1
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Zhao A, Xu W, Han R, Wei J, Yu Q, Wang M, Li H, Li M, Chi G. Role of histone modifications in neurogenesis and neurodegenerative disease development. Ageing Res Rev 2024; 98:102324. [PMID: 38762100 DOI: 10.1016/j.arr.2024.102324] [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: 12/10/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Progressive neuronal dysfunction and death are key features of neurodegenerative diseases; therefore, promoting neurogenesis in neurodegenerative diseases is crucial. With advancements in proteomics and high-throughput sequencing technology, it has been demonstrated that histone post-transcriptional modifications (PTMs) are often altered during neurogenesis when the brain is affected by disease or external stimuli and that the degree of histone modification is closely associated with the development of neurodegenerative diseases. This review aimed to show the regulatory role of histone modifications in neurogenesis and neurodegenerative diseases by discussing the changing patterns and functional significance of histone modifications, including histone methylation, acetylation, ubiquitination, phosphorylation, and lactylation. Finally, we explored the control of neurogenesis and the development of neurodegenerative diseases by artificially modulating histone modifications.
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Affiliation(s)
- Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Rui Han
- Department of Neurovascular Surgery, First Hospital of Jilin University, Changchun, 130021, China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Haokun Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
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2
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Temgire P, Arthur R, Kumar P. Neuroinflammation and the role of epigenetic-based therapies for Huntington's disease management: the new paradigm. Inflammopharmacology 2024; 32:1791-1804. [PMID: 38653938 DOI: 10.1007/s10787-024-01477-0] [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: 06/20/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Huntington's disease (HD) is an inherited, autosomal, neurodegenerative ailment that affects the striatum of the brain. Despite its debilitating effect on its patients, there is no proven cure for HD management as of yet. Neuroinflammation, excitotoxicity, and environmental factors have been reported to influence the regulation of gene expression by modifying epigenetic mechanisms. Aside focusing on the etiology, changes in epigenetic mechanisms have become a crucial factor influencing the interaction between HTT protein and epigenetically transcribed genes involved in neuroinflammation and HD. This review presents relevant literature on epigenetics with special emphasis on neuroinflammation and HD. It summarizes pertinent research on the role of neuroinflammation and post-translational modifications of chromatin, including DNA methylation, histone modification, and miRNAs. To achieve this about 1500 articles were reviewed via databases like PubMed, ScienceDirect, Google Scholar, and Web of Science. They were reduced to 534 using MeSH words like 'epigenetics, neuroinflammation, and HD' coupled with Boolean operators. Results indicated that major contributing factors to the development of HD such as mitochondrial dysfunction, excitotoxicity, neuroinflammation, and apoptosis are affected by epigenetic alterations. However, the association between neuroinflammation-altered epigenetics and the reported transcriptional changes in HD is unknown. Also, the link between epigenetically dysregulated genomic regions and specific DNA sequences suggests the likelihood that transcription factors, chromatin-remodeling proteins, and enzymes that affect gene expression are all disrupted simultaneously. Hence, therapies that target pathogenic pathways in HD, including neuroinflammation, transcriptional dysregulation, triplet instability, vesicle trafficking dysfunction, and protein degradation, need to be developed.
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Affiliation(s)
- Pooja Temgire
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
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3
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Thompson LM, Orr HT. HD and SCA1: Tales from two 30-year journeys since gene discovery. Neuron 2023; 111:3517-3530. [PMID: 37863037 PMCID: PMC10842341 DOI: 10.1016/j.neuron.2023.09.036] [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: 03/24/2023] [Revised: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023]
Abstract
One of the more transformative findings in human genetics was the discovery that the expansion of unstable nucleotide repeats underlies a group of inherited neurological diseases. A subset of these unstable repeat neurodegenerative diseases is due to the expansion of a CAG trinucleotide repeat encoding a stretch of glutamines, i.e., the polyglutamine (polyQ) repeat neurodegenerative diseases. Among the CAG/polyQ repeat diseases are Huntington's disease (HD) and spinocerebellar ataxia type 1 (SCA1), in which the expansions are within widely expressed proteins. Although both HD and SCA1 are autosomal dominantly inherited, and both typically cause mid- to late-life-onset movement disorders with cognitive decline, they each are characterized by distinct clinical characteristics and predominant sites of neuropathology. Importantly, the respective affected proteins, Huntingtin (HTT, HD) and Ataxin 1 (ATXN1, SCA1), have unique functions and biological properties. Here, we review HD and SCA1 with a focus on how their disease-specific and shared features may provide informative insights.
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Affiliation(s)
- Leslie M Thompson
- Department of Psychiatry and Human Behavior, Department of Neurobiology and Behavior, Department of Biological Chemistry, Institute of Memory Impairments and Neurological Disorders, Sue and Bill Gross Stem Cell Center, University of California Irvine, Irvine, CA 92697, USA
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis and Saint Paul, MN 55455, USA.
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4
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Nguyen TB, Miramontes R, Chillon-Marinas C, Maimon R, Vazquez-Sanchez S, Lau AL, McClure NR, England WE, Singha M, Stocksdale JT, Jang KH, Jung S, McKnight JI, Ho LN, Faull RLM, Steffan JS, Reidling JC, Jang C, Lee G, Cleveland DW, Lagier-Tourenne C, Spitale RC, Thompson LM. Aberrant splicing in Huntington's disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565004. [PMID: 37961595 PMCID: PMC10635028 DOI: 10.1101/2023.10.31.565004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene encoding huntingtin. Prior reports have established a correlation between CAG expanded HTT and altered gene expression. However, the mechanisms leading to disruption of RNA processing in HD remain unclear. Here, our analysis of the reported HTT protein interactome identifies interactions with known RNA-binding proteins (RBPs). Total, long-read sequencing and targeted RASL-seq of RNAs from cortex and striatum of the HD mouse model R6/2 reveals increased exon skipping which is confirmed in Q150 and Q175 knock-in mice and in HD human brain. We identify the RBP TDP-43 and the N6-methyladenosine (m6A) writer protein methyltransferase 3 (METTL3) to be upstream regulators of exon skipping in HD. Along with this novel mechanistic insight, we observe decreased nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 in HD mice and human brain. In addition, TDP-43 co-localizes with HTT in human HD brain forming novel nuclear aggregate-like bodies distinct from mutant HTT inclusions or previously observed TDP-43 pathologies. Binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in striatum from HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a novel mechanism underlying alternative splicing/unannotated exon usage in HD and highlights the critical nature of TDP-43 function across multiple neurodegenerative diseases.
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5
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Wang H, Guo B, Guo X. Histone demethylases in neurodevelopment and neurodegenerative diseases. Int J Neurosci 2023:1-11. [PMID: 37902510 DOI: 10.1080/00207454.2023.2276656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023]
Abstract
Neurodevelopment can be precisely regulated by epigenetic mechanisms, including DNA methylations, noncoding RNAs, and histone modifications. Histone methylation was a reversible modification, catalyzed by histone methyltransferases and demethylases. So far, dozens of histone lysine demethylases (KDMs) have been discovered, and they (members from KDM1 to KDM7 family) are important for neurodevelopment by regulating cellular processes, such as chromatin structure and gene transcription. The role of KDM5C and KDM7B in neural development is particularly important, and mutations in both genes are frequently found in human X-linked mental retardation (XLMR). Functional disorders of specific KDMs, such as KDM1A can lead to the development of neurodegenerative diseases, including Alzheimer's disease (AD) and Parkinson's disease (PD). Several KDMs can serve as potential therapeutic targets in the treatment of neurodegenerative diseases. At present, the function of KDMs in neurodegenerative diseases is not fully understood, so more comprehensive and profound studies are needed. Here, the role and mechanism of histone demethylases were summarized in neurodevelopment, and the potential of them was introduced in the treatment of neurodegenerative diseases.
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Affiliation(s)
- Haiying Wang
- Department of Sports Human Sciences, Hebei Social Science Foundation Project Research Group, Hebei Sport University, Shijiazhuang, Hebei, China
| | - Beiyi Guo
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Xiaoqiang Guo
- Department of Sports Human Sciences, Hebei Social Science Foundation Project Research Group, Hebei Sport University, Shijiazhuang, Hebei, China
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6
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Angelopoulou E, Pyrgelis ES, Ahire C, Suman P, Mishra A, Piperi C. Functional Implications of Protein Arginine Methyltransferases (PRMTs) in Neurodegenerative Diseases. BIOLOGY 2023; 12:1257. [PMID: 37759656 PMCID: PMC10525691 DOI: 10.3390/biology12091257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
During the aging of the global population, the prevalence of neurodegenerative diseases will be continuously growing. Although each disorder is characterized by disease-specific protein accumulations, several common pathophysiological mechanisms encompassing both genetic and environmental factors have been detected. Among them, protein arginine methyltransferases (PRMTs), which catalyze the methylation of arginine of various substrates, have been revealed to regulate several cellular mechanisms, including neuronal cell survival and excitability, axonal transport, synaptic maturation, and myelination. Emerging evidence highlights their critical involvement in the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS) spectrum, Huntington's disease (HD), spinal muscular atrophy (SMA) and spinal and bulbar muscular atrophy (SBMA). Underlying mechanisms include the regulation of gene transcription and RNA splicing, as well as their implication in various signaling pathways related to oxidative stress responses, apoptosis, neuroinflammation, vacuole degeneration, abnormal protein accumulation and neurotransmission. The targeting of PRMTs is a therapeutic approach initially developed against various forms of cancer but currently presents a novel potential strategy for neurodegenerative diseases. In this review, we discuss the accumulating evidence on the role of PRMTs in the pathophysiology of neurodegenerative diseases, enlightening their pathogenesis and stimulating future research.
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Affiliation(s)
- Efthalia Angelopoulou
- 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (E.A.); (E.-S.P.)
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Efstratios-Stylianos Pyrgelis
- 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (E.A.); (E.-S.P.)
| | - Chetana Ahire
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, Kamrup 781101, Assam, India; (C.A.); (P.S.)
| | - Prachi Suman
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, Kamrup 781101, Assam, India; (C.A.); (P.S.)
| | - Awanish Mishra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, Kamrup 781101, Assam, India; (C.A.); (P.S.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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7
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Jiang A, Handley RR, Lehnert K, Snell RG. From Pathogenesis to Therapeutics: A Review of 150 Years of Huntington's Disease Research. Int J Mol Sci 2023; 24:13021. [PMID: 37629202 PMCID: PMC10455900 DOI: 10.3390/ijms241613021] [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: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Huntington's disease (HD) is a debilitating neurodegenerative genetic disorder caused by an expanded polyglutamine-coding (CAG) trinucleotide repeat in the huntingtin (HTT) gene. HD behaves as a highly penetrant dominant disorder likely acting through a toxic gain of function by the mutant huntingtin protein. Widespread cellular degeneration of the medium spiny neurons of the caudate nucleus and putamen are responsible for the onset of symptomology that encompasses motor, cognitive, and behavioural abnormalities. Over the past 150 years of HD research since George Huntington published his description, a plethora of pathogenic mechanisms have been proposed with key themes including excitotoxicity, dopaminergic imbalance, mitochondrial dysfunction, metabolic defects, disruption of proteostasis, transcriptional dysregulation, and neuroinflammation. Despite the identification and characterisation of the causative gene and mutation and significant advances in our understanding of the cellular pathology in recent years, a disease-modifying intervention has not yet been clinically approved. This review includes an overview of Huntington's disease, from its genetic aetiology to clinical presentation and its pathogenic manifestation. An updated view of molecular mechanisms and the latest therapeutic developments will also be discussed.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand; (R.R.H.); (K.L.); (R.G.S.)
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8
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Speidell A, Bin Abid N, Yano H. Brain-Derived Neurotrophic Factor Dysregulation as an Essential Pathological Feature in Huntington's Disease: Mechanisms and Potential Therapeutics. Biomedicines 2023; 11:2275. [PMID: 37626771 PMCID: PMC10452871 DOI: 10.3390/biomedicines11082275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a major neurotrophin whose loss or interruption is well established to have numerous intersections with the pathogenesis of progressive neurological disorders. There is perhaps no greater example of disease pathogenesis resulting from the dysregulation of BDNF signaling than Huntington's disease (HD)-an inherited neurodegenerative disorder characterized by motor, psychiatric, and cognitive impairments associated with basal ganglia dysfunction and the ultimate death of striatal projection neurons. Investigation of the collection of mechanisms leading to BDNF loss in HD highlights this neurotrophin's importance to neuronal viability and calls attention to opportunities for therapeutic interventions. Using electronic database searches of existing and forthcoming research, we constructed a literature review with the overarching goal of exploring the diverse set of molecular events that trigger BDNF dysregulation within HD. We highlighted research that investigated these major mechanisms in preclinical models of HD and connected these studies to those evaluating similar endpoints in human HD subjects. We also included a special focus on the growing body of literature detailing key transcriptomic and epigenetic alterations that affect BDNF abundance in HD. Finally, we offer critical evaluation of proposed neurotrophin-directed therapies and assessed clinical trials seeking to correct BDNF expression in HD individuals.
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Affiliation(s)
- Andrew Speidell
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Noman Bin Abid
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Involvement of the H3.3 Histone Variant in the Epigenetic Regulation of Gene Expression in the Nervous System, in Both Physiological and Pathological Conditions. Int J Mol Sci 2023; 24:11028. [PMID: 37446205 DOI: 10.3390/ijms241311028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
All the cells of an organism contain the same genome. However, each cell expresses only a minor fraction of its potential and, in particular, the genes encoding the proteins necessary for basal metabolism and the proteins responsible for its specific phenotype. The ability to use only the right and necessary genes involved in specific functions depends on the structural organization of the nuclear chromatin, which in turn depends on the epigenetic history of each cell, which is stored in the form of a collection of DNA and protein modifications. Among these modifications, DNA methylation and many kinds of post-translational modifications of histones play a key role in organizing the complex indexing of usable genes. In addition, non-canonical histone proteins (also known as histone variants), the synthesis of which is not directly linked with DNA replication, are used to mark specific regions of the genome. Here, we will discuss the role of the H3.3 histone variant, with particular attention to its loading into chromatin in the mammalian nervous system, both in physiological and pathological conditions. Indeed, chromatin modifications that mark cell memory seem to be of special importance for the cells involved in the complex processes of learning and memory.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
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10
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Arancibia-Opazo S, Contreras-Riquelme JS, Sánchez M, Cisternas-Olmedo M, Vidal RL, Martin AJM, Sáez MA. Transcriptional and Histone Acetylation Changes Associated with CRE Elements Expose Key Factors Governing the Regulatory Circuit in the Early Stage of Huntington's Disease Models. Int J Mol Sci 2023; 24:10848. [PMID: 37446028 DOI: 10.3390/ijms241310848] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Huntington's disease (HD) is a disorder caused by an abnormal expansion of trinucleotide CAG repeats within the huntingtin (Htt) gene. Under normal conditions, the CREB Binding Protein interacts with CREB elements and acetylates Lysine 27 of Histone 3 to direct the expression of several genes. However, mutant Htt causes depletion of CBP, which in turn induces altered histone acetylation patterns and transcriptional deregulation. Here, we have studied a differential expression analysis and H3K27ac variation in 4- and 6-week-old R6/2 mice as a model of juvenile HD. The analysis of differential gene expression and acetylation levels were integrated into Gene Regulatory Networks revealing key regulators involved in the altered transcription cascade. Our results show changes in acetylation and gene expression levels that are related to impaired neuronal development, and key regulators clearly defined in 6-week-old mice are proposed to drive the downstream regulatory cascade in HD. Here, we describe the first approach to determine the relationship among epigenetic changes in the early stages of HD. We determined the existence of changes in pre-symptomatic stages of HD as a starting point for early onset indicators of the progression of this disease.
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Affiliation(s)
- Sandra Arancibia-Opazo
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago 8580745, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Universidad San Sebastián, Santiago 8580704, Chile
| | - J Sebastián Contreras-Riquelme
- Plant Genome Regulation Lab, Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Mario Sánchez
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Marisol Cisternas-Olmedo
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Biomedical Neuroscience Institute, University of Chile, Santiago 8380455, Chile
- Center for Geroscience, Brain Health, and Metabolism, Santiago 8380453, Chile
| | - René L Vidal
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Biomedical Neuroscience Institute, University of Chile, Santiago 8380455, Chile
- Center for Geroscience, Brain Health, and Metabolism, Santiago 8380453, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Alberto J M Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Universidad San Sebastián, Santiago 8580704, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 7500000, Chile
| | - Mauricio A Sáez
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Centro de Oncología de Precisión, Facultad de Medicina Universidad Mayor, Santiago 7560908, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco 4813302, Chile
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11
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Burtscher J, Pepe G, Maharjan N, Riguet N, Di Pardo A, Maglione V, Millet GP. Sphingolipids and impaired hypoxic stress responses in Huntington disease. Prog Lipid Res 2023; 90:101224. [PMID: 36898481 DOI: 10.1016/j.plipres.2023.101224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/20/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
Huntington disease (HD) is a debilitating, currently incurable disease. Protein aggregation and metabolic deficits are pathological hallmarks but their link to neurodegeneration and symptoms remains debated. Here, we summarize alterations in the levels of different sphingolipids in an attempt to characterize sphingolipid patterns specific to HD, an additional molecular hallmark of the disease. Based on the crucial role of sphingolipids in maintaining cellular homeostasis, the dynamic regulation of sphingolipids upon insults and their involvement in cellular stress responses, we hypothesize that maladaptations or blunted adaptations, especially following cellular stress due to reduced oxygen supply (hypoxia) contribute to the development of pathology in HD. We review how sphingolipids shape cellular energy metabolism and control proteostasis and suggest how these functions may fail in HD and in combination with additional insults. Finally, we evaluate the potential of improving cellular resilience in HD by conditioning approaches (improving the efficiency of cellular stress responses) and the role of sphingolipids therein. Sphingolipid metabolism is crucial for cellular homeostasis and for adaptations following cellular stress, including hypoxia. Inadequate cellular management of hypoxic stress likely contributes to HD progression, and sphingolipids are potential mediators. Targeting sphingolipids and the hypoxic stress response are novel treatment strategies for HD.
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Affiliation(s)
- Johannes Burtscher
- Institute of Sport Sciences, University of Lausanne, 1015 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland.
| | - Giuseppe Pepe
- IRCCS Neuromed, Via Dell'Elettronica, 86077 Pozzilli, Italy
| | - Niran Maharjan
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland
| | | | - Alba Di Pardo
- IRCCS Neuromed, Via Dell'Elettronica, 86077 Pozzilli, Italy
| | | | - Grégoire P Millet
- Institute of Sport Sciences, University of Lausanne, 1015 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland
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12
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Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
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Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
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13
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Fractalkine/CX3CR1-Dependent Modulation of Synaptic and Network Plasticity in Health and Disease. Neural Plast 2023; 2023:4637073. [PMID: 36644710 PMCID: PMC9833910 DOI: 10.1155/2023/4637073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 01/06/2023] Open
Abstract
CX3CR1 is a G protein-coupled receptor that is expressed exclusively by microglia within the brain parenchyma. The only known physiological CX3CR1 ligand is the chemokine fractalkine (FKN), which is constitutively expressed in neuronal cell membranes and tonically released by them. Through its key role in microglia-neuron communication, the FKN/CX3CR1 axis regulates microglial state, neuronal survival, synaptic plasticity, and a variety of synaptic functions, as well as neuronal excitability via cytokine release modulation, chemotaxis, and phagocytosis. Thus, the absence of CX3CR1 or any failure in the FKN/CX3CR1 axis has been linked to alterations in different brain functions, including changes in synaptic and network plasticity in structures such as the hippocampus, cortex, brainstem, and spinal cord. Since synaptic plasticity is a basic phenomenon in neural circuit integration and adjustment, here, we will review its modulation by the FKN/CX3CR1 axis in diverse brain circuits and its impact on brain function and adaptation in health and disease.
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14
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Mielcarek M, Isalan M. A minimal region of the HSP90AB1 promoter is suitable for ubiquitous expression in different somatic tissues with applicability for gene therapy. Front Mol Biosci 2023; 10:1175407. [PMID: 37138658 PMCID: PMC10149993 DOI: 10.3389/fmolb.2023.1175407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Huntington's disease (HD) is a multi-tissue failure disorder for which there is no cure. We have previously shown an effective therapeutic approach limited mainly to the central nervous system, based on a synthetic zinc finger (ZF) transcription repressor gene therapy, but it would be important to target other tissues as well. In this study, we identify a novel minimal HSP90AB1 promoter region that can efficiently control expression not only in the CNS but also in other affected HD tissues. This promoter-enhancer is effective in driving expression of ZF therapeutic molecules in both HD skeletal muscles and the heart, in the symptomatic R6/1 mouse model. Moreover, for the first time we show that ZF molecules repressing mutant HTT reverse transcriptional pathological remodelling in HD hearts. We conclude that this HSP90AB1 minimal promoter may be used to target multiple HD organs with therapeutic genes. The new promoter has the potential to be added to the portfolio of gene therapy promoters, for use where ubiquitous expression is needed.
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Affiliation(s)
- Michal Mielcarek
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
- *Correspondence: Mark Isalan,
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15
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Lim RG, Al-Dalahmah O, Wu J, Gold MP, Reidling JC, Tang G, Adam M, Dansu DK, Park HJ, Casaccia P, Miramontes R, Reyes-Ortiz AM, Lau A, Hickman RA, Khan F, Paryani F, Tang A, Ofori K, Miyoshi E, Michael N, McClure N, Flowers XE, Vonsattel JP, Davidson S, Menon V, Swarup V, Fraenkel E, Goldman JE, Thompson LM. Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation. Nat Commun 2022; 13:7791. [PMID: 36543778 PMCID: PMC9772349 DOI: 10.1038/s41467-022-35388-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
The complexity of affected brain regions and cell types is a challenge for Huntington's disease (HD) treatment. Here we use single nucleus RNA sequencing to investigate molecular pathology in the cortex and striatum from R6/2 mice and human HD post-mortem tissue. We identify cell type-specific and -agnostic signatures suggesting oligodendrocytes (OLs) and oligodendrocyte precursors (OPCs) are arrested in intermediate maturation states. OL-lineage regulators OLIG1 and OLIG2 are negatively correlated with CAG length in human OPCs, and ATACseq analysis of HD mouse NeuN-negative cells shows decreased accessibility regulated by OL maturation genes. The data implicates glucose and lipid metabolism in abnormal cell maturation and identify PRKCE and Thiamine Pyrophosphokinase 1 (TPK1) as central genes. Thiamine/biotin treatment of R6/1 HD mice to compensate for TPK1 dysregulation restores OL maturation and rescues neuronal pathology. Our insights into HD OL pathology spans multiple brain regions and link OL maturation deficits to abnormal thiamine metabolism.
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Affiliation(s)
- Ryan G Lim
- UCI MIND, University of California Irvine, Irvine, CA, USA
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Maxwell P Gold
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Guomei Tang
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David K Dansu
- Advanced Science Research Center at the City University of New York, New York, NY, USA
| | - Hye-Jin Park
- Advanced Science Research Center at the City University of New York, New York, NY, USA
| | - Patrizia Casaccia
- Advanced Science Research Center at the City University of New York, New York, NY, USA
| | | | - Andrea M Reyes-Ortiz
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Alice Lau
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - Richard A Hickman
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Fatima Khan
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Fahad Paryani
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Alice Tang
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Ofori
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Emily Miyoshi
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Neethu Michael
- Department of Pathology, University of California Irvine, Irvine, CA, USA
| | - Nicolette McClure
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Xena E Flowers
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, New York, NY, USA
| | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, New York, NY, USA
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ, USA
| | - Vilas Menon
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Vivek Swarup
- UCI MIND, University of California Irvine, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, New York, NY, USA.
| | - Leslie M Thompson
- UCI MIND, University of California Irvine, Irvine, CA, USA.
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA.
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA.
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA.
- Sue and Bill Gross Stem Cell Center University of California Irvine, Irvine, CA, USA.
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16
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Integrative Meta-Analysis of Huntington's Disease Transcriptome Landscape. Genes (Basel) 2022; 13:genes13122385. [PMID: 36553652 PMCID: PMC9777612 DOI: 10.3390/genes13122385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder with autosomal dominant inheritance caused by glutamine expansion in the Huntingtin gene (HTT). Striatal projection neurons (SPNs) in HD are more vulnerable to cell death. The executive striatal population is directly connected with the Brodmann Area (BA9), which is mainly involved in motor functions. Analyzing the disease samples from BA9 from the SRA database provides insights related to neuron degeneration, which helps to identify a promising therapeutic strategy. Most gene expression studies examine the changes in expression and associated biological functions. In this study, we elucidate the relationship between variants and their effect on gene/downstream transcript expression. We computed gene and transcript abundance and identified variants from RNA-seq data using various pipelines. We predicted the effect of genome-wide association studies (GWAS)/novel variants on regulatory functions. We found that many variants affect the histone acetylation pattern in HD, thereby perturbing the transcription factor networks. Interestingly, some variants affect miRNA binding as well as their downstream gene expression. Tissue-specific network analysis showed that mitochondrial, neuroinflammation, vasculature, and angiogenesis-related genes are disrupted in HD. From this integrative omics analysis, we propose that abnormal neuroinflammation acts as a two-edged sword that indirectly affects the vasculature and associated energy metabolism. Rehabilitation of blood-brain barrier functionality and energy metabolism may secure the neuron from cell death.
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17
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Zhang L, Liu Y, Lu Y, Wang G. Targeting epigenetics as a promising therapeutic strategy for treatment of neurodegenerative diseases. Biochem Pharmacol 2022; 206:115295. [DOI: 10.1016/j.bcp.2022.115295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
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18
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Altered activity-regulated H3K9 acetylation at TGF-beta signaling genes during egocentric memory in Huntington's disease. Prog Neurobiol 2022; 219:102363. [PMID: 36179935 DOI: 10.1016/j.pneurobio.2022.102363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/25/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022]
Abstract
Molecular mechanisms underlying cognitive deficits in Huntington's disease (HD), a striatal neurodegenerative disorder, are unknown. Here, we generated ChIPseq, 4Cseq and RNAseq data on striatal tissue of HD and control mice during striatum-dependent egocentric memory process. Multi-omics analyses showed altered activity-dependent epigenetic gene reprogramming of neuronal and glial genes regulating striatal plasticity in HD mice, which correlated with memory deficit. First, our data reveal that spatial chromatin re-organization and transcriptional induction of BDNF-related markers, regulating neuronal plasticity, were reduced since memory acquisition in the striatum of HD mice. Second, our data show that epigenetic memory implicating H3K9 acetylation, which established during late phase of memory process (e.g. during consolidation/recall) and contributed to glia-mediated, TGFβ-dependent plasticity, was compromised in HD mouse striatum. Specifically, memory-dependent regulation of H3K9 acetylation was impaired at genes controlling extracellular matrix and myelination. Our study investigating the interplay between epigenetics and memory identifies H3K9 acetylation and TGFβ signaling as new targets of striatal plasticity, which might offer innovative leads to improve HD.
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19
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Song S, Creus Muncunill J, Galicia Aguirre C, Tshilenge KT, Hamilton BW, Gerencser AA, Benlhabib H, Cirnaru MD, Leid M, Mooney SD, Ellerby LM, Ehrlich ME. Postnatal Conditional Deletion of Bcl11b in Striatal Projection Neurons Mimics the Transcriptional Signature of Huntington's Disease. Biomedicines 2022; 10:2377. [PMID: 36289639 PMCID: PMC9598565 DOI: 10.3390/biomedicines10102377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The dysregulation of striatal gene expression and function is linked to multiple diseases, including Huntington's disease (HD), Parkinson's disease, X-linked dystonia-parkinsonism (XDP), addiction, autism, and schizophrenia. Striatal medium spiny neurons (MSNs) make up 90% of the neurons in the striatum and are critical to motor control. The transcription factor, Bcl11b (also known as Ctip2), is required for striatal development, but the function of Bcl11b in adult MSNs in vivo has not been investigated. We conditionally deleted Bcl11b specifically in postnatal MSNs and performed a transcriptomic and behavioral analysis on these mice. Multiple enrichment analyses showed that the D9-Cre-Bcl11btm1.1Leid transcriptional profile was similar to the HD gene expression in mouse and human data sets. A Gene Ontology enrichment analysis linked D9-Cre-Bcl11btm1.1Leid to calcium, synapse organization, specifically including the dopaminergic synapse, protein dephosphorylation, and HDAC-signaling, commonly dysregulated pathways in HD. D9-Cre-Bcl11btm1.1Leid mice had decreased DARPP-32/Ppp1r1b in MSNs and behavioral deficits, demonstrating the dysregulation of a subtype of the dopamine D2 receptor expressing MSNs. Finally, in human HD isogenic MSNs, the mislocalization of BCL11B into nuclear aggregates points to a mechanism for BCL11B loss of function in HD. Our results suggest that BCL11B is important for the function and maintenance of mature MSNs and Bcl11b loss of function drives, in part, the transcriptomic and functional changes in HD.
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Affiliation(s)
- Sicheng Song
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jordi Creus Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Galicia Aguirre
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | | | - B. Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Houda Benlhabib
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Maria-Daniela Cirnaru
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mark Leid
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Lisa M. Ellerby
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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20
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Ebrahimzadeh K, Noroozi R. The emerging role of long non-coding RNAs, microRNAs, and an accelerated epigenetic age in Huntington’s disease. Front Aging Neurosci 2022; 14:987174. [PMID: 36185471 PMCID: PMC9520620 DOI: 10.3389/fnagi.2022.987174] [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: 07/05/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Huntington’s disease (HD) is a dominantly inherited neurodegenerative disease with variable clinical manifestations. Recent studies highlighted the contribution of epigenetic alterations to HD progress and onset. The potential crosstalk between different epigenetic layers and players such as aberrant expression of non-coding RNAs and methylation alterations has been found to affect the pathogenesis of HD or mediate the effects of trinucleotide expansion in its pathophysiology. Also, microRNAs have been assessed for their roles in the modulation of HD manifestations, among them are miR-124, miR-128a, hsa-miR-323b-3p, miR-432, miR-146a, miR-19a, miR-27a, miR-101, miR-9*, miR-22, miR-132, and miR-214. Moreover, long non-coding RNAs such as DNM3OS, NEAT1, Meg3, and Abhd11os are suggested to be involved in the pathogenesis of HD. An accelerated DNA methylation age is another epigenetic signature reported recently for HD. The current literature search collected recent findings of dysregulation of miRNAs or lncRNAs as well as methylation changes and epigenetic age in HD.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Kaveh Ebrahimzadeh,
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Rezvan Noroozi,
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21
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Zhao H, Xie J, Wu S, Sánchez OF, Zhang X, Freeman JL, Yuan C. Pre-differentiation exposure of PFOA induced persistent changes in DNA methylation and mitochondrial morphology in human dopaminergic-like neurons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119684. [PMID: 35764183 DOI: 10.1016/j.envpol.2022.119684] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Perfluorooctanoic acid (PFOA) is abundant in environment due to its historical uses in consumer products and industrial applications. Exposure to low doses of PFOA has been associated with various disease risks, including neurological disorders. The underlying mechanism, however, remains poorly understood. In this study, we examined the effects of low dose PFOA exposure at 0.4 and 4 μg/L on the morphology, epigenome, mitochondrion, and neuronal markers of dopaminergic (DA)-like SH-SY5Y cells. We observed persistent decreases in H3K4me3, H3K27me3 and 5 mC markers in nucleus along with alterations in nuclear size and chromatin compaction percentage in DA-like neurons differentiated from SH-SY5Y cells exposed to 0.4 and 4 μg/L PFOA. Among the selected epigenetic features, DNA methylation pattern can be used to distinguish between PFOA-exposed and naïve populations, suggesting the involvement of epigenetic regulation. Moreover, DA-like neurons with pre-differentiation PFOA exposure exhibit altered network connectivity, mitochondrial volume, and TH expression, implying impairment in DA neuron functionality. Collectively, our results revealed the prolonged effects of developmental PFOA exposure on the fitness of DA-like neurons and identified epigenome and mitochondrion as potential targets for bearing long-lasting changes contributing to increased risks of neurological diseases later in life.
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Affiliation(s)
- Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Shichen Wu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Oscar F Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Xinle Zhang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA.
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22
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Hattori Y, Matsumoto S, Morimoto S, Daini M, Toyofuku M, Matsuda S, Baba R, Murakami K, Iwatani M, Oki H, Iwasaki S, Matsumiya K, Tominari Y, Kimura H, Ito M. Design, synthesis, and structure–activity relationship of TAK-418 and its derivatives as a novel series of LSD1 inhibitors with lowered risk of hematological side effects. Eur J Med Chem 2022; 239:114522. [DOI: 10.1016/j.ejmech.2022.114522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/25/2022] [Accepted: 06/04/2022] [Indexed: 11/04/2022]
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23
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Environmental stimulation in Huntington disease patients and animal models. Neurobiol Dis 2022; 171:105725. [DOI: 10.1016/j.nbd.2022.105725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
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24
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Song Y, Zhang H, Yang X, Shi Y, Yu B. Annual review of lysine-specific demethylase 1 (LSD1/KDM1A) inhibitors in 2021. Eur J Med Chem 2022; 228:114042. [PMID: 34915312 DOI: 10.1016/j.ejmech.2021.114042] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising epigenetic target for disease treatment. Several LSD1 inhibitors have advanced into clinical trials. Following our last annual review on LSD1 inhibitors in 2020 (Eur. J. Med. Chem. 2021, 214, 113254), in this review we aim to update LSD1 inhibitors including natural products, synthetic compounds and cyclic peptides reported during 2021. Design strategies, structure-activity relationships, binding model analysis and modes of action are highlighted. In particular, two FDA-approved antihypertensive drugs raloxifene and fenoldopam were repurposed as reversible LSD1 inhibitors. The clinical candidate TAK-418 for treating neurodevelopmental disorders and PET imaging agent [18F]30 for LSD1 were identified. Moreover, dual inhibitors targeting both LSD1 and HDAC6 or tubulin displayed enhanced anti-cancer effects than single agents. These compounds further enrich the structural types of LSD1 inhibitors.
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100000, China
| | - Huiqing Zhang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoke Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Yuting Shi
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100000, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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25
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Sawant N, Morton H, Kshirsagar S, Reddy AP, Reddy PH. Mitochondrial Abnormalities and Synaptic Damage in Huntington's Disease: a Focus on Defective Mitophagy and Mitochondria-Targeted Therapeutics. Mol Neurobiol 2021; 58:6350-6377. [PMID: 34519969 DOI: 10.1007/s12035-021-02556-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/05/2021] [Indexed: 12/12/2022]
Abstract
Huntington's disease (HD) is a fatal and pure genetic disease with a progressive loss of medium spiny neurons (MSN). HD is caused by expanded polyglutamine repeats in the exon 1 of HD gene. Clinically, HD is characterized by chorea, seizures, involuntary movements, dystonia, cognitive decline, intellectual impairment, and emotional disturbances. Several years of intense research revealed that multiple cellular changes, including defective axonal transport, protein-protein interactions, defective bioenergetics, calcium dyshomeostasis, NMDAR activation, synaptic damage, mitochondrial abnormalities, and selective loss of medium spiny neurons are implicated in HD. Recent research on mutant huntingtin (mHtt) and mitochondria has found that mHtt interacts with the mitochondrial division protein, dynamin-related protein 1 (DRP1), enhances GTPase DRP1 enzymatic activity, and causes excessive mitochondrial fragmentation and abnormal distribution, leading to defective axonal transport of mitochondria and selective synaptic degeneration. Recent research also revealed that failure to remove dead and/or dying mitochondria is an early event in the disease progression. Currently, efforts are being made to reduce abnormal protein interactions and enhance synaptic mitophagy as therapeutic strategies for HD. The purpose of this article is to discuss recent research in HD progression. This article also discusses recent developments of cell and mouse models, cellular changes, mitochondrial abnormalities, DNA damage, bioenergetics, oxidative stress, mitophagy, and therapeutics strategies in HD.
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Affiliation(s)
- Neha Sawant
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Hallie Morton
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Sudhir Kshirsagar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Arubala P Reddy
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Neurology, Department of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Department of Internal Medicine, Cell Biology & Biochemistry, Public Health and School of Health Professions, Texas Tech University Health Sciences Center, Neuroscience & Pharmacology3601 4th Street, NeurologyLubbock, TX, 79430, USA.
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26
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DNA Methylation in Huntington's Disease. Int J Mol Sci 2021; 22:ijms222312736. [PMID: 34884540 PMCID: PMC8657460 DOI: 10.3390/ijms222312736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides is the major DNA modification in mammalian cells that is a key component of stable epigenetic marks. This modification, which on the one hand is reversible, while on the other hand, can be maintained through successive rounds of replication plays roles in gene regulation, genome maintenance, transgenerational epigenetic inheritance, and imprinting. Disturbed DNA methylation contributes to a wide array of human diseases from single-gene disorders to sporadic metabolic diseases or cancer. DNA methylation was also shown to affect several neurodegenerative disorders, including Huntington's disease (HD), a fatal, monogenic inherited disease. HD is caused by a polyglutamine repeat expansion in the Huntingtin protein that brings about a multifaceted pathogenesis affecting several cellular processes. Research of the last decade found complex, genome-wide DNA methylation changes in HD pathogenesis that modulate transcriptional activity and genome stability. This article reviews current evidence that sheds light on the role of DNA methylation in HD.
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27
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Kim C, Yousefian-Jazi A, Choi SH, Chang I, Lee J, Ryu H. Non-Cell Autonomous and Epigenetic Mechanisms of Huntington's Disease. Int J Mol Sci 2021; 22:12499. [PMID: 34830381 PMCID: PMC8617801 DOI: 10.3390/ijms222212499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Huntington's disease (HD) is a rare neurodegenerative disorder caused by an expansion of CAG trinucleotide repeat located in the exon 1 of Huntingtin (HTT) gene in human chromosome 4. The HTT protein is ubiquitously expressed in the brain. Specifically, mutant HTT (mHTT) protein-mediated toxicity leads to a dramatic degeneration of the striatum among many regions of the brain. HD symptoms exhibit a major involuntary movement followed by cognitive and psychiatric dysfunctions. In this review, we address the conventional role of wild type HTT (wtHTT) and how mHTT protein disrupts the function of medium spiny neurons (MSNs). We also discuss how mHTT modulates epigenetic modifications and transcriptional pathways in MSNs. In addition, we define how non-cell autonomous pathways lead to damage and death of MSNs under HD pathological conditions. Lastly, we overview therapeutic approaches for HD. Together, understanding of precise neuropathological mechanisms of HD may improve therapeutic approaches to treat the onset and progression of HD.
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Affiliation(s)
- Chaebin Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Ali Yousefian-Jazi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Seung-Hye Choi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Inyoung Chang
- Department of Biology, Boston University, Boston, MA 02215, USA;
| | - Junghee Lee
- Boston University Alzheimer’s Disease Research Center, Boston University, Boston, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Hoon Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
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28
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Holdgate GA, Bardelle C, Lanne A, Read J, O'Donovan DH, Smith JM, Selmi N, Sheppard R. Drug discovery for epigenetics targets. Drug Discov Today 2021; 27:1088-1098. [PMID: 34728375 DOI: 10.1016/j.drudis.2021.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/19/2021] [Accepted: 10/27/2021] [Indexed: 12/28/2022]
Abstract
Dysregulation of the epigenome is associated with the onset and progression of several diseases, including cancer, autoimmune, cardiovascular, and neurological disorders. Members from the three families of epigenetic proteins (readers, writers, and erasers) have been shown to be druggable using small-molecule inhibitors. Increasing knowledge of the role of epigenetics in disease and the reversibility of these modifications explain why pharmacological intervention is an attractive strategy for tackling epigenetic-based disease. In this review, we provide an overview of epigenetics drug targets, focus on approaches used for initial hit identification, and describe the subsequent role of structure-guided chemistry optimisation of initial hits to clinical candidates. We also highlight current challenges and future potential for epigenetics-based therapies.
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Affiliation(s)
- Geoffrey A Holdgate
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK.
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Jon Read
- Structure and Biophysics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Nidhal Selmi
- iLAB, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Robert Sheppard
- Medicinal Chemistry, Cardiovascular, Renal, Metabolism R&D, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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29
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Malla B, Guo X, Senger G, Chasapopoulou Z, Yildirim F. A Systematic Review of Transcriptional Dysregulation in Huntington's Disease Studied by RNA Sequencing. Front Genet 2021; 12:751033. [PMID: 34721539 PMCID: PMC8554124 DOI: 10.3389/fgene.2021.751033] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease (HD) is a chronic neurodegenerative disorder caused by an expansion of polyglutamine repeats in exon 1 of the Huntingtin gene. Transcriptional dysregulation accompanied by epigenetic alterations is an early and central disease mechanism in HD yet, the exact mechanisms and regulators, and their associated gene expression programs remain incompletely understood. This systematic review investigates genome-wide transcriptional studies that were conducted using RNA sequencing (RNA-seq) technology in HD patients and models. The review protocol was registered at the Open Science Framework (OSF). The biomedical literature and gene expression databases, PubMed and NCBI BioProject, Array Express, European Nucleotide Archive (ENA), European Genome-Phenome Archive (EGA), respectively, were searched using the defined terms specified in the protocol following the PRISMA guidelines. We conducted a complete literature and database search to retrieve all RNA-seq-based gene expression studies in HD published until August 2020, retrieving 288 articles and 237 datasets from PubMed and the databases, respectively. A total of 27 studies meeting the eligibility criteria were included in this review. Collectively, comparative analysis of the datasets revealed frequent genes that are consistently dysregulated in HD. In postmortem brains from HD patients, DNAJB1, HSPA1B and HSPB1 genes were commonly upregulated across all brain regions and cell types except for medium spiny neurons (MSNs) at symptomatic disease stage, and HSPH1 and SAT1 genes were altered in expression in all symptomatic brain datasets, indicating early and sustained changes in the expression of genes related to heat shock response as well as response to misfolded proteins. Specifically in indirect pathway medium spiny neurons (iMSNs), mitochondria related genes were among the top uniquely dysregulated genes. Interestingly, blood from HD patients showed commonly differentially expressed genes with a number of brain regions and cells, with the highest number of overlapping genes with MSNs and BA9 region at symptomatic stage. We also found the differential expression and predicted altered activity of a set of transcription factors and epigenetic regulators, including BCL6, EGR1, FOSL2 and CREBBP, HDAC1, KDM4C, respectively, which may underlie the observed transcriptional changes in HD. Altogether, our work provides a complete overview of the transcriptional studies in HD, and by data synthesis, reveals a number of common and unique gene expression and regulatory changes across different cell and tissue types in HD. These changes could elucidate new insights into molecular mechanisms of differential vulnerability in HD. Systematic Review Registration: https://osf.io/pm3wq.
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Affiliation(s)
- Bimala Malla
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xuanzong Guo
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gökçe Senger
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Zoi Chasapopoulou
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ferah Yildirim
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
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30
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Yildirim F, Foddis M, Blumenau S, Müller S, Kajetan B, Holtgrewe M, Kola V, Beule D, Sassi C. Shared and oppositely regulated transcriptomic signatures in Huntington's disease and brain ischemia confirm known and unveil novel potential neuroprotective genes. Neurobiol Aging 2021; 104:122.e1-122.e17. [PMID: 33875290 DOI: 10.1016/j.neurobiolaging.2021.03.001] [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: 02/23/2020] [Revised: 02/13/2021] [Accepted: 03/02/2021] [Indexed: 11/20/2022]
Abstract
Huntington's disease and subcortical vascular dementia display similar dementing features, shaped by different degrees of striatal atrophy, deep white matter degeneration and tau pathology. To investigate the hypothesis that Huntington's disease transcriptomic hallmarks may provide a window into potential protective genes upregulated during brain acute and subacute ischemia, we compared RNA sequencing signatures in the most affected brain areas of 2 widely used experimental mouse models: Huntington's disease, (R6/2, striatum and cortex and Q175, hippocampus) and brain ischemia-subcortical vascular dementia (BCCAS, striatum, cortex and hippocampus). We identified a cluster of 55 shared genes significantly differentially regulated in both models and we screened these in 2 different mouse models of Alzheimer's disease, and 96 early-onset familial and apparently sporadic small vessel ischemic disease patients. Our data support the prevalent role of transcriptional regulation upon genetic coding variability of known neuroprotective genes (Egr2, Fos, Ptgs2, Itga5, Cdkn1a, Gsn, Npas4, Btg2, Cebpb) and provide a list of potential additional ones likely implicated in different dementing disorders and worth further investigation.
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Affiliation(s)
- Ferah Yildirim
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Foddis
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sonja Blumenau
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Susanne Müller
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Bentele Kajetan
- Berlin Institute of Health, BIH, Core Unit Bioinformatics, Berlin, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health, BIH, Core Unit Bioinformatics, Berlin, Germany
| | - Vasilis Kola
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, BIH, Core Unit Bioinformatics, Berlin, Germany
| | - Celeste Sassi
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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31
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Tan X, Liu Y, Liu Y, Zhang T, Cong S. Dysregulation of long non-coding RNAs and their mechanisms in Huntington's disease. J Neurosci Res 2021; 99:2074-2090. [PMID: 34031910 DOI: 10.1002/jnr.24825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/19/2021] [Accepted: 02/26/2021] [Indexed: 12/31/2022]
Abstract
Extensive alterations in gene regulatory networks are a typical characteristic of Huntington's disease (HD); these include alterations in protein-coding genes and poorly understood non-coding RNAs (ncRNAs), which are associated with pathology caused by mutant huntingtin. Long non-coding RNAs (lncRNAs) are an important class of ncRNAs involved in a variety of biological functions, including transcriptional regulation and post-transcriptional modification of many targets, and likely contributed to the pathogenesis of HD. While a number of changes in lncRNAs expression have been observed in HD, little is currently known about their functions. Here, we discuss their possible mechanisms and molecular functions, with a particular focus on their roles in transcriptional regulation. These findings give us a better insight into HD pathogenesis and may provide new targets for the treatment of this neurodegenerative disease.
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Affiliation(s)
- Xiaoping Tan
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yang Liu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yan Liu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Taiming Zhang
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
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32
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Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
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Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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33
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Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:2020293118. [PMID: 33952696 DOI: 10.1073/pnas.2020293118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Transcriptional dysregulation in Huntington's disease (HD) causes functional deficits in striatal neurons. Here, we performed Patch-sequencing (Patch-seq) in an in vitro HD model to investigate the effects of mutant Huntingtin (Htt) on synaptic transmission and gene transcription in single striatal neurons. We found that expression of mutant Htt decreased the synaptic output of striatal neurons in a cell autonomous fashion and identified a number of genes whose dysregulation was correlated with physiological deficiencies in mutant Htt neurons. In support of a pivotal role for epigenetic mechanisms in HD pathophysiology, we found that inhibiting histone deacetylase 1/3 activities rectified several functional and morphological deficits and alleviated the aberrant transcriptional profiles in mutant Htt neurons. With this study, we demonstrate that Patch-seq technology can be applied both to better understand molecular mechanisms underlying a complex neurological disease at the single-cell level and to provide a platform for screening for therapeutics for the disease.
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34
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Histone Methylation Regulation in Neurodegenerative Disorders. Int J Mol Sci 2021; 22:ijms22094654. [PMID: 33925016 PMCID: PMC8125694 DOI: 10.3390/ijms22094654] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Advances achieved with molecular biology and genomics technologies have permitted investigators to discover epigenetic mechanisms, such as DNA methylation and histone posttranslational modifications, which are critical for gene expression in almost all tissues and in brain health and disease. These advances have influenced much interest in understanding the dysregulation of epigenetic mechanisms in neurodegenerative disorders. Although these disorders diverge in their fundamental causes and pathophysiology, several involve the dysregulation of histone methylation-mediated gene expression. Interestingly, epigenetic remodeling via histone methylation in specific brain regions has been suggested to play a critical function in the neurobiology of psychiatric disorders, including that related to neurodegenerative diseases. Prominently, epigenetic dysregulation currently brings considerable interest as an essential player in neurodegenerative disorders, such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), Amyotrophic lateral sclerosis (ALS) and drugs of abuse, including alcohol abuse disorder, where it may facilitate connections between genetic and environmental risk factors or directly influence disease-specific pathological factors. We have discussed the current state of histone methylation, therapeutic strategies, and future perspectives for these disorders. While not somatically heritable, the enzymes responsible for histone methylation regulation, such as histone methyltransferases and demethylases in neurons, are dynamic and reversible. They have become promising potential therapeutic targets to treat or prevent several neurodegenerative disorders. These findings, along with clinical data, may provide links between molecular-level changes and behavioral differences and provide novel avenues through which the epigenome may be targeted early on in people at risk for neurodegenerative disorders.
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35
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Crittenden JR, Gipson TA, Smith AC, Bowden HA, Yildirim F, Fischer KB, Yim M, Housman DE, Graybiel AM. Striatal transcriptome changes linked to drug-induced repetitive behaviors. Eur J Neurosci 2021; 53:2450-2468. [PMID: 33759265 DOI: 10.1111/ejn.15116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 11/30/2022]
Abstract
Disruptive or excessive repetitive motor patterns (stereotypies) are cardinal symptoms in numerous neuropsychiatric disorders. Stereotypies are also evoked by psychomotor stimulants such as amphetamine. The acquisition of motor sequences is paralleled by changes in activity patterns in the striatum, and stereotypies have been linked to abnormal plasticity in these reinforcement-related circuits. Here, we designed experiments in mice to identify transcriptomic changes that underlie striatal plasticity occurring alongside the development of drug-induced stereotypic behavior. We identified three schedules of amphetamine treatment inducing different degrees of stereotypy and used bulk RNAseq to compare striatal gene expression changes among groups of mice treated with the different drug-dose schedules and vehicle-treated, cage-mate controls. Mice were identified as naïve, sensitized, or tolerant to drug-induced stereotypy. All drug-treated groups exhibited expression changes in genes that encode members of the extracellular signal-regulated kinase (ERK) cascades known to regulate psychomotor stimulant responses. In the sensitized group with the most prolonged stereotypy, we found dysregulation of 20 genes that were not changed in other groups. Gene set enrichment analysis indicated highly significant overlap with genes regulated by neuregulin 1 (Nrg1). Nrg1 is known to be a schizophrenia and autism susceptibility gene that encodes a ligand for Erb-B receptors, which are involved in neuronal migration, myelination, and cell survival, including that of dopamine-containing neurons. Stimulant abuse is a risk factor for schizophrenia onset, and these two disorders share behavioral stereotypy phenotypes. Our results raise the possibility that drug-induced sensitization of the Nrg1 signaling pathway might underlie these links.
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Affiliation(s)
- Jill R Crittenden
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theresa A Gipson
- Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anne C Smith
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
| | - Hilary A Bowden
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ferah Yildirim
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, and NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kyle B Fischer
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael Yim
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David E Housman
- Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ann M Graybiel
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA
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36
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Hattori Y, Matsuda S, Baba R, Matsumiya K, Iwasaki S, Constantinescu CC, Morley TJ, Carroll VM, Papin C, Gouasmat A, Alagille D, Tamagnan G, Koike T. Design, Synthesis, and Evaluation of (2-Aminocyclopropyl)phenyl Derivatives as Novel Positron Emission Tomography Imaging Agents for Lysine-Specific Demethylase 1 in the Brain. J Med Chem 2021; 64:3780-3793. [PMID: 33729758 DOI: 10.1021/acs.jmedchem.0c01937] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Dysregulation of histone H3 lysine 4 (H3K4) methylation is implicated in the pathogenesis of neurodevelopmental disorders. Lysine-specific demethylase 1 (LSD1) determines the methylation status of H3K4 through flavin adenine dinucleotide (FAD)-mediated histone demethylation. Therefore, LSD1 inhibition in the brain can be a novel therapeutic option for treating these disorders. Positron emission tomography (PET) imaging of LSD1 allows for investigating LSD1 expression levels under normal and disease conditions and validating target engagement of therapeutic LSD1 inhibitors. This study designed and synthesized (2-aminocyclopropyl)phenyl derivatives with irreversible binding to LSD1 as PET imaging agents for LSD1 in the brain. We optimized lipophilicity of the lead compound to minimize the risk of nonspecific binding and identified 1e with high selectivity over monoamine oxidase A and B, which are a family of FAD-dependent enzymes homologous to LSD1. PET imaging in a monkey showed a high uptake of [18F]1e to regions enriched with LSD1, indicating its specific binding to LSD1.
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Affiliation(s)
- Yasushi Hattori
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoru Matsuda
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Rina Baba
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kouta Matsumiya
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Shinji Iwasaki
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | | | - Thomas J Morley
- Invicro LLC, 60 Temple Street, Suite 8A, New Haven, Connecticut 06518, United States
| | - Vincent M Carroll
- Invicro LLC, 60 Temple Street, Suite 8A, New Haven, Connecticut 06518, United States
| | - Caroline Papin
- Invicro LLC, 60 Temple Street, Suite 8A, New Haven, Connecticut 06518, United States
| | - Alexandra Gouasmat
- Invicro LLC, 60 Temple Street, Suite 8A, New Haven, Connecticut 06518, United States
| | - David Alagille
- XingImaging LLC, 760 Temple Street, New Haven, Connecticut 06510, United States
| | - Gilles Tamagnan
- XingImaging LLC, 760 Temple Street, New Haven, Connecticut 06510, United States
| | - Tatsuki Koike
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
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37
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Hecklau K, Mueller S, Koch SP, Mehkary MH, Kilic B, Harms C, Boehm-Sturm P, Yildirim F. The Effects of Selective Inhibition of Histone Deacetylase 1 and 3 in Huntington's Disease Mice. Front Mol Neurosci 2021; 14:616886. [PMID: 33679321 PMCID: PMC7925995 DOI: 10.3389/fnmol.2021.616886] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/27/2021] [Indexed: 01/15/2023] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease characterized by a late clinical onset of psychiatric, cognitive, and motor symptoms. Transcriptional dysregulation is an early and central disease mechanism which is accompanied by epigenetic alterations in HD. Previous studies demonstrated that targeting transcriptional changes by inhibition of histone deacetylases (HDACs), especially the class I HDACs, provides therapeutic effects. Yet, their exact mechanisms of action and the features of HD pathology, on which these inhibitors act remain to be elucidated. Here, using transcriptional profiling, we found that selective inhibition of HDAC1 and HDAC3 by RGFP109 alleviated transcriptional dysregulation of a number of genes, including the transcription factor genes Neurod2 and Nr4a2, and gene sets and programs, especially those that are associated to insulin-like growth factor pathway, in the striatum of R6/1 mice. RGFP109 treatment led to a modest improvement of the motor skill learning and coordination deficit on the RotaRod test, while it did not alter the locomotor and anxiety-like phenotypes in R6/1 animals. We also found, by volumetric MRI, a widespread brain atrophy in the R6/1 mice at the symptomatic disease stage, on which RGFP109 showed no significant effects. Collectively, our combined work suggests that specific HDAC1 and HDAC3 inhibition may offer benefits for alleviating the motor phenotypic deficits and transcriptional dysregulation in HD.
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Affiliation(s)
- Katharina Hecklau
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Mueller
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Paul Koch
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mustafa Hussain Mehkary
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Busra Kilic
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Harms
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Boehm-Sturm
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ferah Yildirim
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité – Universitätsmedizin Berlin, Berlin, Germany
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38
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Iida T, Itoh Y, Takahashi Y, Yamashita Y, Kurohara T, Miyake Y, Oba M, Suzuki T. Design, Synthesis, and Biological Evaluation of Lysine Demethylase 5 C Degraders. ChemMedChem 2021; 16:1609-1618. [PMID: 33470543 DOI: 10.1002/cmdc.202000933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/18/2022]
Abstract
Lysine demethylase 5 C (KDM5C) controls epigenetic gene expression and is attracting great interest in the field of chemical epigenetics. KDM5C has emerged as a therapeutic target for anti-prostate cancer agents, and recently we identified triazole 1 as an inhibitor of KDM5C. Compound 1 exhibited highly potent KDM5C-inhibitory activity in in vitro enzyme assays, but did not show strong anticancer effects. Therefore, a different approach is needed for the development of anticancer agents targeting KDM5C. Here, we attempted to identify KDM5C degraders by focusing on a protein-knockdown strategy. Compound 3 b, which was designed based on compound 1, degraded KDM5C and inhibited the growth of prostate cancer PC-3 cells more strongly than compound 1. These findings suggest that KDM5C degraders are more effective as anticancer agents than compounds that only inhibit the catalytic activity of KDM5C.
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Affiliation(s)
- Tetsuya Iida
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yukihiro Itoh
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yukari Takahashi
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yasunobu Yamashita
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Takashi Kurohara
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Yuka Miyake
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Makoto Oba
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
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39
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Alcalá-Vida R, Seguin J, Lotz C, Molitor AM, Irastorza-Azcarate I, Awada A, Karasu N, Bombardier A, Cosquer B, Skarmeta JLG, Cassel JC, Boutillier AL, Sexton T, Merienne K. Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington's disease mice. Nat Commun 2021; 12:364. [PMID: 33441541 PMCID: PMC7807045 DOI: 10.1038/s41467-020-20605-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022] Open
Abstract
Temporal dynamics and mechanisms underlying epigenetic changes in Huntington's disease (HD), a neurodegenerative disease primarily affecting the striatum, remain unclear. Using a slowly progressing knockin mouse model, we profile the HD striatal chromatin landscape at two early disease stages. Data integration with cell type-specific striatal enhancer and transcriptomic databases demonstrates acceleration of age-related epigenetic remodelling and transcriptional changes at neuronal- and glial-specific genes from prodromal stage, before the onset of motor deficits. We also find that 3D chromatin architecture, while generally preserved at neuronal enhancers, is altered at the disease locus. Specifically, we find that the HD mutation, a CAG expansion in the Htt gene, locally impairs the spatial chromatin organization and proximal gene regulation. Thus, our data provide evidence for two early and distinct mechanisms underlying chromatin structure changes in the HD striatum, correlating with transcriptional changes: the HD mutation globally accelerates age-dependent epigenetic and transcriptional reprogramming of brain cell identities, and locally affects 3D chromatin organization.
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Affiliation(s)
- Rafael Alcalá-Vida
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Jonathan Seguin
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Caroline Lotz
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Anne M Molitor
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Ibai Irastorza-Azcarate
- Berlin Institute of Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ali Awada
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Nezih Karasu
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Aurélie Bombardier
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Brigitte Cosquer
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Jose Luis Gomez Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Jean-Christophe Cassel
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Anne-Laurence Boutillier
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Thomas Sexton
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Karine Merienne
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France.
- CNRS UMR 7364, 67000, Strasbourg, France.
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40
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Yokotsuka-Ishida S, Nakamura M, Tomiyasu Y, Nagai M, Kato Y, Tomiyasu A, Umehara H, Hayashi T, Sasaki N, Ueno SI, Sano A. Positional cloning and comprehensive mutation analysis identified a novel KDM2B mutation in a Japanese family with minor malformations, intellectual disability, and schizophrenia. J Hum Genet 2021; 66:597-606. [PMID: 33402700 DOI: 10.1038/s10038-020-00889-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 11/09/2022]
Abstract
The importance of epigenetic control in the development of the central nervous system has recently been attracting attention. Methylation patterns of lysine 4 and lysine 36 in histone H3 (H3K4 and H3K36) in the central nervous system are highly conserved among species. Numerous complications of body malformations and neuropsychiatric disorders are due to abnormal histone H3 methylation modifiers. In this study, we analyzed a Japanese family with a dominant inheritance of symptoms including Marfan syndrome-like minor physical anomalies (MPAs), intellectual disability, and schizophrenia (SCZ). We performed positional cloning for this family using a single nucleotide polymorphism (SNP) array and whole-exome sequencing, which revealed a missense coding strand mutation (rs1555289644, NM_032590.4: c.2173G>A, p.A725T) in exon 15 on the plant homeodomain of the KDM2B gene as a possible cause of the disease in the family. The exome sequencing revealed that within the coding region, only a point mutation in KDM2B was present in the region with the highest logarithm of odds score of 2.41 resulting from whole genome linkage analysis. Haplotype analysis revealed co-segregation with four affected family members (IV-9, III-4, IV-5, and IV-8). Lymphoblastoid cell lines from the proband with this mutation showed approximately halved KDM2B expression in comparison with healthy controls. KDM2B acts as an H3K4 and H3K36 histone demethylase. Our findings suggest that haploinsufficiency of KDM2B in the process of development, like other H3K4 and H3K36 methylation modifiers, may have caused MPAs, intellectual disability, and SCZ in this Japanese family.
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Affiliation(s)
- Saeko Yokotsuka-Ishida
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masayuki Nakamura
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.
| | - Yoko Tomiyasu
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Mio Nagai
- Division of Psychiatry, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Yuko Kato
- Division of Psychiatry, Jiundo Hospital, Tokyo, Japan
| | - Akiyuki Tomiyasu
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiromi Umehara
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Takehiro Hayashi
- Department of Social Welfare, The International University of Kagoshima, Kagoshima, Japan
| | - Natsuki Sasaki
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Ehime University Graduate School of Medicine Toon, Kagoshima, Japan
| | - Akira Sano
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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41
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Mu MD, Qian ZM, Yang SX, Rong KL, Yung WH, Ke Y. Therapeutic effect of a histone demethylase inhibitor in Parkinson's disease. Cell Death Dis 2020; 11:927. [PMID: 33116116 PMCID: PMC7595123 DOI: 10.1038/s41419-020-03105-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 12/30/2022]
Abstract
Iron accumulation in the substantia nigra is recognized as a hallmark of Parkinson's disease (PD). Therefore, reducing accumulated iron and associated oxidative stress is considered a promising therapeutic strategy for PD. However, current iron chelators have poor membrane permeability and lack cell-type specificity. Here we identified GSK-J4, a histone demethylase inhibitor with the ability to cross blood brain barrier, as a potent iron suppressor. Only a trace amount of GSK-J4 significantly and selectively reduced intracellular labile iron in dopaminergic neurons, and suppressed H2O2 and 6-OHDA-induced cell death in vitro. The iron-suppressive effect was mainly mediated by inducing an increase in the expression of the iron exporter ferroportin-1. In parallel, GSK-J4 rescued dopaminergic neuron loss and motor defects in 6-OHDA-induced PD rats, which was accompanied by reduction of oxidative stress. Importantly, GSK-J4 rescued the abnormal changes of histone methylation, H3K4me3 and H3K27me3 during 6-OHDA treatment although the iron-suppressive and neuroprotective effects were sensitive to H3K4me3 inhibition only. Also, upregulating H3K4me3 increased ferroportin-1 expression and neuroprotection. Taken together, we demonstrate a previously unappreciated action of GSK-J4 on cell-specific iron suppression and neuroprotection via epigenetic mechanism. Compared with conventional iron chelators, this compound has a stronger therapeutic potential for PD.
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Affiliation(s)
- Ming-Dao Mu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Zhong-Ming Qian
- Institute of Translational and Precision Medicine, Nantong University, Nantong 226001, China
| | - Sheng-Xi Yang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Kang-Lin Rong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Wing-Ho Yung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China. .,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
| | - Ya Ke
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China. .,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
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42
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Alcalà-Vida R, Awada A, Boutillier AL, Merienne K. Epigenetic mechanisms underlying enhancer modulation of neuronal identity, neuronal activity and neurodegeneration. Neurobiol Dis 2020; 147:105155. [PMID: 33127472 DOI: 10.1016/j.nbd.2020.105155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
Neurodegenerative diseases, including Huntington's disease (HD) and Alzheimer's disease (AD), are progressive conditions characterized by selective, disease-dependent loss of neuronal regions and/or subpopulations. Neuronal loss is preceded by a long period of neuronal dysfunction, during which glial cells also undergo major changes, including neuroinflammatory response. Those dramatic changes affecting both neuronal and glial cells associate with epigenetic and transcriptional dysregulations, characterized by defined cell-type-specific signatures. Notably, increasing studies support the view that altered regulation of transcriptional enhancers, which are distal regulatory regions of the genome capable of modulating the activity of promoters through chromatin looping, play a critical role in transcriptional dysregulation in HD and AD. We review current knowledge on enhancers in HD and AD, and highlight challenging issues to better decipher the epigenetic code of neurodegenerative diseases.
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Affiliation(s)
- Rafael Alcalà-Vida
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | - Ali Awada
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | | | - Karine Merienne
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France.
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43
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Kedaigle AJ, Reidling JC, Lim RG, Adam M, Wu J, Wassie B, Stocksdale JT, Casale MS, Fraenkel E, Thompson LM. Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice. Hum Mol Genet 2020; 29:202-215. [PMID: 31696228 DOI: 10.1093/hmg/ddz264] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/20/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Transcriptional and epigenetic alterations occur early in Huntington's disease (HD), and treatment with epigenetic modulators is beneficial in several HD animal models. The drug JQ1, which inhibits histone acetyl-lysine reader bromodomains, has shown promise for multiple cancers and neurodegenerative disease. We tested whether JQ1 could improve behavioral phenotypes in the R6/2 mouse model of HD and modulate HD-associated changes in transcription and epigenomics. R6/2 and non-transgenic (NT) mice were treated with JQ1 daily from 5 to 11 weeks of age and behavioral phenotypes evaluated over this period. Following the trial, cortex and striatum were isolated and subjected to mRNA-seq and ChIP-seq for the histone marks H3K4me3 and H3K27ac. Initially, JQ1 enhanced motor performance in NT mice. In R6/2 mice, however, JQ1 had no effect on rotarod or grip strength but exacerbated weight loss and worsened performance on the pole test. JQ1-induced gene expression changes in NT mice were distinct from those in R6/2 and primarily involved protein translation and bioenergetics pathways. Dysregulation of HD-related pathways in striatum was exacerbated by JQ1 in R6/2 mice, but not in NTs, and JQ1 caused a corresponding increase in the formation of a mutant huntingtin protein-dependent high molecular weight species associated with pathogenesis. This study suggests that drugs predicted to be beneficial based on their mode of action and effects in wild-type or in other neurodegenerative disease models may have an altered impact in the HD context. These observations have important implications in the development of epigenetic modulators as therapies for HD.
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Affiliation(s)
| | | | - Ryan G Lim
- Memory Impairment and Neurological Disorders Research Unit
| | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jie Wu
- Memory Impairment and Neurological Disorders Research Unit
| | - Brook Wassie
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | | | - Ernest Fraenkel
- Computational and Systems Biology Program.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leslie M Thompson
- Memory Impairment and Neurological Disorders Research Unit.,Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
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44
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Zovkic IB. Epigenetics and memory: an expanded role for chromatin dynamics. Curr Opin Neurobiol 2020; 67:58-65. [PMID: 32905876 DOI: 10.1016/j.conb.2020.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
Abstract
Nearly two decades of research on epigenetic mechanisms in the brain have demonstrated that epigenetic marks that were once thought to be relatively static are dynamically and reversibly regulated in the brain during memory formation. Here, we focus on new research that has further expanded the dynamic nature of chromatin in memory formation through three key mechanisms. First, we discuss the emerging role of histone variants, which undergo learning-induced turnover or exchange, a process in which one histone type replaces another in chromatin. Next, we focus on chromatin remodeling complexes, which are tightly intertwined with all aspects of chromatin regulation and as such, can reposition or evict nucleosomes to promote transcriptional induction, and mediate histone variant exchange. Finally, we discuss how differential distribution of histone marks to localized narrow genomic regions and/or broadly distributed chromatin domains impact transcriptional outcomes and memory formation. Together, these studies mark a shift toward unraveling the complexity of chromatin function in memory and offer new strategies for fine tuning transcriptional outcomes to modify longevity, specificity and strength of memories.
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Affiliation(s)
- Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Canada.
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45
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Crapser JD, Ochaba J, Soni N, Reidling JC, Thompson LM, Green KN. Microglial depletion prevents extracellular matrix changes and striatal volume reduction in a model of Huntington's disease. Brain 2020; 143:266-288. [PMID: 31848580 DOI: 10.1093/brain/awz363] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/22/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
Huntington's disease is associated with a reactive microglial response and consequent inflammation. To address the role of these cells in disease pathogenesis, we depleted microglia from R6/2 mice, a rapidly progressing model of Huntington's disease marked by behavioural impairment, mutant huntingtin (mHTT) accumulation, and early death, through colony-stimulating factor 1 receptor inhibition (CSF1Ri) with pexidartinib (PLX3397) for the duration of disease. Although we observed an interferon gene signature in addition to downregulated neuritogenic and synaptic gene pathways with disease, overt inflammation was not evident by microglial morphology or cytokine transcript levels in R6/2 mice. Nonetheless, CSF1Ri-induced microglial elimination reduced or prevented disease-related grip strength and object recognition deficits, mHTT accumulation, astrogliosis, and striatal volume loss, the latter of which was not associated with reductions in cell number but with the extracellular accumulation of chondroitin sulphate proteoglycans (CSPGs)-a primary component of glial scars. A concurrent loss of proteoglycan-containing perineuronal nets was also evident in R6/2 mice, and microglial elimination not only prevented this but also strikingly increased perineuronal nets in the brains of naïve littermates, suggesting a new role for microglia as homeostatic regulators of perineuronal net formation and integrity.
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Affiliation(s)
- Joshua D Crapser
- Department of Neurobiology and Behavior, University of California, Irvine (UCI), Irvine, CA, USA.,Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Joseph Ochaba
- Department of Neurobiology and Behavior, University of California, Irvine (UCI), Irvine, CA, USA.,Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Neelakshi Soni
- Department of Neurobiology and Behavior, University of California, Irvine (UCI), Irvine, CA, USA.,Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Jack C Reidling
- Department of Neurobiology and Behavior, University of California, Irvine (UCI), Irvine, CA, USA.,Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Leslie M Thompson
- Department of Neurobiology and Behavior, University of California, Irvine (UCI), Irvine, CA, USA.,Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA.,Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Kim N Green
- Department of Neurobiology and Behavior, University of California, Irvine (UCI), Irvine, CA, USA.,Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
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46
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Chen W, Hu Y, Ju D. Gene therapy for neurodegenerative disorders: advances, insights and prospects. Acta Pharm Sin B 2020; 10:1347-1359. [PMID: 32963936 PMCID: PMC7488363 DOI: 10.1016/j.apsb.2020.01.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/09/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Gene therapy is rapidly emerging as a powerful therapeutic strategy for a wide range of neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease (PD) and Huntington's disease (HD). Some early clinical trials have failed to achieve satisfactory therapeutic effects. Efforts to enhance effectiveness are now concentrating on three major fields: identification of new vectors, novel therapeutic targets, and reliable of delivery routes for transgenes. These approaches are being assessed closely in preclinical and clinical trials, which may ultimately provide powerful treatments for patients. Here, we discuss advances and challenges of gene therapy for neurodegenerative disorders, highlighting promising technologies, targets, and future prospects.
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Key Words
- AADC, aromatic-l-amino-acid
- AAVs, adeno-associated viruses
- AD, Alzheimer's disease
- ARSA, arylsulfatase A
- ASOs, antisense oligonucleotides
- ASPA, aspartoacylase
- Adeno-associated viruses
- Adv, adenovirus
- BBB, blood–brain barrier
- BCSFB, blood–cerebrospinal fluid barrier
- BRB, blood–retina barrier
- Bip, glucose regulated protein 78
- CHOP, CCAAT/enhancer binding homologous protein
- CLN6, ceroidlipofuscinosis neuronal protein 6
- CNS, central nervous system
- CSF, cerebrospinal fluid
- Central nervous system
- Delivery routes
- ER, endoplasmic reticulum
- FDA, U.S. Food and Drug Administration
- GAA, lysosomal acid α-glucosidase
- GAD, glutamic acid decarboxylase
- GDNF, glial derived neurotrophic factor
- Gene therapy
- HD, Huntington's disease
- HSPGs, heparin sulfate proteoglycans
- HTT, mutant huntingtin
- IDS, iduronate 2-sulfatase
- LVs, retrovirus/lentivirus
- Lamp2a, lysosomal-associated membrane protein 2a
- NGF, nerve growth factor
- Neurodegenerative disorders
- PD, Parkinson's disease
- PGRN, Progranulin
- PINK1, putative kinase 1
- PTEN, phosphatase and tensin homolog
- RGCs, retinal ganglion cells
- RNAi, RNA interference
- RPE, retinal pigmented epithelial
- SGSH, lysosomal heparan-N-sulfamidase gene
- SMN, survival motor neuron
- SOD, superoxide dismutase
- SUMF, sulfatase-modifying factor
- TFEB, transcription factor EB
- TPP1, tripeptidyl peptidase 1
- TREM2, triggering receptor expressed on myeloid cells 2
- UPR, unfolded protein response
- ZFPs, zinc finger proteins
- mTOR, mammalian target of rapamycin
- siRNA, small interfering RNA
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Affiliation(s)
- Wei Chen
- Department of Biological Medicines, Fudan University School of Pharmacy, Shanghai 201203, China
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yang Hu
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Dianwen Ju
- Department of Biological Medicines, Fudan University School of Pharmacy, Shanghai 201203, China
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Pourshafie N, Masati E, Bunker E, Nickolls AR, Thepmankorn P, Johnson K, Feng X, Ekins T, Grunseich C, Fischbeck KH. Linking epigenetic dysregulation, mitochondrial impairment, and metabolic dysfunction in SBMA motor neurons. JCI Insight 2020; 5:136539. [PMID: 32641584 PMCID: PMC7406250 DOI: 10.1172/jci.insight.136539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/21/2020] [Indexed: 12/19/2022] Open
Abstract
Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disorder caused by a polyglutamine expansion in the androgen receptor (AR). Using gene expression analysis and ChIP sequencing, we mapped transcriptional changes in genetically engineered patient stem cell-derived motor neurons. We found that transcriptional dysregulation in SBMA can occur through AR-mediated histone modification. We detected reduced histone acetylation, along with decreased expression of genes encoding compensatory metabolic proteins and reduced substrate availability for mitochondrial function. Furthermore, we found that pyruvate supplementation corrected this deficiency and improved mitochondrial function and SBMA motor neuron viability. We propose that epigenetic dysregulation of metabolic genes contributes to reduced mitochondrial ATP production. Our results show a molecular link between altered epigenetic regulation and mitochondrial metabolism that contributes to neurodegeneration.
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Affiliation(s)
- Naemeh Pourshafie
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
- George Washington University, Institute of Biomedical Sciences, Washington, DC, USA
| | - Ester Masati
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Eric Bunker
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Alec R. Nickolls
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
- Brown University, Department of Neuroscience, Providence, Rhode Island, USA
- National Center for Complementary and Integrative Health, NIH, Bethesda, Maryland, USA
| | - Parisorn Thepmankorn
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Kory Johnson
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Xia Feng
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
- Johns Hopkins University, Department of Psychiatry and Behavioral Sciences, Baltimore, Maryland, USA
| | - Tyler Ekins
- Brown University, Department of Neuroscience, Providence, Rhode Island, USA
- Program in Developmental Neuroscience, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Kenneth H. Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
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48
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Kim A, García-García E, Straccia M, Comella-Bolla A, Miguez A, Masana M, Alberch J, Canals JM, Rodríguez MJ. Reduced Fractalkine Levels Lead to Striatal Synaptic Plasticity Deficits in Huntington's Disease. Front Cell Neurosci 2020; 14:163. [PMID: 32625064 PMCID: PMC7314984 DOI: 10.3389/fncel.2020.00163] [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: 03/29/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder in which the striatum is the most affected brain region. Although a chronic inflammatory microglial reaction that amplifies disease progression has been described in HD patients, some murine models develop symptoms without inflammatory microglial activation. Thus, dysfunction of non-inflammatory microglial activity could also contribute to the early HD pathological process. Here, we show the involvement of microglia and particularly fractalkine signaling in the striatal synaptic dysfunction of R6/1 mice. We found reduced fractalkine gene expression and protein concentration in R6/1 striata from 8 to 20 weeks of age. Consistently, we also observed a down-regulation of fractalkine levels in the putamen of HD patients and in HD patient hiPSC-derived neurons. Automated cell morphology analysis showed a non-inflammatory ramified microglia in the striatum of R6/1 mice. However, we found increased PSD-95-positive puncta inside microglia, indicative of synaptic pruning, before HD motor symptoms start to manifest. Indeed, microglia appeared to be essential for striatal synaptic function, as the inhibition of microglial activity with minocycline impaired the induction of corticostriatal long-term depression (LTD) in wild-type mice. Notably, fractalkine administration restored impaired corticostriatal LTD in R6/1 mice. Our results unveil a role for fractalkine-dependent neuron-microglia interactions in the early striatal synaptic dysfunction characteristic of HD.
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Affiliation(s)
- Anya Kim
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain
| | - Esther García-García
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain
| | - Marco Straccia
- Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain.,Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain.,Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
| | - Andrea Comella-Bolla
- Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain.,Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain.,Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
| | - Andrés Miguez
- Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain.,Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain.,Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
| | - Mercè Masana
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain
| | - Jordi Alberch
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain.,Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
| | - Josep M Canals
- Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain.,Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain.,Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
| | - Manuel J Rodríguez
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain.,Network Center for Biomedical Research in Neurodegenerative Diseases, Barcelona, Spain
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49
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Miyazaki H, Yamanaka T, Oyama F, Kino Y, Kurosawa M, Yamada-Kurosawa M, Yamano R, Shimogori T, Hattori N, Nukina N. FACS-array-based cell purification yields a specific transcriptome of striatal medium spiny neurons in a murine Huntington disease model. J Biol Chem 2020; 295:9768-9785. [PMID: 32499373 DOI: 10.1074/jbc.ra120.012983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/21/2020] [Indexed: 12/27/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder caused by expanded CAG repeats in the Huntingtin gene. Results from previous studies have suggested that transcriptional dysregulation is one of the key mechanisms underlying striatal medium spiny neuron (MSN) degeneration in HD. However, some of the critical genes involved in HD etiology or pathology could be masked in a common expression profiling assay because of contamination with non-MSN cells. To gain insight into the MSN-specific gene expression changes in presymptomatic R6/2 mice, a common HD mouse model, here we used a transgenic fluorescent protein marker of MSNs for purification via FACS before profiling gene expression with gene microarrays and compared the results of this "FACS-array" with those obtained with homogenized striatal samples (STR-array). We identified hundreds of differentially expressed genes (DEGs) and enhanced detection of MSN-specific DEGs by comparing the results of the FACS-array with those of the STR-array. The gene sets obtained included genes ubiquitously expressed in both MSNs and non-MSN cells of the brain and associated with transcriptional regulation and DNA damage responses. We proposed that the comparative gene expression approach using the FACS-array may be useful for uncovering the gene cascades affected in MSNs during HD pathogenesis.
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Affiliation(s)
- Haruko Miyazaki
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoyuki Yamanaka
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Fumitaka Oyama
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Department of Chemistry and Life Science, Kogakuin University, Tokyo, Japan
| | - Yoshihiro Kino
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Masaru Kurosawa
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Institute for Environmental and Gender-specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | | | - Risa Yamano
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan
| | - Tomomi Shimogori
- Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuyuki Nukina
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan .,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
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50
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Merienne N, Meunier C, Schneider A, Seguin J, Nair SS, Rocher AB, Le Gras S, Keime C, Faull R, Pellerin L, Chatton JY, Neri C, Merienne K, Déglon N. Cell-Type-Specific Gene Expression Profiling in Adult Mouse Brain Reveals Normal and Disease-State Signatures. Cell Rep 2020; 26:2477-2493.e9. [PMID: 30811995 DOI: 10.1016/j.celrep.2019.02.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/21/2018] [Accepted: 02/01/2019] [Indexed: 12/21/2022] Open
Abstract
The role of brain cell-type-specific functions and profiles in pathological and non-pathological contexts is still poorly defined. Such cell-type-specific gene expression profiles in solid, adult tissues would benefit from approaches that avoid cellular stress during isolation. Here, we developed such an approach and identified highly selective transcriptomic signatures in adult mouse striatal direct and indirect spiny projection neurons, astrocytes, and microglia. Integrating transcriptomic and epigenetic data, we obtained a comprehensive model for cell-type-specific regulation of gene expression in the mouse striatum. A cross-analysis with transcriptomic and epigenomic data generated from mouse and human Huntington's disease (HD) brains shows that opposite epigenetic mechanisms govern the transcriptional regulation of striatal neurons and glial cells and may contribute to pathogenic and compensatory mechanisms. Overall, these data validate this less stressful method for the investigation of cellular specificity in the adult mouse brain and demonstrate the potential of integrative studies using multiple databases.
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Affiliation(s)
- Nicolas Merienne
- Department of Clinical Neurosciences, Laboratory of Neurotherapies and Neuromodulation (LNTM), Lausanne University Hospital, 1011 Lausanne, Switzerland; Neuroscience Research Center, LNTM, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Cécile Meunier
- Department of Physiology, Laboratory of Neuroenergetics, University of Lausanne, 1005 Lausanne, Switzerland
| | - Anne Schneider
- University of Strasbourg, CNRS, UMR 7364, Laboratory of Cognitive and Adaptive Neuroscience, 67000 Strasbourg, France
| | - Jonathan Seguin
- University of Strasbourg, CNRS, UMR 7364, Laboratory of Cognitive and Adaptive Neuroscience, 67000 Strasbourg, France
| | - Satish S Nair
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging, Team Compensation in Neurodegenerative Diseases and Aging, 75252 Paris, France
| | - Anne B Rocher
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Stéphanie Le Gras
- University of Strasbourg, CNRS, INSERM, UMR 7104, Microarray and Sequencing Platform, Institute of Genetic and Molecular and Cellular Biology, 67404 Illkirch, France
| | - Céline Keime
- University of Strasbourg, CNRS, INSERM, UMR 7104, Microarray and Sequencing Platform, Institute of Genetic and Molecular and Cellular Biology, 67404 Illkirch, France
| | - Richard Faull
- Centre for Brain Research, Faculty of Medical and Health Science, The University of Auckland, Auckland 1023, New Zealand
| | - Luc Pellerin
- Department of Physiology, Laboratory of Neuroenergetics, University of Lausanne, 1005 Lausanne, Switzerland; Centre de Résonance Magnétique des Systèmes Biologiques UMR 5536, CNRS-Université de Bordeaux, 146 rue Léo Saignat, Bordeaux, France
| | - Jean-Yves Chatton
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland; Cellular Imaging Facility, University of Lausanne, 1005 Lausanne, Switzerland
| | - Christian Neri
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging, Team Compensation in Neurodegenerative Diseases and Aging, 75252 Paris, France
| | - Karine Merienne
- University of Strasbourg, CNRS, UMR 7364, Laboratory of Cognitive and Adaptive Neuroscience, 67000 Strasbourg, France
| | - Nicole Déglon
- Department of Clinical Neurosciences, Laboratory of Neurotherapies and Neuromodulation (LNTM), Lausanne University Hospital, 1011 Lausanne, Switzerland; Neuroscience Research Center, LNTM, Lausanne University Hospital, 1011 Lausanne, Switzerland.
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