia. Histone deacetylase (HDAC) enzyme activity is a major component of corepressor function. HDAC inhibition using suberoylanilide hydroxamic acid or MS-275 significantly increased MCSFR and GMCSFR expression in leukemia cell lines that express PU.1 and mutated or translocated RUNX1. RUNX1 deficiency is associated with persistent corepressor interaction with PU.1. Thus, inhibiting HDAC can partly compensate for the functional consequences of RUNX1 deficiency.
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Wang H, Cheng F, Woan K, Sahakian E, Merino O, Rock-Klotz J, Vicente-Suarez I, Pinilla-Ibarz J, Wright KL, Seto E, Bhalla K, Villagra A, Sotomayor EM. Histone deacetylase inhibitor LAQ824 augments inflammatory responses in macrophages through transcriptional regulation of IL-10. THE JOURNAL OF IMMUNOLOGY 2011; 186:3986-96. [PMID: 21368229 DOI: 10.4049/jimmunol.1001101] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
APCs are important in the initiation of productive Ag-specific T cell responses and the induction of T cell anergy. The inflammatory status of the APC at the time of encounter with Ag-specific T cells plays a central role in determining such divergent T cell outcomes. A better understanding of the regulation of proinflammatory and anti-inflammatory genes in its natural setting, the chromatin substrate, might provide novel insights to overcome anergic mechanisms mediated by APCs. In this study, we show for the first time, to our knowledge, that treatment of BALB/c murine macrophages with the histone deacetylase inhibitor LAQ824 induces chromatin changes at the level of the IL-10 gene promoter that lead to enhanced recruitment of the transcriptional repressors HDAC11 and PU.1. Such an effect is associated with diminished IL-10 production and induction of inflammatory cells able of priming naive Ag-specific T cells, but more importantly, capable of restoring the responsiveness of anergized Ag-specific CD4(+) T cells.
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Affiliation(s)
- Hongwei Wang
- Department of Immunology and Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL 33613, USA
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Lee HA, Hong SH, Kim JW, Jang IS. Possible involvement of DNA methylation in NKCC1 gene expression during postnatal development and in response to ischemia. J Neurochem 2010; 114:520-9. [PMID: 20456012 DOI: 10.1111/j.1471-4159.2010.06772.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In CNS, GABA(A) receptor-mediated responses switch from depolarization to hyperpolarization during postnatal development. This switch is mediated by developmental down-regulation of inwardly directed Na(+)-K(+)-2Cl(-) co-transporter type 1 (NKCC1) and up-regulation of outwardly directed K(+)-Cl(-) co-transporter type 2. While several factors have been shown to regulate K(+)-Cl(-) co-transporter type 2 expression, little is known about the mechanisms by which the expression of NKCC1 is regulated during postnatal development. Here, we report a novel epigenetic mechanism underlying the developmental regulation of NKCC1 gene expression in the rat cerebral cortex. In vitro DNA methylation of the NKCC1 promoter region, which contains a high density of cytosine-phosphodiester-guanine islands, significantly decreased the expression of NKCC1 mRNA, and the degree of methylation of the NKCC1 promoter region significantly increased during postnatal development. In addition, treatment with 5-aza-2'-deoxycytidine, a specific DNA methyltransferase inhibitor, elicited an increase in the expression of NKCC1 mRNA and protein in cortical slice cultures. Focal ischemic injury induced by the occlusion of the middle cerebral artery led to the re-expression of NKCC1 mRNA and protein even in the mature rat cortex. The re-expression of NKCC1 mRNA and protein in the injured cerebral cortex was related to a decrease in the methylation status of the NKCC1 promoter region. Our results indicate that epigenetic mechanisms, such as DNA methylation, might be involved in the regulation of NKCC1 gene expression during postnatal development as well as under pathological conditions.
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Affiliation(s)
- Hae-Ahm Lee
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, Korea
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37
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Ghosh RP, Nikitina T, Horowitz-Scherer RA, Gierasch LM, Uversky VN, Hite K, Hansen JC, Woodcock CL. Unique physical properties and interactions of the domains of methylated DNA binding protein 2. Biochemistry 2010; 49:4395-410. [PMID: 20405910 DOI: 10.1021/bi9019753] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylated DNA binding protein 2 (MeCP2) is a methyl CpG binding protein whose key role is the recognition of epigenetic information encoded in DNA methylation patterns. Mutation or misregulation of MeCP2 function leads to Rett syndrome as well as a variety of other autism spectrum disorders. Here, we have analyzed in detail the properties of six individually expressed human MeCP2 domains spanning the entire protein with emphasis on their interactions with each other, with DNA, and with nucleosomal arrays. Each domain contributes uniquely to the structure and function of the full-length protein. MeCP2 is approximately 60% unstructured, with nine interspersed alpha-molecular recognition features (alpha-MoRFs), which are polypeptide segments predicted to acquire secondary structure upon forming complexes with binding partners. Large increases in secondary structure content are induced in some of the isolated MeCP2 domains and in the full-length protein by binding to DNA. Interactions between some MeCP2 domains in cis and trans seen in our assays likely contribute to the structure and function of the intact protein. We also show that MeCP2 has two functional halves. The N-terminal portion contains the methylated DNA binding domain (MBD) and two highly disordered flanking domains that modulate MBD-mediated DNA binding. One of these flanking domains is also capable of autonomous DNA binding. In contrast, the C-terminal portion of the protein that harbors at least two independent DNA binding domains and a chromatin-specific binding domain is largely responsible for mediating nucleosomal array compaction and oligomerization. These findings led to new mechanistic and biochemical insights regarding the conformational modulations of this intrinsically disordered protein, and its context-dependent in vivo roles.
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Affiliation(s)
- Rajarshi P Ghosh
- Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
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38
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Alvarez-Saavedra M, Carrasco L, Sura-Trueba S, Demarchi Aiello V, Walz K, Neto JX, Young JI. Elevated expression of MeCP2 in cardiac and skeletal tissues is detrimental for normal development. Hum Mol Genet 2010; 19:2177-90. [PMID: 20203171 DOI: 10.1093/hmg/ddq096] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
MeCP2 plays a critical role in interpreting epigenetic signatures that command chromatin conformation and regulation of gene transcription. In spite of MeCP2's ubiquitous expression, its functions have always been considered in the context of brain physiology. In this study, we demonstrate that alterations of the normal pattern of expression of MeCP2 in cardiac and skeletal tissues are detrimental for normal development. Overexpression of MeCP2 in the mouse heart leads to embryonic lethality with cardiac septum hypertrophy and dysregulated expression of MeCP2 in skeletal tissue produces severe malformations. We further show that MeCP2's expression in the heart is developmentally regulated; further suggesting that it plays a key role in regulating transcriptional programs in non-neural tissues.
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Imoto A, Okada M, Okazaki T, Kitasato H, Harigae H, Takahashi S. Metallothionein-1 isoforms and vimentin are direct PU.1 downstream target genes in leukemia cells. J Biol Chem 2010; 285:10300-9. [PMID: 20139074 DOI: 10.1074/jbc.m109.095810] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
PU.1 is a key transcription factor for hematopoiesis and plays important roles in various hematological malignancies. To clarify the molecular function of PU.1, we initially tried to identify bona fide target genes regulated by PU.1. Dual microarrays were employed for this study to compare PU.1-knockdown K562 cells (K562PU.1KD) stably expressing PU.1 short inhibitory RNAs versus control cells and PU.1-overexpressing K562 cells (K562PU.1OE) versus control cells. In these analyses, we found that several genes, including metallothionein (MT)-1 isoforms (MT-1G and MT-1A) and vimentin (VIM), were markedly induced while Jun dimerization protein (JDP) 2 was suppressed in K562PU.1KD cells. Furthermore, the mRNA expressions of the MT-1 and VIM genes were inversely correlated and the mRNA expression of JDP2 was positively correlated with PU.1 mRNA expression in 43 primary acute myeloid leukemia specimens (MT-1G: R = -0.50, p < 0.001; MT-1A: R = -0.58, p < 0.0005; VIM: R = -0.39, p < 0.01; and JDP2: R = 0.30, p < 0.05). Next, we analyzed the regulation of the MT-1 and VIM genes. We observed increased associations of acetylated histones H3 and H4 with the promoters of these genes in K562PU.1KD cells. Sequence analyses of the regions approximately 1 kb upstream from the transcription start sites of these genes revealed numerous CpG sites, which are potential targets for DNA methylation. Chromatin immunoprecipitation assays revealed that methyl CpG-binding protein 2 (MeCP2) and PU.1 bound to the CpG-rich regions in the MT-1 and VIM promoters. Bisulfite sequencing analyses of the PU.1-bound regions of these promoters revealed that the proportions of methylated CpG sites were tightly related to the PU.1 expression levels.
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Affiliation(s)
- Akemi Imoto
- Division of Molecular Hematology, Kitasato University Graduate School of Medical Sciences, 1-15-1 Kitasato, Minamiku, Sagamihara 252-0373, Japan
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Thambirajah AA, Ausió J. A moment's pause: putative nucleosome-based influences on MeCP2 regulation. Biochem Cell Biol 2010; 87:791-8. [PMID: 19898528 DOI: 10.1139/o09-054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
There has been a hotbed of activity surrounding MeCP2 research in the past number of years. Despite better characterizing the functions and nature of this protein, it has become abundantly clear that MeCP2 is involved in far more complex activities than perhaps initially anticipated. Recent publications have shown that MeCP2 is dynamically post-translationally modified, and it is possible that these marks permit MeCP2 to inhabit very diverse chromatin environments. It is also of interest to consider how nucleosome composition differs in these varying chromatin regions, and how the chromatin template itself contributes to diversifying the regulatory roles of MeCP2. These will be critical points to examine when seeking to understand how MeCP2 behaviour differentiates in tissues other than the brain. By understanding the chromatin and (or) tissue context in which MeCP2 interacts, it may be possible to discern the specific etiology of diseases linked to MeCP2 dysfunction.
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Affiliation(s)
- Anita A Thambirajah
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W3P6, Canada
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MicroRNAs and epigenetic regulation in the mammalian inner ear: implications for deafness. Mamm Genome 2009; 20:581-603. [PMID: 19876605 DOI: 10.1007/s00335-009-9230-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 09/30/2009] [Indexed: 01/19/2023]
Abstract
Sensorineural hearing loss is the most common sensory disorder in humans and derives, in most cases, from inner-ear defects or degeneration of the cochlear sensory neuroepithelial hair cells. Genetic factors make a significant contribution to hearing impairment. While mutations in 51 genes have been associated with hereditary sensorineural nonsyndromic hearing loss (NSHL) in humans, the responsible mutations in many other chromosomal loci linked with NSHL have not been identified yet. Recently, mutations in a noncoding microRNA (miRNA) gene, MIR96, which is expressed specifically in the inner-ear hair cells, were linked with progressive hearing loss in humans and mice. Furthermore, additional miRNAs were found to have essential roles in the development and survival of inner-ear hair cells. Epigenetic mechanisms, in particular, DNA methylation and histone modifications, have also been implicated in human deafness, suggesting that several layers of noncoding genes that have never been studied systematically in the inner-ear sensory epithelia are required for normal hearing. This review aims to summarize the current knowledge about the roles of miRNAs and epigenetic regulatory mechanisms in the development, survival, and function of the inner ear, specifically in the sensory epithelia, tectorial membrane, and innervation, and their contribution to hearing.
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Desai S, Bolick SCE, Maurin M, Wright KL. PU.1 regulates positive regulatory domain I-binding factor 1/Blimp-1 transcription in lymphoma cells. THE JOURNAL OF IMMUNOLOGY 2009; 183:5778-87. [PMID: 19828640 DOI: 10.4049/jimmunol.0901120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The human positive regulatory domain I-binding factor 1 (PRDI-BF1) and its murine homolog Blimp-1 promote differentiation of mature B cells into Ab-secreting plasma cells. In contrast, ectopic expression of PRDI-BF1 in lymphoma cells can lead to inhibition of proliferation or apoptosis. However, little is currently known about the regulation of PRDM1, the gene encoding PRDI-BF1. This report establishes that in lymphoma cells stimulation through the BCR rapidly induces endogenous PRDM1 at the level of transcription with minor changes in mRNA stability. The induced PRDM1-encoded protein localizes to its target genes in vivo and suppresses their expression. In vivo genomic footprinting of the PRDM1 promoter in unstimulated lymphoma and myeloma cells reveals multiple common in vivo occupied elements throughout the promoter. Further functional and structural analysis of the promoter reveals that the promoter is preloaded and poised for activation in the B cell lines. The transcription factor PU.1 is shown to be required for the BCR-induced expression of PRDM1 in lymphoma cells and in PU.1-positive myeloma cells. Activation of PRDM1 is associated with loss of the corepressor transducin-like enhancer of split 4 from the PU.1 complex. These findings indicate that PRDM1 is poised for activation in lymphoma cells and therefore may be a potential therapeutic target to inhibit lymphoma cell proliferation and survival.
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Affiliation(s)
- Shruti Desai
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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Ishii H, Du H, Zhang Z, Henderson A, Sen R, Pazin MJ. Mi2beta shows chromatin enzyme specificity by erasing a DNase I-hypersensitive site established by ACF. J Biol Chem 2009; 284:7533-41. [PMID: 19158090 DOI: 10.1074/jbc.m807617200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ATP-dependent chromatin-remodeling enzymes are linked to changes in gene expression; however, it is not clear how the multiple remodeling enzymes found in eukaryotes differ in function and work together. In this report, we demonstrate that the ATP-dependent remodeling enzymes ACF and Mi2beta can direct consecutive, opposing chromatin-remodeling events, when recruited to chromatin by different transcription factors. In a cell-free system based on the immunoglobulin heavy chain gene enhancer, we show that TFE3 induces a DNase I-hypersensitive site in an ATP-dependent reaction that requires ACF following transcription factor binding to chromatin. In a second step, PU.1 directs Mi2beta to erase an established DNase I-hypersensitive site, in an ATP-dependent reaction subsequent to PU.1 binding to chromatin, whereas ACF will not support erasure. Erasure occurred without displacing the transcription factor that initiated the site. Other tested enzymes were unable to erase the DNase I-hypersensitive site. Establishing and erasing the DNase I-hypersensitive site required transcriptional activation domains from TFE3 and PU.1, respectively. Together, these results provide important new mechanistic insight into the combinatorial control of chromatin structure.
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Affiliation(s)
- Haruhiko Ishii
- Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454, USA
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Villagra A, Cheng F, Wang HW, Suarez I, Glozak M, Maurin M, Nguyen D, Wright KL, Atadja PW, Bhalla K, Pinilla-Ibarz J, Seto E, Sotomayor EM. The histone deacetylase HDAC11 regulates the expression of interleukin 10 and immune tolerance. Nat Immunol 2008; 10:92-100. [PMID: 19011628 DOI: 10.1038/ni.1673] [Citation(s) in RCA: 330] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 10/07/2008] [Indexed: 12/12/2022]
Abstract
Antigen-presenting cells (APCs) induce T cell activation as well as T cell tolerance. The molecular basis of the regulation of this critical 'decision' is not well understood. Here we show that HDAC11, a member of the HDAC histone deacetylase family with no prior defined physiological function, negatively regulated expression of the gene encoding interleukin 10 (IL-10) in APCs. Overexpression of HDAC11 inhibited IL-10 expression and induced inflammatory APCs that were able to prime naive T cells and restore the responsiveness of tolerant CD4+ T cells. Conversely, disruption of HDAC11 in APCs led to upregulation of expression of the gene encoding IL-10 and impairment of antigen-specific T cell responses. Thus, HDAC11 represents a molecular target that influences immune activation versus immune tolerance, a critical 'decision' with substantial implications in autoimmunity, transplantation and cancer immunotherapy.
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Affiliation(s)
- Alejandro Villagra
- Division of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
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Uchiumi F, Sakakibara G, Sato J, Tanuma SI. Characterization of the promoter region of the humanPARGgene and its response to PU.1 during differentiation of HL-60 cells. Genes Cells 2008; 13:1229-47. [DOI: 10.1111/j.1365-2443.2008.01240.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
The methyl-CpG-binding protein MeCP2 was discovered over 15 years ago as part of a search for proteins that selectively bind methylated DNA. It is a nuclear protein that is largely chromatin-bound and has a strong preference for binding to methylated DNA sequences in vivo. Evidence from model systems shows that MeCP2 can recruit the Sin3a co-repressor complex to promoters leading to transcriptional repression, therefore suggesting that MeCP2 can interpret the DNA methylation signal to bring about gene silencing. Mutations in the human MECP2 gene cause the autism spectrum disorder Rett Syndrome. MeCP2 is most highly expressed in neurons, and mice lacking this protein show symptoms that strikingly parallel those of Rett patients. Surprisingly, these symptoms are efficiently reversed by delayed activation of a ‘stopped’ Mecp2 gene, raising hopes that human Rett syndrome may also be reversible. Future studies of MeCP2 promise to shed light upon brain function, neurological disease and the biology of DNA methylation.
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Spi-B inhibits human plasma cell differentiation by repressing BLIMP1 and XBP-1 expression. Blood 2008; 112:1804-12. [PMID: 18552212 DOI: 10.1182/blood-2008-01-136440] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The terminal differentiation of B cells into antibody-secreting plasma cells is tightly regulated by a complex network of transcription factors. Here we evaluated the role of the Ets factor Spi-B during terminal differentiation of human B cells. All mature tonsil and peripheral blood B-cell subsets expressed Spi-B, with the exception of plasma cells. Overexpression of Spi-B in CD19(+) B cells inhibited, similar to the known inhibitor BCL-6, the expression of plasma cell-associated surface markers and transcription factors as well as immunoglobulin production, ie, in vitro plasma cell differentiation. The arrest in B-cell differentiation enforced by Spi-B was independent of the transactivation domain, but dependent on the Ets-domain. By chromatin immunoprecipitation and assays using an inducible Spi-B construct BLIMP1 and XBP-1 were identified as direct target genes of Spi-B mediated repression. We propose a novel role for Spi-B in maintenance of germinal center and memory B cells by direct repression of major plasma cell factors and thereby plasma cell differentiation.
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Kumar A, Kamboj S, Malone BM, Kudo S, Twiss JL, Czymmek KJ, LaSalle JM, Schanen NC. Analysis of protein domains and Rett syndrome mutations indicate that multiple regions influence chromatin-binding dynamics of the chromatin-associated protein MECP2 in vivo. J Cell Sci 2008; 121:1128-37. [PMID: 18334558 DOI: 10.1242/jcs.016865] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The methyl-CpG-binding protein 2 (MECP2) serves both organizational and transcriptional functions in the nucleus, with two well-characterized domains integrally related to these functions. The recognition of methylated CpG dinucleotides is accomplished by the methyl-binding domain (MBD), and the transcriptional repression domain (TRD) facilitates protein-protein interactions with chromatin remodeling proteins. For each known function of MECP2, chromatin binding is a crucial activity. Here, we apply photobleaching strategies within the nucleus using domain-deleted MECP2 proteins as well as naturally occurring point mutations identified in individuals with the neurodevelopmental disorder Rett syndrome (RTT). These studies reveal that MECP2 is transiently associated with chromatin in vivo and confirm a central role for the MBD in directing the protein to heterochromatin. In addition, we report for the first time that the small region between the MBD and the TRD, known as the interdomain region (ID), stabilizes chromatin binding by MECP2 independently of the MBD. The TRD of MECP2 also contributes towards chromatin binding, whereas the N- and C-termini do not. Some common RTT missense and nonsense mutations significantly affect binding kinetics, suggesting that alterations in chromatin binding can result in protein dysfunction and hence a disease phenotype.
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Affiliation(s)
- Asmita Kumar
- Nemours Biomedical Research, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
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Rice KL, Hormaeche I, Licht JD. Epigenetic regulation of normal and malignant hematopoiesis. Oncogene 2007; 26:6697-714. [PMID: 17934479 DOI: 10.1038/sj.onc.1210755] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The molecular processes governing hematopoiesis involve the interplay between lineage-specific transcription factors and a series of epigenetic tags, including DNA methylation and covalent histone tail modifications, such as acetylation, methylation, phosphorylation, SUMOylation and ubiquitylation. These post-translational modifications, which collectively constitute the 'histone code', are capable of affecting chromatin structure and gene transcription and are catalysed by opposing families of enzymes, allowing the developmental potential of hematopoietic stem cells to be dynamically regulated. The essential role of these enzymes in regulating normal blood development is highlighted by the finding that members from all families of chromatin regulators are targets for dysregulation in many hematological malignancies, and that patterns of histone modification are globally affected in cancer as well as the regulatory regions of specific oncogenes and tumor suppressors. The discovery that these epigenetic marks can be reversed by compounds targeting aberrant transcription factor/co-activator/co-repressor interactions and histone-modifying activities, provides the basis for an exciting field in which the epigenome of cancer cells may be manipulated with potential therapeutic benefits.
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Affiliation(s)
- K L Rice
- Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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Yamada T, Shimizu T, Suzuki M, Kihara-Negishi F, Nanashima N, Sakurai T, Fan Y, Akita M, Oikawa T, Tsuchida S. Interaction between the homeodomain protein HOXC13 and ETS family transcription factor PU.1 and its implication in the differentiation of murine erythroleukemia cells. Exp Cell Res 2007; 314:847-58. [PMID: 18076876 DOI: 10.1016/j.yexcr.2007.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 11/05/2007] [Accepted: 11/08/2007] [Indexed: 01/25/2023]
Abstract
Some of homeodomain proteins and the ETS family of transcription factors are involved in hematopoiesis. RT-PCR analysis revealed that the HOXC13 and PU.1 genes were expressed in murine erythroleukemia (MEL) cells and their levels decreased during DMSO-induced differentiation into erythroid cells. HOXC13 bound to the ETS domain of PU.1 through a region encompassing the C-terminal part of the homeodomain and the most C-terminal region and enhanced the transcriptional activity of PU.1. Enforced expression of HOXC13 in MEL cells resulted in the suppression of beta-globin gene expression. In MEL cells overexpressing HOXC13 and PU.1, which also inhibits the differentiation of MEL cells, no synergistic effect on the suppression of beta-globin gene expression was observed. However, in the presence of DMSO, the expression levels of the beta-globin gene in the cells overexpressing HOXC13 and PU.1 were, unexpectedly, higher than those in the cells overexpressing PU.1 alone. The levels of PU.1 protein were markedly decreased despite that the levels of mRNA were preserved in the cells overexpressing PU.1 and HOXC13. It was, thus, suggested that although HOXC13 negatively regulates the differentiation of MEL cells into erythroid cells, it antagonizes PU.1 possibly by down-regulation of PU.1 protein in the presence of a differentiation stimulus.
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Affiliation(s)
- Toshiyuki Yamada
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
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