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Bibbò F, Asadzadeh F, Boccia A, Sorice C, Bianco O, Saccà CD, Majello B, Donofrio V, Bifano D, De Martino L, Quaglietta L, Cristofano A, Covelli EM, Cinalli G, Ferrucci V, De Antonellis P, Zollo M. Targeting Group 3 Medulloblastoma by the Anti-PRUNE-1 and Anti-LSD1/KDM1A Epigenetic Molecules. Int J Mol Sci 2024; 25:3917. [PMID: 38612726 PMCID: PMC11011515 DOI: 10.3390/ijms25073917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Medulloblastoma (MB) is a highly malignant childhood brain tumor. Group 3 MB (Gr3 MB) is considered to have the most metastatic potential, and tailored therapies for Gr3 MB are currently lacking. Gr3 MB is driven by PRUNE-1 amplification or overexpression. In this paper, we found that PRUNE-1 was transcriptionally regulated by lysine demethylase LSD1/KDM1A. This study aimed to investigate the therapeutic potential of inhibiting both PRUNE-1 and LSD1/KDM1A with the selective inhibitors AA7.1 and SP-2577, respectively. We found that the pharmacological inhibition had a substantial efficacy on targeting the metastatic axis driven by PRUNE-1 (PRUNE-1-OTX2-TGFβ-PTEN) in Gr3 MB. Using RNA seq transcriptomic feature data in Gr3 MB primary cells, we provide evidence that the combination of AA7.1 and SP-2577 positively affects neuronal commitment, confirmed by glial fibrillary acidic protein (GFAP)-positive differentiation and the inhibition of the cytotoxic components of the tumor microenvironment and the epithelial-mesenchymal transition (EMT) by the down-regulation of N-Cadherin protein expression. We also identified an impairing action on the mitochondrial metabolism and, consequently, oxidative phosphorylation, thus depriving tumors cells of an important source of energy. Furthermore, by overlapping the genomic mutational signatures through WES sequence analyses with RNA seq transcriptomic feature data, we propose in this paper that the combination of these two small molecules can be used in a second-line treatment in advanced therapeutics against Gr3 MB. Our study demonstrates that the usage of PRUNE-1 and LSD1/KDM1A inhibitors in combination represents a novel therapeutic approach for these highly aggressive metastatic MB tumors.
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Affiliation(s)
- Francesca Bibbò
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Fatemeh Asadzadeh
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
- SEMM European School of Molecular Medicine, 20139 Milan, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Carmen Sorice
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Orazio Bianco
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Carmen Daniela Saccà
- Department of Biology, University Federico II of Naples, 80138 Naples, Italy; (C.D.S.); (B.M.)
| | - Barbara Majello
- Department of Biology, University Federico II of Naples, 80138 Naples, Italy; (C.D.S.); (B.M.)
| | - Vittoria Donofrio
- Department of Pathology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (V.D.); (D.B.)
| | - Delfina Bifano
- Department of Pathology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (V.D.); (D.B.)
| | - Lucia De Martino
- Pediatric Neuro-Oncology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (L.D.M.); (L.Q.)
| | - Lucia Quaglietta
- Pediatric Neuro-Oncology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (L.D.M.); (L.Q.)
| | - Adriana Cristofano
- Pediatric Neuroradiology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (A.C.); (E.M.C.)
| | - Eugenio Maria Covelli
- Pediatric Neuroradiology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (A.C.); (E.M.C.)
| | - Giuseppe Cinalli
- Pediatric Neurosurgery, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy;
| | - Veronica Ferrucci
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Pasqualino De Antonellis
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Massimo Zollo
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
- DAI Medicina di Laboratorio e Trasfusionale, ‘AOU Federico II Policlinico’, 80131 Naples, Italy
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Xu H, Yu X, Xie R, Wang Y, Li C. RCOR1 improves neurobehaviors and neuron injury in rat cerebral palsy by Endothelin-1 targeting-induced Akt/GSK-3β pathway upregulation. Brain Dev 2024; 46:93-102. [PMID: 37978036 DOI: 10.1016/j.braindev.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/27/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND RE1 Silencing Transcription factor (REST) corepressor 1 (RCOR1) has been reported to orchestrate neurogenesis, while its role in cerebral palsy (CP) remains elusive. Besides, RCOR1 can interact with Endothelin-1 (EDN1), and EDN1 expression is related to brain damage. Therefore, this study aimed to explore the effects of RCOR1/EDN1 on brain damage during the progression of CP. METHODS CP rats were established via hypoxia-ischemia insult, and injected with lentivirus-RCOR1, followed by examination of brain pathological conditions. The RCOR1 and EDN1 interaction was recognized using hTFtarget. Healthy rat cortical neuron cells received interference of RCOR1/EDN1 expression, and underwent oxygen-glucose deprivation/reoxygenation (OGD/R) treatment, after which phenotypic and molecular assays were conducted through the biochemical method, qRT-PCR and/or western blot. RESULTS RCOR1 was low-expressed but EDN1 was high-expressed in CP model rats and OGD/R-treated neurons. RCOR1 overexpression ameliorated rat neurobehaviors, alleviated brain pathological conditions, reduced TUNEL-positive cells, decreased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA), increased superoxide dismutase (SOD) level and repressed EDN1 expression in the brains of CP model rats. In neurons, RCOR1 overexpression counteracted OGD/R-induced viability decrease, reduction of the levels of RCOR1, SOD, Bcl-2, caspase-3, p-Akt/Akt and p-GSK-3β/GSK-3β, and elevation of the levels of EDN1, ROS, Bax, and cleaved caspase-3, while EDN1 overexpression did contrarily on these events. Moreover, there was a negative interplay between RCOR1 overexpression and EDN1 overexpression in OGD/R-induced neurons. CONCLUSION RCOR1 ameliorates neurobehaviors and suppresses neuronal apoptosis and oxidative stress in CP through EDN1 targeting-mediated upregulation of Akt/GSK-3β.
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Affiliation(s)
- Hai Xu
- Department of Rehabilitation Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Wulumuqi City, Xinjiang Uygur Autonomous Region 830001, China
| | - Xuetao Yu
- Department of Rehabilitation Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Wulumuqi City, Xinjiang Uygur Autonomous Region 830001, China
| | - Rong Xie
- Department of Rehabilitation Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Wulumuqi City, Xinjiang Uygur Autonomous Region 830001, China
| | - Yangyang Wang
- Department of Rehabilitation Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Wulumuqi City, Xinjiang Uygur Autonomous Region 830001, China
| | - Chunli Li
- Department of Rehabilitation Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Wulumuqi City, Xinjiang Uygur Autonomous Region 830001, China.
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Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun 2023; 14:2300. [PMID: 37085539 PMCID: PMC10121654 DOI: 10.1038/s41467-023-38044-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/13/2023] [Indexed: 04/23/2023] Open
Abstract
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aylin Camgöz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Owen Chapman
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sameena Wani
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Abhijit Chakraborty
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Meghana Pagadala
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Rosalind Bump
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sahaana Chandran
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Rocio Acuna-Hidalgo
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Derek Reid
- Arima Genomics, Inc, San Diego, CA, 92121, USA
| | | | - Monika Mauermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Edwin F Juarez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Anne Jenseit
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - James T Robinson
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Petra Fiesel
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ling Morgan
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sunita Sridhar
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Michael Levy
- Neurosurgery, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Denise Malicki
- Pathology, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Stephen Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, NYU Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - John Crawford
- Department of Neurosciences, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Robert J Wechsler-Reya
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jennifer Cotter
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - George Michaiel
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Gudrun Fleischhack
- German Cancer Consortium (DKTK), West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Hannah Carter
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kulandaimanuvel Antony Michealraj
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Sachin A Kumar
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Jeremy Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany
| | - Jill P Mesirov
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ferhat Ay
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Jesse R Dixon
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Lukas Chavez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA.
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA.
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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Mao F, Shi YG. Targeting the LSD1/KDM1 Family of Lysine Demethylases in Cancer and Other Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:15-49. [PMID: 37751134 DOI: 10.1007/978-3-031-38176-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase discovered and the founding member of the flavin-dependent lysine demethylase family (KDM1). The human KDM1 family includes KDM1A and KDM1B, which primarily catalyze demethylation of histone H3K4me1/2. The KDM1 family is involved in epigenetic gene regulation and plays important roles in various biological and disease pathogenesis processes, including cell differentiation, embryonic development, hormone signaling, and carcinogenesis. Malfunction of many epigenetic regulators results in complex human diseases, including cancers. Regulators such as KDM1 have become potential therapeutic targets because of the reversibility of epigenetic control of genome function. Indeed, several classes of KDM1-selective small molecule inhibitors have been developed, some of which are currently in clinical trials to treat various cancers. In this chapter, we review the discovery, biochemical, and molecular mechanisms, atomic structure, genetics, biology, and pathology of the KDM1 family of lysine demethylases. Focusing on cancer, we also provide a comprehensive summary of recently developed KDM1 inhibitors and related preclinical and clinical studies to provide a better understanding of the mechanisms of action and applications of these KDM1-specific inhibitors in therapeutic treatment.
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Affiliation(s)
- Fei Mao
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yujiang Geno Shi
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China.
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Li Y, Zhao Y, Li X, Zhai L, Zheng H, Yan Y, Fu Q, Ma J, Fu H, Zhang Z, Li Z. Biological and therapeutic role of LSD1 in Alzheimer’s diseases. Front Pharmacol 2022; 13:1020556. [PMID: 36386192 PMCID: PMC9640401 DOI: 10.3389/fphar.2022.1020556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Alzheimer’s disease (AD) is a common chronic neurodegenerative disease characterized by cognitive learning and memory impairments, however, current treatments only provide symptomatic relief. Lysine-specific demethylase 1 (LSD1), regulating the homeostasis of histone methylation, plays an important role in the pathogenesis of many neurodegenerative disorders. LSD1 functions in regulating gene expression via transcriptional repression or activation, and is involved in initiation and progression of AD. Pharmacological inhibition of LSD1 has shown promising therapeutic benefits for AD treatment. In this review, we attempt to elaborate on the role of LSD1 in some aspects of AD including neuroinflammation, autophagy, neurotransmitters, ferroptosis, tau protein, as well as LSD1 inhibitors under clinical assessments for AD treatment.
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Affiliation(s)
- Yu Li
- Department of Pharmacy, Yellow River Central Hospital of Yellow River Conservancy Commission, Zhengzhou, China
| | - Yuanyuan Zhao
- Department of Pharmacy, Yellow River Central Hospital of Yellow River Conservancy Commission, Zhengzhou, China
| | - Xiaona Li
- Department of Pharmacy, Yellow River Central Hospital of Yellow River Conservancy Commission, Zhengzhou, China
| | - Liuqun Zhai
- Department of Pharmacy, Yellow River Central Hospital of Yellow River Conservancy Commission, Zhengzhou, China
| | - Hua Zheng
- Department of Pharmacy, Yellow River Central Hospital of Yellow River Conservancy Commission, Zhengzhou, China
| | - Ying Yan
- Department of Pharmacy, Yellow River Central Hospital of Yellow River Conservancy Commission, Zhengzhou, China
| | - Qiang Fu
- Department of Pharmacy, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinlian Ma
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Haier Fu
- Department of Pharmacy, Yellow River Central Hospital of Yellow River Conservancy Commission, Zhengzhou, China
- *Correspondence: Haier Fu, ; Zhenqiang Zhang, ; Zhonghua Li,
| | - Zhenqiang Zhang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
- *Correspondence: Haier Fu, ; Zhenqiang Zhang, ; Zhonghua Li,
| | - Zhonghua Li
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
- *Correspondence: Haier Fu, ; Zhenqiang Zhang, ; Zhonghua Li,
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Rivera C, Verbel-Vergara D, Arancibia D, Lappala A, González M, Guzmán F, Merello G, Lee JT, Andrés ME. Revealing RCOR2 as a regulatory component of nuclear speckles. Epigenetics Chromatin 2021; 14:51. [PMID: 34819154 PMCID: PMC8611983 DOI: 10.1186/s13072-021-00425-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/31/2021] [Indexed: 12/26/2022] Open
Abstract
Background Nuclear processes such as transcription and RNA maturation can be impacted by subnuclear compartmentalization in condensates and nuclear bodies. Here, we characterize the nature of nuclear granules formed by REST corepressor 2 (RCOR2), a nuclear protein essential for pluripotency maintenance and central nervous system development. Results Using biochemical approaches and high-resolution microscopy, we reveal that RCOR2 is localized in nuclear speckles across multiple cell types, including neurons in the brain. RCOR2 forms complexes with nuclear speckle components such as SON, SRSF7, and SRRM2. When cells are exposed to chemical stress, RCOR2 behaves as a core component of the nuclear speckle and is stabilized by RNA. In turn, nuclear speckle morphology appears to depend on RCOR2. Specifically, RCOR2 knockdown results larger nuclear speckles, whereas overexpressing RCOR2 leads to smaller and rounder nuclear speckles. Conclusion Our study suggests that RCOR2 is a regulatory component of the nuclear speckle bodies, setting this co-repressor protein as a factor that controls nuclear speckles behavior. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00425-4.
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Affiliation(s)
- Carlos Rivera
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile.,Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6624, Boston, MA, 02114, USA.,Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02114, USA
| | - Daniel Verbel-Vergara
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Duxan Arancibia
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Anna Lappala
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6624, Boston, MA, 02114, USA.,Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02114, USA
| | - Marcela González
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Fabián Guzmán
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Gianluca Merello
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6624, Boston, MA, 02114, USA. .,Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02114, USA.
| | - María Estela Andrés
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile.
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8
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Chen L, Zhang M, Fang L, Yang X, Cao N, Xu L, Shi L, Cao Y. Coordinated regulation of the ribosome and proteasome by PRMT1 in the maintenance of neural stemness in cancer cells and neural stem cells. J Biol Chem 2021; 297:101275. [PMID: 34619150 PMCID: PMC8546425 DOI: 10.1016/j.jbc.2021.101275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/19/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022] Open
Abstract
Previous studies suggested that cancer cells resemble neural stem/progenitor cells in regulatory network, tumorigenicity, and differentiation potential, and that neural stemness might represent the ground or basal state of differentiation and tumorigenicity. The neural ground state is reflected in the upregulation and enrichment of basic cell machineries and developmental programs, such as cell cycle, ribosomes, proteasomes, and epigenetic factors, in cancers and in embryonic neural or neural stem cells. However, how these machineries are concertedly regulated is unclear. Here, we show that loss of neural stemness in cancer or neural stem cells via muscle-like differentiation or neuronal differentiation, respectively, caused downregulation of ribosome and proteasome components and major epigenetic factors, including PRMT1, EZH2, and LSD1. Furthermore, inhibition of PRMT1, an oncoprotein that is enriched in neural cells during embryogenesis, caused neuronal-like differentiation, downregulation of a similar set of proteins downregulated by differentiation, and alteration of subcellular distribution of ribosome and proteasome components. By contrast, PRMT1 overexpression led to an upregulation of these proteins. PRMT1 interacted with these components and protected them from degradation via recruitment of the deubiquitinase USP7, also known to promote cancer and enriched in embryonic neural cells, thereby maintaining a high level of epigenetic factors that maintain neural stemness, such as EZH2 and LSD1. Taken together, our data indicate that PRMT1 inhibition resulted in repression of cell tumorigenicity. We conclude that PRMT1 coordinates ribosome and proteasome activity to match the needs for high production and homeostasis of proteins that maintain stemness in cancer and neural stem cells.
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Affiliation(s)
- Lu Chen
- Research Institute of Nanjing University in Shenzhen, Shenzhen, China; MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China
| | - Min Zhang
- Research Institute of Nanjing University in Shenzhen, Shenzhen, China; MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China
| | - Xiaoli Yang
- Research Institute of Nanjing University in Shenzhen, Shenzhen, China; MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China
| | - Ning Cao
- Research Institute of Nanjing University in Shenzhen, Shenzhen, China; MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China
| | - Liyang Xu
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China
| | - Lihua Shi
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China
| | - Ying Cao
- Research Institute of Nanjing University in Shenzhen, Shenzhen, China; MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine of the Medical School, Nanjing University, Nanjing, China.
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9
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Nandakumar S, Shahani P, Datta I, Pal R. Interventional Strategies for Parkinson Disease: Can Neural Precursor Cells Forge a Path Ahead? ACS Chem Neurosci 2021; 12:3785-3794. [PMID: 34628850 DOI: 10.1021/acschemneuro.1c00525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neural precursor cells (NPCs), derived from pluripotent stem cells (PSCs), with their unique ability to generate multiple neuronal and glial cell types are extremely useful for understanding biological mechanisms in normal and diseased states. However, generation of specific neuronal subtypes (mature) from NPCs in large numbers adequate for cell therapy is challenging due to lack of a thorough understanding of the cues that govern their differentiation. Interestingly, neural stem cells (NSCs) themselves are in consideration for therapy given their potency to form different neural cell types, release of trophic factors, and immunomodulatory effects that confer neuroprotection. With the recent COVID-19 outbreak and its accompanying neurological indications, the immunomodulatory role of NSCs may gain additional significance in the prevention of disease progression in vulnerable populations. In this regard, small-molecule mediated NPC generation from PSCs via NSC formation has become an important strategy that ensures consistency and robustness of the process. The development of the mammalian brain occurs along the rostro-caudal axis, and the establishment of anterior identity is an early event. Wnt signaling, along with fibroblast growth factor and retinoic acid, acts as a caudalization signal. Further, the increasing amount of epigenetic data available from human fetal brain development has enhanced both our understanding of and ability to experimentally manipulate these developmental regulatory programs in vitro. However, the impact on homing and engraftment after transplantation and subsequently on therapeutic efficacy of NPCs based on their derivation strategy is not yet clear. Another formidable challenge in cell replacement therapy for neurodegenerative disorders is the mode of delivery. In this Perspective, we discuss these core ideas with insights from our preliminary studies exploring the role of PSC-derived NPCs in rat models of MPTP-induced Parkinson's disease following intranasal injections.
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Affiliation(s)
- Swapna Nandakumar
- Eyestem Research, Centre for Cellular and Molecular Platforms (C-CAMP), Bengaluru 560065, Karnataka, India
| | - Pradnya Shahani
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru 560029, Karnataka, India
| | - Indrani Datta
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru 560029, Karnataka, India
| | - Rajarshi Pal
- Eyestem Research, Centre for Cellular and Molecular Platforms (C-CAMP), Bengaluru 560065, Karnataka, India
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10
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Noches V, Rivera C, González MP, Merello G, Olivares-Costa M, Andrés ME. Pilocarpine-induced seizures associate with modifications of LSD1/CoREST/HDAC1/2 epigenetic complex and repressive chromatin in mice hippocampus. Biochem Biophys Rep 2021; 25:100889. [PMID: 33426312 PMCID: PMC7779720 DOI: 10.1016/j.bbrep.2020.100889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 11/28/2022] Open
Abstract
Epilepsy is a neurological disorder of genetic or environmental origin characterized by recurrent spontaneous seizures. A rodent model of temporal lobe epilepsy is induced by a single administration of pilocarpine, a non-selective cholinergic muscarinic receptor agonist. The molecular changes associated with pilocarpine-induced seizures are still poorly described. Epigenetic multiprotein complexes that regulate gene expression by changing the structure of chromatin impose transcriptional memories. Among the epigenetic enzymes relevant to the epileptogenic process is lysine-specific demethylase 1 (LSD1, KDM1A), which regulates the expression of genes that control neuronal excitability. LSD1 forms complexes with the CoREST family of transcriptional corepressors, which are molecular bridges that bring HDAC1/2 and LSD1 enzymes to deacetylate and demethylate the tail of nucleosomal histone H3. To test the hypothesis that LSD1-complexes are involved in initial modifications associated with pilocarpine-induced epilepsy, we studied the expression of main components of LSD1-complexes and the associated epigenetic marks on isolated neurons and the hippocampus of pilocarpine-treated mice. Using a single injection of 300 mg/kg of pilocarpine and after 24 h, we found that protein levels of LSD1, CoREST2, and HDAC1/2 increased, while CoREST1 decreased in the hippocampus. In addition, we observed increased histone H3 lysine 9 di- and trimethylation (H3K9me2/3) and decreased histone H3 lysine 4 di and trimethylation (H3K4me2/3). Similar findings were observed in cultured hippocampal neurons and HT-22 hippocampal cell line treated with pilocarpine. In conclusion, our data show that muscarinic receptor activation by pilocarpine induces a global repressive state of chromatin and prevalence of LSD1-CoREST2 epigenetic complexes, modifications that could underlie the pathophysiological processes leading to epilepsy.
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Key Words
- CoREST, Corepressor for element-1 silencing transcription factor
- H3K4me2
- H3K4me2, histone H3 lysine 4 dimethylation
- H3K4me3, histone H3 lysine 4 trimethylation
- H3K9me2
- H3K9me2, histone H3 lysine 9 dimethylation
- H3K9me3, histone H3 lysine 9 trimethylation
- H3ac, Histone H3 acetylated
- HDAC, Histone deacetylase
- HP1α, heterochromatin protein 1α
- LCH Complex, LSD1/CoREST/HDACs complex
- LCH complex
- LSD1, lysine-specific demethylase 1
- Muscarinic receptors
- Pilo, Pilocarpine
- Pilocarpine
- SMN, Scopolamine Methyl Nitrate
- Status epilepticus
- TLE, Temporal Lobe Epilepsy
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Affiliation(s)
- Verónica Noches
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Rivera
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela P González
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gianluca Merello
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Montserrat Olivares-Costa
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Estela Andrés
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
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11
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More than a Corepressor: The Role of CoREST Proteins in Neurodevelopment. eNeuro 2020; 7:ENEURO.0337-19.2020. [PMID: 32075869 PMCID: PMC7070449 DOI: 10.1523/eneuro.0337-19.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/19/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The molecular mechanisms governing normal neurodevelopment are tightly regulated by the action of transcription factors. Repressor element 1 (RE1) silencing transcription factor (REST) is widely documented as a regulator of neurogenesis that acts by recruiting corepressor proteins and repressing neuronal gene expression in non-neuronal cells. The REST corepressor 1 (CoREST1), CoREST2, and CoREST3 are best described for their role as part of the REST complex. However, recent evidence has shown the proteins have the ability to repress expression of distinct target genes in a REST-independent manner. These findings indicate that each CoREST paralogue may have distinct and critical roles in regulating neurodevelopment and are more than simply “REST corepressors,” whereby they act as independent repressors orchestrating biological processes during neurodevelopment.
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12
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Kidnapillai S, Wade B, Bortolasci CC, Panizzutti B, Spolding B, Connor T, Crowley T, Jamain S, Gray L, Leboyer M, Berk M, Walder K. Drugs used to treat bipolar disorder act via microRNAs to regulate expression of genes involved in neurite outgrowth. J Psychopharmacol 2020; 34:370-379. [PMID: 31913086 DOI: 10.1177/0269881119895534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND The drugs commonly used to treat bipolar disorder have limited efficacy and drug discovery is hampered by the paucity of knowledge of the pathophysiology of this disease. This study aims to explore the role of microRNAs in bipolar disorder and understand the molecular mechanisms of action of commonly used bipolar disorder drugs. METHODS The transcriptional effects of bipolar disorder drug combination (lithium, valproate, lamotrigine and quetiapine) in cultured human neuronal cells were studied using next generation sequencing. Differential expression of genes (n=20) and microRNAs (n=6) was assessed and the differentially expressed microRNAs were confirmed with TaqMan MicroRNA Assays. The expression of the differentially expressed microRNAs were inhibited to determine bipolar disorder drug effects on their target genes (n=8). Independent samples t-test was used for normally distributed data and Kruskal-Wallis/Mann-Whitney U test was used for data not distributed normally. Significance levels were set at p<0.05. RESULTS We found that bipolar disorder drugs tended to increase the expression of miR-128 and miR-378 (p<0.05). Putative target genes of these microRNAs targeted pathways including those identified as "neuron projection development" and "axonogenesis". Many of the target genes are inhibitors of neurite outgrowth and neurogenesis and were downregulated following bipolar disorder drug combination treatment (all p<0.05). The bipolar disorder drug combination tended to decrease the expression of the target genes (NOVA1, GRIN3A, and VIM), however this effect could be reversed by the application of microRNA inhibitors. CONCLUSIONS We conclude that at a transcriptional level, bipolar disorder drugs affect several genes in concert that would increase neurite outgrowth and neurogenesis and hence neural plasticity, and that this effect is mediated (at least in part) by modulation of the expression of these two key microRNAs.
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Affiliation(s)
| | - Ben Wade
- Centre for Molecular and Medical Research, Deakin University, Geelong, VIC, Australia
| | - Chiara C Bortolasci
- Centre for Molecular and Medical Research, Deakin University, Geelong, VIC, Australia
| | - Bruna Panizzutti
- Laboratory of Molecular Psychiatry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Briana Spolding
- Centre for Molecular and Medical Research, Deakin University, Geelong, VIC, Australia
| | - Timothy Connor
- Centre for Molecular and Medical Research, Deakin University, Geelong, VIC, Australia
| | - Tamsyn Crowley
- Centre for Molecular and Medical Research, Deakin University, Geelong, VIC, Australia.,Bioinformatics Core Research Facility (BCRF), Deakin University, Geelong, VIC, Australia
| | | | - Laura Gray
- Centre for Molecular and Medical Research, Deakin University, Geelong, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | | | - Michael Berk
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia.,Orygen, National Centre of Excellence in Youth Mental Health, Parkville, VIC, Australia
| | - Ken Walder
- Centre for Molecular and Medical Research, Deakin University, Geelong, VIC, Australia
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13
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Monestime CM, Taibi A, Gates KP, Jiang K, Sirotkin HI. CoRest1 regulates neurogenesis in a stage‐dependent manner. Dev Dyn 2019; 248:918-930. [DOI: 10.1002/dvdy.86] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Andrew Taibi
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Keith P. Gates
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Karen Jiang
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Howard I. Sirotkin
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
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14
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Lei A, Chen L, Zhang M, Yang X, Xu L, Cao N, Zhang Z, Cao Y. EZH2 Regulates Protein Stability via Recruiting USP7 to Mediate Neuronal Gene Expression in Cancer Cells. Front Genet 2019; 10:422. [PMID: 31130994 PMCID: PMC6510286 DOI: 10.3389/fgene.2019.00422] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
Misexpression of chromatin modification factors and changed epigenetic modifications play crucial roles for tumorigenesis. Our previous studies demonstrated that inhibition of epigenetic modification enzymes EZH2, LSD1, DNMTs, and HDACs caused post-mitotic neuron-like differentiation in different cancer cells. However, how they regulate neuronal differentiation in cancer cells was unknown. Here, we show that EZH2, LSD1, DNMT1, and HDAC1 form interactions themselves, meanwhile, they also interact with SMAD proteins and β-CATENIN in cancer cells. Chemical inhibition of these enzymes leads to reduced level of proteins except HDAC1. The change in protein level and/or enzymatic activities further result in changed chromatin modifications on neuronal gene promoters, and activation of neuronal genes. Inhibition of these enzymes in neural progenitor cells (NPCs) also caused neuronal differentiation, similar to cancer cells. Particularly, EZH2 interacts with and required for the stability of LSD1, HDAC1, DNMT1, β-CATENIN, or SMAD2/4, via recruitment of deubiquitinase USP7. Reduced EZH2 leads to enhanced ubiquitination and degradation of these proteins, and decreased binding of LSD1, HDAC1, and DNMT1 to neuronal gene promoters, and lessened Wnt and TGFβ target gene activation. Hence, EZH2 sustains a series of proteins that promote tumorigenesis, in addition to its original function of histone methylation. Considering together with other studies, we conclude that these chromatin modification factors function in the same way in cancer cells as in neural progenitor/stem cells. The similarity between cancer cells and neural progenitor/stem cells provides an insight into the essence and unified framework for cancer initiation and progression, and are suggestive for novel strategies of cancer therapy.
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Affiliation(s)
- Anhua Lei
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Lu Chen
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Min Zhang
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Xiaoli Yang
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Liyang Xu
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Ning Cao
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Zan Zhang
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Ying Cao
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
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15
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PIASγ controls stability and facilitates SUMO-2 conjugation to CoREST family of transcriptional co-repressors. Biochem J 2018; 475:1441-1454. [PMID: 29555846 DOI: 10.1042/bcj20170983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 02/05/2023]
Abstract
CoREST family of transcriptional co-repressors regulates gene expression and cell fate determination during development. CoREST co-repressors recruit with different affinity the histone demethylase LSD1 (KDM1A) and the deacetylases HDAC1/2 to repress with variable strength the expression of target genes. CoREST protein levels are differentially regulated during cell fate determination and in mature tissues. However, regulatory mechanisms of CoREST co-repressors at the protein level have not been studied. Here, we report that CoREST (CoREST1, RCOR1) and its homologs CoREST2 (RCOR2) and CoREST3 (RCOR3) interact with PIASγ (protein inhibitor of activated STAT), a SUMO (small ubiquitin-like modifier)-E3-ligase. PIASγ increases the stability of CoREST proteins and facilitates their SUMOylation by SUMO-2. Interestingly, the SUMO-conjugating enzyme, Ubc9 also facilitates the SUMOylation of CoREST proteins. However, it does not change their protein levels. Specificity was shown using the null enzymatic form of PIASγ (PIASγ-C342A) and the SUMO protease SENP-1, which reversed SUMOylation and the increment of CoREST protein levels induced by PIASγ. The major SUMO acceptor lysines are different and are localized in nonconserved sequences among CoREST proteins. SUMOylation-deficient CoREST1 and CoREST3 mutants maintain a similar interaction profile with LSD1 and HDAC1/2, and consequently maintain similar repressor capacity compared with wild-type counterparts. In conclusion, CoREST co-repressors form protein complexes with PIASγ, which acts both as SUMO E3-ligase and as a protein stabilizer for CoREST proteins. This novel regulation of CoREST by PIASγ interaction and SUMOylation may serve to control cell fate determination during development.
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16
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Wang L, Yang H, Lin X, Cao Y, Gao P, Zheng Y, Fan Z. KDM1A regulated the osteo/dentinogenic differentiation process of the stem cells of the apical papilla via binding with PLOD2. Cell Prolif 2018; 51:e12459. [PMID: 29656462 DOI: 10.1111/cpr.12459] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/14/2018] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Dental tissue-derived mesenchymal stem cells (MSCs)-mediated pulp-dentin regeneration is considered a potential approach for the regeneration of damaged teeth. Enhancing MSC-mediated pulp-dentin regeneration is based on an understanding of the molecular mechanisms underlying directed cell differentiation process. Histone demethylation enzyme, lysine demethylase 1A (KDM1A) can regulate the differentiation of some MSCs, but its role in dental tissue-derived MSCs is unclear. MATERIAL AND METHODS We obtained SCAPs from immature teeth. Alkaline phosphatase (ALP) activity assay, Alizarin red staining, quantitative calcium analysis, osteogenesis-related genes expression and in vivo transplantation experiment were used to explore the osteo/dentinogenic differentiation. Co-immunoprecipitation (Co-IP) assay was used to investigate the binding protein. RESULTS Knock-down of KDM1A reduced ALP activity and mineralization, promoted the expressions of osteo/dentinogenic differentiation markers DSPP, DMP1, BSP and key transcript factors, RUNX2, OSX, DLX2 in SCAPs, and also enhanced the osteo/dentinogenesis in vivo. In addition, KDM1A could associate with PLOD2 to form protein complex. And knock-down of PLOD2 inhibited ALP activity and mineralization, and promoted the expressions of DSPP, DMP1, BSP, RUNX2, OSX and DLX2 in SCAPs. CONCLUSIONS KDM1A might have different role in different stages of osteo/dentinogenic differentiation process by binding partner with PLOD2, and finally resulted in the inhibited function for the osteo/dentinogenesis in SCAPs. Our studies provided a further understanding of the regulatory mechanisms of dynamic osteo/dentinogenic differentiation process in dental tissue MSCs.
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Affiliation(s)
- Lijun Wang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Endodontics, Capital Medical University School of Stomatology, Beijing, China
| | - Haoqing Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Xiao Lin
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Implant Dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Yangyang Cao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Peipei Gao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Ying Zheng
- Department of Endodontics, Capital Medical University School of Stomatology, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
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Podobinska M, Szablowska-Gadomska I, Augustyniak J, Sandvig I, Sandvig A, Buzanska L. Epigenetic Modulation of Stem Cells in Neurodevelopment: The Role of Methylation and Acetylation. Front Cell Neurosci 2017; 11:23. [PMID: 28223921 PMCID: PMC5293809 DOI: 10.3389/fncel.2017.00023] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022] Open
Abstract
The coordinated development of the nervous system requires fidelity in the expression of specific genes determining the different neural cell phenotypes. Stem cell fate decisions during neurodevelopment are strictly correlated with their epigenetic status. The epigenetic regulatory processes, such as DNA methylation and histone modifications discussed in this review article, may impact both neural stem cell (NSC) self-renewal and differentiation and thus play an important role in neurodevelopment. At the same time, stem cell decisions regarding fate commitment and differentiation are highly dependent on the temporospatial expression of specific genes contingent on the developmental stage of the nervous system. An interplay between the above, as well as basic cell processes, such as transcription regulation, DNA replication, cell cycle regulation and DNA repair therefore determine the accuracy and function of neuronal connections. This may significantly impact embryonic health and development as well as cognitive processes such as neuroplasticity and memory formation later in the adult.
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Affiliation(s)
- Martyna Podobinska
- Stem Cell Bioengineering Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences Warsaw, Poland
| | | | - Justyna Augustyniak
- Stem Cell Bioengineering Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences Warsaw, Poland
| | - Ioanna Sandvig
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU) Trondheim, Norway
| | - Axel Sandvig
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU) Trondheim, Norway
| | - Leonora Buzanska
- Stem Cell Bioengineering Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences Warsaw, Poland
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Ferreira RC, Popova EY, James J, Briones MRS, Zhang SS, Barnstable CJ. Histone Deacetylase 1 Is Essential for Rod Photoreceptor Differentiation by Regulating Acetylation at Histone H3 Lysine 9 and Histone H4 Lysine 12 in the Mouse Retina. J Biol Chem 2016; 292:2422-2440. [PMID: 28028172 DOI: 10.1074/jbc.m116.756643] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/22/2016] [Indexed: 01/19/2023] Open
Abstract
Histone acetylation has a regulatory role in gene expression and is necessary for proper tissue development. To investigate the specific roles of histone deacetylases (HDACs) in rod differentiation in neonatal mouse retinas, we used a pharmacological approach that showed that inhibition of class I but not class IIa HDACs caused the same phenotypic changes seen with broad spectrum HDAC inhibitors, most notably a block in the differentiation of rod photoreceptors. Inhibition of HDAC1 resulted in increase of acetylation of lysine 9 of histone 3 (H3K9) and lysine 12 of histone 4 (H4K12) but not lysine 27 of histone 3 (H3K27) and led to maintained expression of progenitor-specific genes such as Vsx2 and Hes1 with concomitant block of expression of rod-specific genes. ChiP experiments confirmed these changes in the promoters of a group of progenitor genes. Based on our results, we suggest that HDAC1-specific inhibition prevents progenitor cells of the retina from exiting the cell cycle and differentiating. HDAC1 may be an essential epigenetic regulator of the transition from progenitor cells to terminally differentiated photoreceptors.
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Affiliation(s)
- Renata C Ferreira
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Laboratory of Evolutionary Genomics and Biocomplexity, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Evgenya Y Popova
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
| | - Jessica James
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033
| | - Marcelo R S Briones
- Laboratory of Evolutionary Genomics and Biocomplexity, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Samuel S Zhang
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
| | - Colin J Barnstable
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033, .,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
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Garay PM, Wallner MA, Iwase S. Yin-yang actions of histone methylation regulatory complexes in the brain. Epigenomics 2016; 8:1689-1708. [PMID: 27855486 PMCID: PMC5289040 DOI: 10.2217/epi-2016-0090] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/05/2016] [Indexed: 02/07/2023] Open
Abstract
Dysregulation of histone methylation has emerged as a major driver of neurodevelopmental disorders including intellectual disabilities and autism spectrum disorders. Histone methyl writer and eraser enzymes generally act within multisubunit complexes rather than in isolation. However, it remains largely elusive how such complexes cooperate to achieve the precise spatiotemporal gene expression in the developing brain. Histone H3K4 methylation (H3K4me) is a chromatin signature associated with active gene-regulatory elements. We review a body of literature that supports a model in which the RAI1-containing H3K4me writer complex counterbalances the LSD1-containing H3K4me eraser complex to ensure normal brain development. This model predicts H3K4me as the nexus of previously unrelated neurodevelopmental disorders.
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Affiliation(s)
- Patricia Marie Garay
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Shigeki Iwase
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI 48109, USA
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20
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Speranzini V, Pilotto S, Sixma TK, Mattevi A. Touch, act and go: landing and operating on nucleosomes. EMBO J 2016; 35:376-88. [PMID: 26787641 DOI: 10.15252/embj.201593377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022] Open
Abstract
Chromatin-associated enzymes are responsible for the installation, removal and reading of precise post-translation modifications on DNA and histone proteins. They are specifically recruited to the target gene by associated factors, and as a result of their activity, they contribute in modulating cell identity and differentiation. Structural and biophysical approaches are broadening our knowledge on these processes, demonstrating that DNA, histone tails and histone surfaces can each function as distinct yet functionally interconnected anchoring points promoting nucleosome binding and modification. The mechanisms underlying nucleosome recognition have been described for many histone modifiers and related readers. Here, we review the recent literature on the structural organization of these nucleosome-associated proteins, the binding properties that drive nucleosome modification and the methodological advances in their analysis. The overarching conclusion is that besides acting on the same substrate (the nucleosome), each system functions through characteristic modes of action, which bring about specific biological functions in gene expression regulation.
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Affiliation(s)
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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21
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Correction: Decreased Expression of CoREST1 and CoREST2 Together with LSD1 and HDAC1/2 during Neuronal Differentiation. PLoS One 2015; 10:e0133555. [PMID: 26186538 PMCID: PMC4505873 DOI: 10.1371/journal.pone.0133555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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