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Zhao T, Hong Y, Yan B, Huang S, Ming GL, Song H. Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a. Nat Commun 2024; 15:5674. [PMID: 38971831 PMCID: PMC11227589 DOI: 10.1038/s41467-024-50010-y] [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: 01/30/2024] [Accepted: 06/25/2024] [Indexed: 07/08/2024] Open
Abstract
Quiescence, a hallmark of adult neural stem cells (NSCs), is required for maintaining the NSC pool to support life-long continuous neurogenesis in the adult dentate gyrus (DG). Whether long-lasting epigenetic modifications maintain NSC quiescence over the long term in the adult DG is not well-understood. Here we show that mice with haploinsufficiency of Setd1a, a schizophrenia risk gene encoding a histone H3K4 methyltransferase, develop an enlarged DG with more dentate granule cells after young adulthood. Deletion of Setd1a specifically in quiescent NSCs in the adult DG promotes their activation and neurogenesis, which is countered by inhibition of the histone demethylase LSD1. Mechanistically, RNA-sequencing and CUT & RUN analyses of cultured quiescent adult NSCs reveal Setd1a deletion-induced transcriptional changes and many Setd1a targets, among which down-regulation of Bhlhe40 promotes quiescent NSC activation in the adult DG in vivo. Together, our study reveals a Setd1a-dependent epigenetic mechanism that sustains NSC quiescence in the adult DG.
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Affiliation(s)
- Ting Zhao
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA
| | - Yan Hong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA
| | - Bowen Yan
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Suming Huang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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2
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Zhang H, Peyton L, McCarroll A, de León Guerrerro SD, Zhang S, Gowda P, Sirkin D, El Achwah M, Duhe A, Wood WG, Jamison B, Tracy G, Pollak R, Hart RP, Pato CN, Mulle JG, Sanders AR, Pang ZP, Duan J. Scaled and Efficient Derivation of Loss of Function Alleles in Risk Genes for Neurodevelopmental and Psychiatric Disorders in Human iPSC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585542. [PMID: 38562852 PMCID: PMC10983959 DOI: 10.1101/2024.03.18.585542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Translating genetic findings for neurodevelopmental and psychiatric disorders (NPD) into actionable disease biology would benefit from large-scale and unbiased functional studies of NPD genes. Leveraging the cytosine base editing (CBE) system, here we developed a pipeline for clonal loss-of-function (LoF) allele mutagenesis in human induced pluripotent stem cells (hiPSCs) by introducing premature stop-codons (iSTOP) that lead to mRNA nonsense-mediated-decay (NMD) or protein truncation. We tested the pipeline for 23 NPD genes on 3 hiPSC lines and achieved highly reproducible, efficient iSTOP editing in 22 NPD genes. Using RNAseq, we confirmed their pluripotency, absence of chromosomal abnormalities, and NMD. Interestingly, for three schizophrenia risk genes (SETD1A, TRIO, CUL1), despite the high efficiency of base editing, we only obtained heterozygous LoF alleles, suggesting their essential roles for cell growth. We replicated the reported neural phenotypes of SHANK3-haploinsufficiency and found CUL1-LoF reduced neurite branches and synaptic puncta density. This iSTOP pipeline enables a scaled and efficient LoF mutagenesis of NPD genes, yielding an invaluable shareable resource.
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Affiliation(s)
- Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Lilia Peyton
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Ada McCarroll
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Sol Díaz de León Guerrerro
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
| | - Prarthana Gowda
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - David Sirkin
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Mahmoud El Achwah
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Alexandra Duhe
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Whitney G Wood
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Brandon Jamison
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Gregory Tracy
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Rebecca Pollak
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University
| | - Carlos N Pato
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
| | - Jennifer G Mulle
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
- Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Alan R Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
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3
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Zhang Z, Wang R, Zhou H, Wu D, Cao Y, Zhang C, Sun H, Mu C, Hao Z, Ren H, Wang N, Yu S, Zhang J, Tao M, Wang C, Liu Y, Liu L, Liu Y, Zang J, Wang G. Inhibition of EHMT1/2 rescues synaptic damage and motor impairment in a PD mouse model. Cell Mol Life Sci 2024; 81:128. [PMID: 38472451 DOI: 10.1007/s00018-024-05176-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Epigenetic dysregulation that leads to alterations in gene expression and is suggested to be one of the key pathophysiological factors of Parkinson's disease (PD). Here, we found that α-synuclein preformed fibrils (PFFs) induced histone H3 dimethylation at lysine 9 (H3K9me2) and increased the euchromatic histone methyltransferases EHMT1 and EHMT2, which were accompanied by neuronal synaptic damage, including loss of synapses and diminished expression levels of synaptic-related proteins. Furthermore, the levels of H3K9me2 at promoters in genes that encode the synaptic-related proteins SNAP25, PSD95, Synapsin 1 and vGLUT1 were increased in primary neurons after PFF treatment, which suggests a linkage between H3K9 dimethylation and synaptic dysfunction. Inhibition of EHMT1/2 with the specific inhibitor A-366 or shRNA suppressed histone methylation and alleviated synaptic damage in primary neurons that were treated with PFFs. In addition, the synaptic damage and motor impairment in mice that were injected with PFFs were repressed by treatment with the EHMT1/2 inhibitor A-366. Thus, our findings reveal the role of histone H3 modification by EHMT1/2 in synaptic damage and motor impairment in a PFF animal model, suggesting the involvement of epigenetic dysregulation in PD pathogenesis.
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Affiliation(s)
- Zhixiong Zhang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Rui Wang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Hui Zhou
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Dan Wu
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Yifan Cao
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Chuang Zhang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Hongyang Sun
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Chenchen Mu
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Zongbing Hao
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Haigang Ren
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
- Jiangsu Provincial Medical Innovation Center of Trauma Medicine, Institute of Trauma Medicine, Soochow University, Suzhou, 215123, Jiangsu, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Nana Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Shuang Yu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Jingzhong Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Mengdan Tao
- School of Pharmacy, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Can Wang
- School of Pharmacy, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yan Liu
- School of Pharmacy, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Liu Liu
- Department of Pharmacy, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, China
| | - Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, 230026, Anhui, China
| | - Guanghui Wang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Soochow University, Suzhou, 215123, Jiangsu, China.
- Center of Translational Medicine, First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Suzhou, 215400, China.
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4
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Tian Y, Zheng X, Li R, Hu L, Shui X, Wang L, Chen D, Lee TH, Zhang T. Quantitative Proteomic and Phosphoproteomic Analyses Reveal a Role of Death-Associated Protein Kinase 1 in Regulating Hippocampal Synapse. Mol Neurobiol 2024; 61:1794-1806. [PMID: 37775722 DOI: 10.1007/s12035-023-03674-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Death-associated protein kinase 1 (DAPK1) is a stress-responsive calcium/calmodulin (CaM)-regulated serine/threonine protein kinase that is actively involved in stress-induced cell death. The dysregulation of DAPK1 has been established in various neurological disorders such as epilepsy, Alzheimer's disease (AD), and Parkinson's disease (PD). Recent research indicates a synaptic localization of DAPK1 in neurons, suggesting a potential role of DAPK1 in modulating synaptic structure and function. However, the key molecules and pathways underlying the influence of DAPK1 on synapses remain elusive. We utilized quantitative proteomic and phosphoproteomic analyses to compare the differences in protein expression and phosphorylation in hippocampal tissues of wild-type (WT) and DAPK1-knockout (KO) mice. Bioinformatic analysis of differentially expressed proteins and phosphoproteins revealed a preferential enrichment of proteins involved in regulating synaptic function, cytoskeletal structure, and neurotransmission. Gene set enrichment analysis (GESA) highlighted altered presynaptic functions including synaptic vesicle priming and glutamate secretion in KO mice. Besides, we observed that proteins with potential phosphorylation motifs of ERK and DAPK1 were overrepresented among the differential phosphoproteins and were highly enriched in neuronal function-related pathways. Furthermore, Western blot analysis validated differences in the expression of several proteins closely associated with presynaptic organization, dendrites and calcium transmembrane transport between KO and WT mice, further corroborating the potential involvement of DAPK1 in the regulation of synaptic functions. Overall, our data provide molecular evidence to elucidate the physiological links between DAPK1 and neuronal functions and help clarify the role of DAPK1 in the pathogenesis of neurodevelopmental and neurodegenerative diseases.
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Affiliation(s)
- Yuan Tian
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Xiaoqing Zheng
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Ruomeng Li
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Li Hu
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Xindong Shui
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Long Wang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Dongmei Chen
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Tae Ho Lee
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China.
| | - Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China.
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5
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Colijn MA, Carrion P, Poirier-Morency G, Rogic S, Torres I, Menon M, Lisonek M, Cook C, DeGraaf A, Thammaiah SP, Neelakant H, Willaeys V, Leonova O, White RF, Yip S, Mungall AJ, MacLeod PM, Gibson WT, Sullivan PF, Honer WG, Pavlidis P, Stowe RM. SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases. Prog Neuropsychopharmacol Biol Psychiatry 2024; 129:110888. [PMID: 37918557 DOI: 10.1016/j.pnpbp.2023.110888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/18/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023]
Abstract
OBJECTIVE SETD1A encodes a histone methyltransferase involved in various cell cycle regulatory processes. Loss-of-function SETD1A variants have been associated with numerous neurodevelopmental phenotypes, including intellectual disability and schizophrenia. While the association between rare coding variants in SETD1A and schizophrenia has achieved genome-wide significance by rare variant burden testing, only a few studies have described the psychiatric phenomenology of such individuals in detail. This systematic review and case report aims to characterize the neurodevelopmental and psychiatric phenotypes of SETD1A variant-associated schizophrenia. METHODS A PubMed search was completed in July 2022 and updated in May 2023. Only studies that reported individuals with a SETD1A variant as well as a primary psychotic disorder were ultimately included. Additionally, another two previously unpublished cases of SETD1A variant-associated psychosis from our own sequencing cohort are described. RESULTS The search yielded 32 articles. While 15 articles met inclusion criteria, only five provided case descriptions. In total, phenotypic information was available for 11 individuals, in addition to our own two unpublished cases. Our findings suggest that although individuals with SETD1A variant-associated schizophrenia may share a number of common features, phenotypic variability nonetheless exists. Moreover, although such individuals may exhibit numerous other neurodevelopmental features suggestive of the syndrome, their psychiatric presentations appear to be similar to those of general schizophrenia populations. CONCLUSIONS Loss-of-function SETD1A variants may underlie the development of psychosis in a small percentage of individuals with schizophrenia. Identifying such individuals may become increasingly important, given the potential for advances in precision medicine treatment approaches.
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Affiliation(s)
- Mark A Colijn
- Department of Psychiatry, Hotchkiss Brain Institute, and Mathison Centre for Mental Health Research & Education, University of Calgary, Calgary, AB, Canada.
| | - Prescilla Carrion
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | | | - Sanja Rogic
- Department of Psychiatry and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Ivan Torres
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; BC Mental Health and Substance Use Services, Vancouver, BC, Canada
| | - Mahesh Menon
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | | | - Courtney Cook
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ashley DeGraaf
- Heart Centre, St. Paul's Hospital and Providence Health, Vancouver, BC, Canada
| | | | - Harish Neelakant
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Veerle Willaeys
- BC Psychosis Program, British Columbia Mental Health & Substance Use Services, Vancouver, BC, Canada
| | - Olga Leonova
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Randall F White
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Patrick M MacLeod
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia and BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Patrick F Sullivan
- Psychiatry and Genetics, University of North Carolina at Chapel Hill, NC, USA; Karolinska Institut, Stockholm, Sweden
| | - William G Honer
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; BC Mental Health and Substance Use Services Research Institute, Vancouver, BC, Canada
| | - Paul Pavlidis
- Department of Psychiatry, Michael Smith Laboratories, and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Robert M Stowe
- Departments of Psychiatry and Neurology (Medicine), BC Neuropsychiatry Program, and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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6
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Lewerissa EI, Nadif Kasri N, Linda K. Epigenetic regulation of autophagy-related genes: Implications for neurodevelopmental disorders. Autophagy 2024; 20:15-28. [PMID: 37674294 PMCID: PMC10761153 DOI: 10.1080/15548627.2023.2250217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionarily highly conserved catabolic process that is important for the clearance of cytosolic contents to maintain cellular homeostasis and survival. Recent findings point toward a critical role for autophagy in brain function, not only by preserving neuronal health, but especially by controlling different aspects of neuronal development and functioning. In line with this, mutations in autophagy-related genes are linked to various key characteristics and symptoms of neurodevelopmental disorders (NDDs), including autism, micro-/macrocephaly, and epilepsy. However, the group of NDDs caused by mutations in autophagy-related genes is relatively small. A significant proportion of NDDs are associated with mutations in genes encoding epigenetic regulatory proteins that modulate gene expression, so-called chromatinopathies. Intriguingly, several of the NDD-linked chromatinopathy genes have been shown to regulate autophagy-related genes, albeit in non-neuronal contexts. From these studies it becomes evident that tight transcriptional regulation of autophagy-related genes is crucial to control autophagic activity. This opens the exciting possibility that aberrant autophagic regulation might underly nervous system impairments in NDDs with disturbed epigenetic regulation. We here summarize NDD-related chromatinopathy genes that are known to regulate transcriptional regulation of autophagy-related genes. Thereby, we want to highlight autophagy as a candidate key hub mechanism in NDD-related chromatinopathies.Abbreviations: ADNP: activity dependent neuroprotector homeobox; ASD: autism spectrum disorder; ATG: AutTophaGy related; CpG: cytosine-guanine dinucleotide; DNMT: DNA methyltransferase; EHMT: euchromatic histone lysine methyltransferase; EP300: E1A binding protein p300; EZH2: enhancer of zeste 2 polycomb repressive complex 2 subunit; H3K4me3: histone 3 lysine 4 trimethylation; H3K9me1/2/3: histone 3 lysine 9 mono-, di-, or trimethylation; H3K27me2/3: histone 3 lysine 27 di-, or trimethylation; hiPSCs: human induced pluripotent stem cells; HSP: hereditary spastic paraplegia; ID: intellectual disability; KANSL1: KAT8 regulatory NSL complex subunit 1; KAT8: lysine acetyltransferase 8; KDM1A/LSD1: lysine demethylase 1A; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin complex 1; NDD: neurodevelopmental disorder; PHF8: PHD finger protein 8; PHF8-XLID: PHF8-X linked intellectual disability syndrome; PTM: post-translational modification; SESN2: sestrin 2; YY1: YY1 transcription factor; YY1AP1: YY1 associated protein 1.
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Affiliation(s)
- Elly I. Lewerissa
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, Nijmegen, Gelderland, The Netherlands
| | - Katrin Linda
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Flemish Brabant, Belgium
- Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Flemish Brabant, Belgium
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7
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Perlee S, Kikuchi S, Nakadai T, Masuda T, Ohtsuki S, Matsumoto M, Rahmutulla B, Fukuyo M, Cifani P, Kentsis A, Roeder RG, Kaneda A, Hoshii T. SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3. EMBO Rep 2023; 24:e57108. [PMID: 37535603 PMCID: PMC10561176 DOI: 10.15252/embr.202357108] [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: 03/02/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023] Open
Abstract
The H3K4 methyltransferase SETD1A plays a crucial role in leukemia cell survival through its noncatalytic FLOS domain-mediated recruitment of cyclin K and regulation of DNA damage response genes. In this study, we identify a functional nuclear localization signal in and interaction partners of the FLOS domain. Our screen for FLOS domain-binding partners reveals that the SETD1A FLOS domain binds mitosis-associated proteins BuGZ/BUB3. Inhibition of both cyclin K and BuGZ/BUB3-binding motifs in SETD1A shows synergistic antileukemic effects. BuGZ/BUB3 localize to SETD1A-bound promoter-TSS regions and SETD1A-negative H3K4me1-positive enhancer regions adjacent to SETD1A target genes. The GLEBS motif and intrinsically disordered region of BuGZ are required for both SETD1A-binding and leukemia cell proliferation. Cell-cycle-specific SETD1A restoration assays indicate that SETD1A expression at the G1/S phase of the cell cycle promotes both the expression of DNA damage response genes and cell cycle progression in leukemia cells.
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Affiliation(s)
- Sarah Perlee
- Department of Cancer Biology and GeneticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Gerstner Graduate School of Biomedical SciencesMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Sota Kikuchi
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Takeshi Masuda
- Laboratory of Pharmaceutical Microbiology, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaJapan
| | - Sumio Ohtsuki
- Laboratory of Pharmaceutical Microbiology, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Paolo Cifani
- Molecular Pharmacology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Alex Kentsis
- Molecular Pharmacology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
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8
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Farsi Z, Sheng M. Molecular mechanisms of schizophrenia: Insights from human genetics. Curr Opin Neurobiol 2023; 81:102731. [PMID: 37245257 DOI: 10.1016/j.conb.2023.102731] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/30/2023]
Abstract
Schizophrenia is a debilitating psychiatric disorder that affects millions of people worldwide; however, its etiology is poorly understood at the molecular and neurobiological levels. A particularly important advance in recent years is the discovery of rare genetic variants associated with a greatly increased risk of developing schizophrenia. These primarily loss-of-function variants are found in genes that overlap with those implicated by common variants and are involved in the regulation of glutamate signaling, synaptic function, DNA transcription, and chromatin remodeling. Animal models harboring mutations in these large-effect schizophrenia risk genes show promise in providing additional insights into the molecular mechanisms of the disease.
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Affiliation(s)
- Zohreh Farsi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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9
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Obi-Nagata K, Suzuki N, Miyake R, MacDonald ML, Fish KN, Ozawa K, Nagahama K, Okimura T, Tanaka S, Kano M, Fukazawa Y, Sweet RA, Hayashi-Takagi A. Distorted neurocomputation by a small number of extra-large spines in psychiatric disorders. SCIENCE ADVANCES 2023; 9:eade5973. [PMID: 37294752 PMCID: PMC10256173 DOI: 10.1126/sciadv.ade5973] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/05/2023] [Indexed: 06/11/2023]
Abstract
Human genetics strongly support the involvement of synaptopathy in psychiatric disorders. However, trans-scale causality linking synapse pathology to behavioral changes is lacking. To address this question, we examined the effects of synaptic inputs on dendrites, cells, and behaviors of mice with knockdown of SETD1A and DISC1, which are validated animal models of schizophrenia. Both models exhibited an overrepresentation of extra-large (XL) synapses, which evoked supralinear dendritic and somatic integration, resulting in increased neuronal firing. The probability of XL spines correlated negatively with working memory, and the optical prevention of XL spine generation restored working memory impairment. Furthermore, XL synapses were more abundant in the postmortem brains of patients with schizophrenia than in those of matched controls. Our findings suggest that working memory performance, a pivotal aspect of psychiatric symptoms, is shaped by distorted dendritic and somatic integration via XL spines.
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Affiliation(s)
- Kisho Obi-Nagata
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
- Gunma University Graduate School of Medicine, Maebashi City, Gunma 371-8512, Japan
| | - Norimitsu Suzuki
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
| | - Ryuhei Miyake
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
| | - Matthew L. MacDonald
- Departments of Psychiatry, Neurology, Statistics, and Neurobiology, Translational Neuroscience Program, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Kenneth N. Fish
- Departments of Psychiatry, Neurology, Statistics, and Neurobiology, Translational Neuroscience Program, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Katsuya Ozawa
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
| | - Kenichiro Nagahama
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Tsukasa Okimura
- Medical Institute of Developmental Disabilities Research, Showa University, Tokyo 157-8577, Japan
| | - Shoji Tanaka
- Department of Information and Communication Sciences, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Yugo Fukazawa
- Division of Brain Structure and Function, Faculty of Medical Science, University of Fukui, Yoshida, Fukui, 910-1193, Japan
| | - Robert A. Sweet
- Departments of Psychiatry, Neurology, Statistics, and Neurobiology, Translational Neuroscience Program, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Akiko Hayashi-Takagi
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
- Gunma University Graduate School of Medicine, Maebashi City, Gunma 371-8512, Japan
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10
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Nakamura T, Takata A. The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research. Mol Psychiatry 2023; 28:1868-1889. [PMID: 36878965 PMCID: PMC10575785 DOI: 10.1038/s41380-023-02005-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Despite enormous efforts employing various approaches, the molecular pathology in the schizophrenia brain remains elusive. On the other hand, the knowledge of the association between the disease risk and changes in the DNA sequences, in other words, our understanding of the genetic pathology of schizophrenia, has dramatically improved over the past two decades. As the consequence, now we can explain more than 20% of the liability to schizophrenia by considering all analyzable common genetic variants including those with weak or no statistically significant association. Also, a large-scale exome sequencing study identified single genes whose rare mutations substantially increase the risk for schizophrenia, of which six genes (SETD1A, CUL1, XPO7, GRIA3, GRIN2A, and RB1CC1) showed odds ratios larger than ten. Based on these findings together with the preceding discovery of copy number variants (CNVs) with similarly large effect sizes, multiple disease models with high etiological validity have been generated and analyzed. Studies of the brains of these models, as well as transcriptomic and epigenomic analyses of patient postmortem tissues, have provided new insights into the molecular pathology of schizophrenia. In this review, we overview the current knowledge acquired from these studies, their limitations, and directions for future research that may redefine schizophrenia based on biological alterations in the responsible organ rather than operationalized criteria.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
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11
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Santarriaga S, Gerlovin K, Layadi Y, Karmacharya R. Human stem cell-based models to study synaptic dysfunction and cognition in schizophrenia: A narrative review. Schizophr Res 2023:S0920-9964(23)00084-1. [PMID: 36925354 PMCID: PMC10500041 DOI: 10.1016/j.schres.2023.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
Cognitive impairment is the strongest predictor of functional outcomes in schizophrenia and is hypothesized to result from synaptic dysfunction. However, targeting synaptic plasticity and cognitive deficits in patients remains a significant clinical challenge. A comprehensive understanding of synaptic plasticity and the molecular basis of learning and memory in a disease context can provide specific targets for the development of novel therapeutics targeting cognitive impairments in schizophrenia. Here, we describe the role of synaptic plasticity in cognition, summarize evidence for synaptic dysfunction in schizophrenia and demonstrate the use of patient derived induced-pluripotent stem cells for studying synaptic plasticity in vitro. Lastly, we discuss current advances and future technologies for bridging basic science research of synaptic dysfunction with clinical and translational research that can be used to predict treatment response and develop novel therapeutics.
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Affiliation(s)
- Stephanie Santarriaga
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chemical Biology and Therapeutic Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Kaia Gerlovin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chemical Biology and Therapeutic Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yasmine Layadi
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chimie ParisTech, Université Paris Sciences et Lettres, Paris, France
| | - Rakesh Karmacharya
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chemical Biology and Therapeutic Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Schizophrenia and Bipolar Disorder Program, McLean Hospital, Belmont, MA, USA.
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12
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Wawrzczak-Bargieła A, Bilecki W, Maćkowiak M. Epigenetic Targets in Schizophrenia Development and Therapy. Brain Sci 2023; 13:brainsci13030426. [PMID: 36979236 PMCID: PMC10046502 DOI: 10.3390/brainsci13030426] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Schizophrenia is regarded as a neurodevelopmental disorder with its course progressing throughout life. However, the aetiology and development of schizophrenia are still under investigation. Several data suggest that the dysfunction of epigenetic mechanisms is known to be involved in the pathomechanism of this mental disorder. The present article revised the epigenetic background of schizophrenia based on the data available in online databases (PubMed, Scopus). This paper focused on the role of epigenetic regulation, such as DNA methylation, histone modifications, and interference of non-coding RNAs, in schizophrenia development. The article also reviewed the available data related to epigenetic regulation that may modify the severity of the disease as a possible target for schizophrenia pharmacotherapy. Moreover, the effects of antipsychotics on epigenetic malfunction in schizophrenia are discussed based on preclinical and clinical results. The obtainable data suggest alterations of epigenetic regulation in schizophrenia. Moreover, they also showed the important role of epigenetic modifications in antipsychotic action. There is a need for more data to establish the role of epigenetic mechanisms in schizophrenia therapy. It would be of special interest to find and develop new targets for schizophrenia therapy because patients with schizophrenia could show little or no response to current pharmacotherapy and have treatment-resistant schizophrenia.
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13
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Shmakova AA, Semina EV, Neyfeld EA, Tsygankov BD, Karagyaur MN. [An analysis of the relationship between genetic factors and the risk of schizophrenia]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:26-36. [PMID: 36843456 DOI: 10.17116/jnevro202312302126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The etiology and pathogenesis of schizophrenia remain poorly understood, but it has been established that the contribution of heredity to the development of the disease is about 80-85%. Over the past decade, significant progress has been made in the search for specific genetic variants associated with the development of schizophrenia. The review discusses the results of modern large-scale studies aimed at searching for genetic associations with schizophrenia: genome-wide association studies (GWAS) and the search for rare variants (mutations or copy number variations, CNV), including the use of whole exome sequencing. We synthesize data on currently known genes that are significantly associated with schizophrenia and discuss their biological functions in order to identify the main molecular pathways involved in the pathophysiology of schizophrenia.
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Affiliation(s)
- A A Shmakova
- Koltzov Institute of Developmental Biology, Moscow, Russia
| | - E V Semina
- Lomonosov Moscow State University, Moscow, Russia.,Institute for Regenerative Medicine - Lomonosov Moscow State University, Moscow, Russia
| | - E A Neyfeld
- Lomonosov Moscow State University, Moscow, Russia
| | | | - M N Karagyaur
- Lomonosov Moscow State University, Moscow, Russia.,Institute for Regenerative Medicine - Lomonosov Moscow State University, Moscow, Russia
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14
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Nozawa O, Miyata M, Shiotani H, Kameyama T, Komaki R, Shimizu T, Kuriu T, Kashiwagi Y, Sato Y, Koebisu M, Aiba A, Okabe S, Mizutani K, Takai Y. Necl2/3-mediated mechanism for tripartite synapse formation. Development 2023; 150:285820. [PMID: 36458527 DOI: 10.1242/dev.200931] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Ramified, polarized protoplasmic astrocytes interact with synapses via perisynaptic astrocyte processes (PAPs) to form tripartite synapses. These astrocyte-synapse interactions mutually regulate their structures and functions. However, molecular mechanisms for tripartite synapse formation remain elusive. We developed an in vitro co-culture system for mouse astrocytes and neurons that induced astrocyte ramifications and PAP formation. Co-cultured neurons were required for astrocyte ramifications in a neuronal activity-dependent manner, and synaptically-released glutamate and activation of astrocytic mGluR5 metabotropic glutamate receptor were likely involved in astrocyte ramifications. Astrocytic Necl2 trans-interacted with axonal Necl3, inducing astrocyte-synapse interactions and astrocyte functional polarization by recruiting EAAT1/2 glutamate transporters and Kir4.1 K+ channel to the PAPs, without affecting astrocyte ramifications. This Necl2/3 trans-interaction increased functional synapse number. Thus, astrocytic Necl2, synaptically-released glutamate and axonal Necl3 cooperatively formed tripartite glutamatergic synapses in vitro. Studies on hippocampal mossy fiber synapses in Necl3 knockout and Necl2/3 double knockout mice confirmed these previously unreported mechanisms for astrocyte-synapse interactions and astrocyte functional polarization in vivo.
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Affiliation(s)
- Osamu Nozawa
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Muneaki Miyata
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Hajime Shiotani
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Takeshi Kameyama
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Ryouhei Komaki
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Tatsuhiro Shimizu
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Toshihiko Kuriu
- Osaka Medical and Pharmaceutical University, Research and Development Center, Takatsuki, Osaka 569-8686, Japan
| | - Yutaro Kashiwagi
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuka Sato
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Michinori Koebisu
- Section of Animal Research and Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Atsu Aiba
- Section of Animal Research and Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kiyohito Mizutani
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
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15
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Ritchie FD, Lizarraga SB. The role of histone methyltransferases in neurocognitive disorders associated with brain size abnormalities. Front Neurosci 2023; 17:989109. [PMID: 36845425 PMCID: PMC9950662 DOI: 10.3389/fnins.2023.989109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Brain size is controlled by several factors during neuronal development, including neural progenitor proliferation, neuronal arborization, gliogenesis, cell death, and synaptogenesis. Multiple neurodevelopmental disorders have co-morbid brain size abnormalities, such as microcephaly and macrocephaly. Mutations in histone methyltransferases that modify histone H3 on Lysine 36 and Lysine 4 (H3K36 and H3K4) have been identified in neurodevelopmental disorders involving both microcephaly and macrocephaly. H3K36 and H3K4 methylation are both associated with transcriptional activation and are proposed to sterically hinder the repressive activity of the Polycomb Repressor Complex 2 (PRC2). During neuronal development, tri-methylation of H3K27 (H3K27me3) by PRC2 leads to genome wide transcriptional repression of genes that regulate cell fate transitions and neuronal arborization. Here we provide a review of neurodevelopmental processes and disorders associated with H3K36 and H3K4 histone methyltransferases, with emphasis on processes that contribute to brain size abnormalities. Additionally, we discuss how the counteracting activities of H3K36 and H3K4 modifying enzymes vs. PRC2 could contribute to brain size abnormalities which is an underexplored mechanism in relation to brain size control.
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16
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Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. A CpG island-encoded mechanism protects genes from premature transcription termination. Nat Commun 2023; 14:726. [PMID: 36759609 PMCID: PMC9911701 DOI: 10.1038/s41467-023-36236-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
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Affiliation(s)
- Amy L Hughes
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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17
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Roth C, Kilpinen H, Kurian MA, Barral S. Histone lysine methyltransferase-related neurodevelopmental disorders: current knowledge and saRNA future therapies. Front Cell Dev Biol 2023; 11:1090046. [PMID: 36923252 PMCID: PMC10009263 DOI: 10.3389/fcell.2023.1090046] [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: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
Neurodevelopmental disorders encompass a group of debilitating diseases presenting with motor and cognitive dysfunction, with variable age of onset and disease severity. Advances in genetic diagnostic tools have facilitated the identification of several monogenic chromatin remodeling diseases that cause Neurodevelopmental disorders. Chromatin remodelers play a key role in the neuro-epigenetic landscape and regulation of brain development; it is therefore not surprising that mutations, leading to loss of protein function, result in aberrant neurodevelopment. Heterozygous, usually de novo mutations in histone lysine methyltransferases have been described in patients leading to haploinsufficiency, dysregulated protein levels and impaired protein function. Studies in animal models and patient-derived cell lines, have highlighted the role of histone lysine methyltransferases in the regulation of cell self-renewal, cell fate specification and apoptosis. To date, in depth studies of histone lysine methyltransferases in oncology have provided strong evidence of histone lysine methyltransferase dysregulation as a determinant of cancer progression and drug resistance. As a result, histone lysine methyltransferases have become an important therapeutic target for the treatment of different cancer forms. Despite recent advances, we still lack knowledge about the role of histone lysine methyltransferases in neuronal development. This has hampered both the study and development of precision therapies for histone lysine methyltransferases-related Neurodevelopmental disorders. In this review, we will discuss the current knowledge of the role of histone lysine methyltransferases in neuronal development and disease progression. We will also discuss how RNA-based technologies using small-activating RNAs could potentially provide a novel therapeutic approach for the future treatment of histone lysine methyltransferase haploinsufficiency in these Neurodevelopmental disorders, and how they could be first tested in state-of-the-art patient-derived neuronal models.
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Affiliation(s)
- Charlotte Roth
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Helena Kilpinen
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Serena Barral
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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18
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Chong ZS, Khong ZJ, Tay SH, Ng SY. Metabolic contributions to neuronal deficits caused by genomic disruption of schizophrenia risk gene SETD1A. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:115. [PMID: 36581615 PMCID: PMC9800576 DOI: 10.1038/s41537-022-00326-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
Regulation of neuronal metabolism during early brain development is crucial for directing synaptic plasticity and proper circuit formation. Alterations in neuronal glycolysis or mitochondrial function are associated with several neuropsychiatric disorders, including schizophrenia. Recently, loss-of-function mutations in SETD1A, a histone methyltransferase, have been linked to increased schizophrenia risk and global developmental delay. Here, we show that heterozygous disruption of SETD1A in human induced pluripotent stem cell (hiPSC)-derived neurons results in reduced neurite outgrowth and spontaneous activity, two phenotypes commonly associated with schizophrenia, as well as alterations in metabolic capacity. Furthermore, supplementing culture media with metabolic intermediates ameliorated changes in neurite outgrowth and spontaneous activity, suggesting that metabolic dysfunction contributes to neuronal phenotypes caused by SETD1A haploinsufficiency. These findings highlight a previously unknown connection between SETD1A function, metabolic regulation, and neuron development, and identifies alternative avenues for therapeutic development.
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Affiliation(s)
- Zheng-Shan Chong
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Zi Jian Khong
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, Singapore, Singapore
| | - Shermaine Huiping Tay
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Shi-Yan Ng
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431National University of Singapore, Yong Loo Lin School of Medicine (Department of Physiology, Singapore, Singapore ,grid.276809.20000 0004 0636 696XNational Neuroscience Institute, Singapore, Singapore
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19
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Günther A, Hanganu-Opatz IL. Neuronal oscillations: early biomarkers of psychiatric disease? Front Behav Neurosci 2022; 16:1038981. [PMID: 36600993 PMCID: PMC9806131 DOI: 10.3389/fnbeh.2022.1038981] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Our understanding of the environmental and genetic factors contributing to the wide spectrum of neuropsychiatric disorders has significantly increased in recent years. Impairment of neuronal network activity during early development has been suggested as a contributor to the emergence of neuropsychiatric pathologies later in life. Still, the neurobiological substrates underlying these disorders remain yet to be fully understood and the lack of biomarkers for early diagnosis has impeded research into curative treatment options. Here, we briefly review current knowledge on potential biomarkers for emerging neuropsychiatric disease. Moreover, we summarize recent findings on aberrant activity patterns in the context of psychiatric disease, with a particular focus on their potential as early biomarkers of neuropathologies, an essential step towards pre-symptomatic diagnosis and, thus, early intervention.
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20
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Abstract
Verifying causal effects of neural circuits is essential for proving a direct circuit-behavior relationship. However, techniques for tagging only active neurons with high spatiotemporal precision remain at the beginning stages. Here we develop the soma-targeted Cal-Light (ST-Cal-Light) which selectively converts somatic calcium rise triggered by action potentials into gene expression. Such modification simultaneously increases the signal-to-noise ratio of reporter gene expression and reduces the light requirement for successful labeling. Because of the enhanced efficacy, the ST-Cal-Light enables the tagging of functionally engaged neurons in various forms of behaviors, including context-dependent fear conditioning, lever-pressing choice behavior, and social interaction behaviors. We also target kainic acid-sensitive neuronal populations in the hippocampus which subsequently suppress seizure symptoms, suggesting ST-Cal-Light's applicability in controlling disease-related neurons. Furthermore, the generation of a conditional ST-Cal-Light knock-in mouse provides an opportunity to tag active neurons in a region- or cell-type specific manner via crossing with other Cre-driver lines. Thus, the versatile ST-Cal-Light system links somatic action potentials to behaviors with high temporal precision, and ultimately allows functional circuit dissection at a single cell resolution.
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21
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SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia. Cell Rep 2022; 41:111727. [PMID: 36450243 PMCID: PMC9771694 DOI: 10.1016/j.celrep.2022.111727] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/08/2022] [Accepted: 11/03/2022] [Indexed: 12/02/2022] Open
Abstract
Histone methyltransferase SETD1A is critical for acute myeloid leukemia (AML) cell survival, but the molecular mechanism driving SETD1A gene regulation remains elusive. To delineate the role of SETD1A, we utilize a protein degrader technology to induce rapid SETD1A degradation in AML cell lines. SETD1A degradation results in immediate downregulation of transcripts associated with DNA repair and heme biosynthesis pathways. CRISPR-based functional analyses and metabolomics reveal an essential role of SETD1A to maintain mitochondrial respiration in AML cells. These SETD1A targets are enriched in head-to-head (H2H) genes. SETD1A degradation disrupts a non-enzymatic SETD1A domain-dependent cyclin K function, increases the Ser5P RNA polymerase II (RNAPII) at the transcriptional start site (TSS), and induces the promoter-proximal pausing of RNAPII in a strand-specific manner. This study reveals a non-enzymatic role for SETD1A in transcriptional pause release and provides insight into the mechanism of RNAPII pausing and its function in cancer.
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22
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Clapcote SJ. How can we obtain truly translational mouse models to improve clinical outcomes in schizophrenia? Dis Model Mech 2022; 15:dmm049970. [PMID: 36441105 PMCID: PMC10655820 DOI: 10.1242/dmm.049970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Schizophrenia is a serious mental illness affecting 0.7% of the world's population. Despite over 50 years of schizophrenia drug identification and development, there have been no fundamental advances in the treatment of schizophrenia since the 1980s. Complex genetic aetiology and elusive pathomechanisms have made it difficult for researchers to develop models that sufficiently reflect pathophysiology to support effective drug discovery. However, recent large-scale, well-powered genomic studies have identified risk genes that represent tractable entry points to decipher disease mechanisms in heterogeneous patient populations and develop targeted treatments. Replicating schizophrenia-associated gene variants in mouse models is an important strategy to start understanding their pathogenicity and role in disease biology. Furthermore, longitudinal studies in a wide range of genetic mouse models from early postnatal life are required to assess the progression of this disease through developmental stages to improve early diagnostic strategies and enable preventative measures. By expanding and refining our approach to schizophrenia research, we can improve prevention strategies and treatment of this debilitating disease.
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23
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Griffin A, Mahesh A, Tiwari VK. Disruption of the gene regulatory programme in neurodevelopmental disorders. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194860. [PMID: 36007842 DOI: 10.1016/j.bbagrm.2022.194860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Cortical development consists of a series of synchronised events, including fate transition of cortical progenitors, neuronal migration, specification and connectivity. It is becoming clear that gene expression programs governing these events rely on the interplay between signalling molecules, transcription factors and epigenetic mechanisms. When genetic or environmental factors disrupt expression of genes involved in important brain development processes, neurodevelopmental disorders can occur. This review aims to highlight how recent advances in technologies have helped uncover and imitate the gene regulatory mechanisms commonly disrupted in neurodevelopmental disorders.
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Affiliation(s)
- Aoife Griffin
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom
| | - Arun Mahesh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom.
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24
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Clifton NE, Bosworth ML, Haan N, Rees E, Holmans PA, Wilkinson LS, Isles AR, Collins MO, Hall J. Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function. Hum Mol Genet 2022; 31:3095-3106. [PMID: 35531971 PMCID: PMC9476630 DOI: 10.1093/hmg/ddac105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Large-scale genomic studies of schizophrenia implicate genes involved in the epigenetic regulation of transcription by histone methylation and genes encoding components of the synapse. However, the interactions between these pathways in conferring risk to psychiatric illness are unknown. Loss-of-function (LoF) mutations in the gene encoding histone methyltransferase, SETD1A, confer substantial risk to schizophrenia. Among several roles, SETD1A is thought to be involved in the development and function of neuronal circuits. Here, we employed a multi-omics approach to study the effects of heterozygous Setd1a LoF on gene expression and synaptic composition in mouse cortex across five developmental timepoints from embryonic day 14 to postnatal day 70. Using RNA sequencing, we observed that Setd1a LoF resulted in the consistent downregulation of genes enriched for mitochondrial pathways. This effect extended to the synaptosome, in which we found age-specific disruption to both mitochondrial and synaptic proteins. Using large-scale patient genomics data, we observed no enrichment for genetic association with schizophrenia within differentially expressed transcripts or proteins, suggesting they derive from a distinct mechanism of risk from that implicated by genomic studies. This study highlights biological pathways through which SETD1A LOF may confer risk to schizophrenia. Further work is required to determine whether the effects observed in this model reflect human pathology.
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Affiliation(s)
- Nicholas E Clifton
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK.,University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK.,Neuroscience and Mental Health Research Institute, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Matthew L Bosworth
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Niels Haan
- Neuroscience and Mental Health Research Institute, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Peter A Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Lawrence S Wilkinson
- Neuroscience and Mental Health Research Institute, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Anthony R Isles
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jeremy Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK.,Neuroscience and Mental Health Research Institute, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
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25
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Park J, Lee K, Kim K, Yi SJ. The role of histone modifications: from neurodevelopment to neurodiseases. Signal Transduct Target Ther 2022; 7:217. [PMID: 35794091 PMCID: PMC9259618 DOI: 10.1038/s41392-022-01078-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/11/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulatory mechanisms, including DNA methylation, histone modification, chromatin remodeling, and microRNA expression, play critical roles in cell differentiation and organ development through spatial and temporal gene regulation. Neurogenesis is a sophisticated and complex process by which neural stem cells differentiate into specialized brain cell types at specific times and regions of the brain. A growing body of evidence suggests that epigenetic mechanisms, such as histone modifications, allow the fine-tuning and coordination of spatiotemporal gene expressions during neurogenesis. Aberrant histone modifications contribute to the development of neurodegenerative and neuropsychiatric diseases. Herein, recent progress in understanding histone modifications in regulating embryonic and adult neurogenesis is comprehensively reviewed. The histone modifications implicated in neurodegenerative and neuropsychiatric diseases are also covered, and future directions in this area are provided.
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Affiliation(s)
- Jisu Park
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyubin Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
| | - Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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26
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Bayley R, Borel V, Moss RJ, Sweatman E, Ruis P, Ormrod A, Goula A, Mottram RMA, Stanage T, Hewitt G, Saponaro M, Stewart GS, Boulton SJ, Higgs MR. H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ. Mol Cell 2022; 82:1924-1939.e10. [PMID: 35439434 PMCID: PMC9616806 DOI: 10.1016/j.molcel.2022.03.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/14/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.
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Affiliation(s)
- Rachel Bayley
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Valerie Borel
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Rhiannon J Moss
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ellie Sweatman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Philip Ruis
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Alice Ormrod
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Amalia Goula
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Rachel M A Mottram
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tyler Stanage
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Graeme Hewitt
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK.
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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27
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Wang S, Rhijn JRV, Akkouh I, Kogo N, Maas N, Bleeck A, Ortiz IS, Lewerissa E, Wu KM, Schoenmaker C, Djurovic S, van Bokhoven H, Kleefstra T, Nadif Kasri N, Schubert D. Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway. Cell Rep 2022; 39:110790. [PMID: 35508131 PMCID: PMC7615788 DOI: 10.1016/j.celrep.2022.110790] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/20/2022] [Accepted: 04/15/2022] [Indexed: 12/11/2022] Open
Abstract
Heterozygous loss-of-function (LoF) mutations in SETD1A, which encodes a subunit of histone H3 lysine 4 methyltransferase, cause a neurodevelopmental syndrome and increase the risk for schizophrenia. Using CRISPR-Cas9, we generate excitatory/inhibitory neuronal networks from human induced pluripotent stem cells with a SETD1A heterozygous LoF mutation (SETD1A+/-). Our data show that SETD1A haploinsufficiency results in morphologically increased dendritic complexity and functionally increased bursting activity. This network phenotype is primarily driven by SETD1A haploinsufficiency in glutamatergic neurons. In accordance with the functional changes, transcriptomic profiling reveals perturbations in gene sets associated with glutamatergic synaptic function. At the molecular level, we identify specific changes in the cyclic AMP (cAMP)/Protein Kinase A pathway pointing toward a hyperactive cAMP pathway in SETD1A+/- neurons. Finally, by pharmacologically targeting the cAMP pathway, we are able to rescue the network deficits in SETD1A+/- cultures. Our results demonstrate a link between SETD1A and the cAMP-dependent pathway in human neurons.
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Affiliation(s)
- Shan Wang
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Jon-Ruben van Rhijn
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Ibrahim Akkouh
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway; NORMENT, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Naoki Kogo
- Department of Human Genetics, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands; Department of Biophysics, Donders Institute for Brain Cognition and Behaviour, 6525 AJ Nijmegen, the Netherlands
| | - Nadine Maas
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Anna Bleeck
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Irene Santisteban Ortiz
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Elly Lewerissa
- Department of Human Genetics, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands
| | - Ka Man Wu
- Department of Human Genetics, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands
| | - Chantal Schoenmaker
- Department of Human Genetics, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway; NORMENT, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Hans van Bokhoven
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands; Department of Human Genetics, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands
| | - Nael Nadif Kasri
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands; Department of Human Genetics, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands
| | - Dirk Schubert
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands.
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28
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Shiwaku H, Katayama S, Kondo K, Nakano Y, Tanaka H, Yoshioka Y, Fujita K, Tamaki H, Takebayashi H, Terasaki O, Nagase Y, Nagase T, Kubota T, Ishikawa K, Okazawa H, Takahashi H. Autoantibodies against NCAM1 from patients with schizophrenia cause schizophrenia-related behavior and changes in synapses in mice. Cell Rep Med 2022; 3:100597. [PMID: 35492247 PMCID: PMC9043990 DOI: 10.1016/j.xcrm.2022.100597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
From genetic and etiological studies, autoimmune mechanisms underlying schizophrenia are suspected; however, the details remain unclear. In this study, we describe autoantibodies against neural cell adhesion molecule (NCAM1) in patients with schizophrenia (5.4%, cell-based assay; 6.7%, ELISA) in a Japanese cohort (n = 223). Anti-NCAM1 autoantibody disrupts both NCAM1-NCAM1 and NCAM1-glial cell line-derived neurotrophic factor (GDNF) interactions. Furthermore, the anti-NCAM1 antibody purified from patients with schizophrenia interrupts NCAM1-Fyn interaction and inhibits phosphorylation of FAK, MEK1, and ERK1 when introduced into the cerebrospinal fluid of mice and also reduces the number of spines and synapses in frontal cortex. In addition, it induces schizophrenia-related behavior in mice, including deficient pre-pulse inhibition and cognitive impairment. In conclusion, anti-NCAM1 autoantibodies in patients with schizophrenia cause schizophrenia-related behavior and changes in synapses in mice. These antibodies may be a potential therapeutic target and serve as a biomarker to distinguish a small but treatable subgroup in heterogeneous patients with schizophrenia. Some patients with schizophrenia are positive for anti-NCAM1 autoantibodies Anti-NCAM1 antibody from schizophrenia patients inhibits NCAM1-NCAM1 interactions Anti-NCAM1 antibody from schizophrenia patients reduces spines and synapses in mice Anti-NCAM1 antibody from patients induces schizophrenia-related behavior in mice
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Affiliation(s)
- Hiroki Shiwaku
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo 113-8510, Japan.
| | - Shingo Katayama
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo 113-8510, Japan
| | - Kanoh Kondo
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Yuri Nakano
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo 113-8510, Japan
| | - Hikari Tanaka
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Yuki Yoshioka
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kyota Fujita
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Haruna Tamaki
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University Graduate School, Tokyo 113-8510, Japan
| | | | | | | | | | - Tetsuo Kubota
- Department of Medical Technology, Tsukuba International University, Ibaraki 300-0051, Japan
| | - Kinya Ishikawa
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hitoshi Okazawa
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hidehiko Takahashi
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo 113-8510, Japan.
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29
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Morikawa R, Watanabe Y, Igeta H, Arta RK, Ikeda M, Okazaki S, Hoya S, Saito T, Otsuka I, Egawa J, Tanifuji T, Iwata N, Someya T. Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis. Psychiatry Res 2022; 310:114481. [PMID: 35235885 DOI: 10.1016/j.psychres.2022.114481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/29/2022]
Abstract
SETD1A has been identified as a substantial risk gene for schizophrenia. To further investigate the role of SETD1A in the genetic etiology of schizophrenia in the Japanese population, we performed resequencing and association analyses. First, we resequenced the SETD1A coding regions of 974 patients with schizophrenia. Then, we genotyped variants, prioritized via resequencing, in 2,027 patients with schizophrenia and 2,664 controls. Next, we examined the association between SETD1A and schizophrenia in 3,001 patients with schizophrenia and 2,664 controls. Finally, we performed a retrospective chart review of patients with prioritized SETD1A variants. We identified two novel missense variants (p.Ser575Pro and p.Glu857Gln) via resequencing. We did not detect these variants in 4,691 individuals via genotyping. These variants were not significantly associated with schizophrenia in the association analysis. Additionally, we found that a schizophrenia patient with the p.Glu857Gln variant had developmental delays. In conclusion, novel SETD1A missense variants were exclusively identified in Japanese patients with schizophrenia. However, our study does not provide evidence for the contribution of these variants to the genetic etiology of schizophrenia in the Japanese population.
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Affiliation(s)
- Ryo Morikawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata 951-8510, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata 951-8510, Japan.
| | - Hirofumi Igeta
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata 951-8510, Japan
| | - Reza K Arta
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata 951-8510, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Satoshi Hoya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata 951-8510, Japan
| | - Takeo Saito
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata 951-8510, Japan
| | - Takaki Tanifuji
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata 951-8510, Japan
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30
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Chen R, Liu Y, Djekidel MN, Chen W, Bhattacherjee A, Chen Z, Scolnick E, Zhang Y. Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis. SCIENCE ADVANCES 2022; 8:eabm1077. [PMID: 35245111 PMCID: PMC8896793 DOI: 10.1126/sciadv.abm1077] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/13/2022] [Indexed: 05/30/2023]
Abstract
Schizophrenia (SCZ) is a chronic, serious mental disorder. Although more than 200 SCZ-associated genes have been identified, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a (SET domain containing 1A) haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression in brain regions highly relevant to SCZ. Single-cell RNA sequencing revealed that Setd1a heterozygosity causes highly variable transcriptional adaptations across different cell types in prefrontal cortex (PFC) and striatum. The Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with changes in histone H3 lysine 4 trimethylation. Many of the genes dysregulated in Setd1a+/- mice are involved in neuron morphogenesis and synaptic function. Consistently, Setd1a+/- mice exhibit certain behavioral features of patients with SCZ. Collectively, our study establishes Setd1a+/- mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific dysregulation that potentially underlies SCZ pathogenesis.
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Affiliation(s)
- Renchao Chen
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Yiqiong Liu
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Mohamed N. Djekidel
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Wenqiang Chen
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Aritra Bhattacherjee
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Ed Scolnick
- The Stanley Center for Psychiatric Research at Broad Institute, Cambridge, MA 02142, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA
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31
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Wang S, Bleeck A, Nadif Kasri N, Kleefstra T, van Rhijn JR, Schubert D. SETD1A Mediated H3K4 Methylation and Its Role in Neurodevelopmental and Neuropsychiatric Disorders. Front Mol Neurosci 2021; 14:772000. [PMID: 34803610 PMCID: PMC8595121 DOI: 10.3389/fnmol.2021.772000] [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: 09/08/2021] [Accepted: 10/12/2021] [Indexed: 01/07/2023] Open
Abstract
Posttranslational modification of histones and related gene regulation are shown to be affected in an increasing number of neurological disorders. SETD1A is a chromatin remodeler that influences gene expression through the modulation of mono- di- and trimethylation marks on Histone-H3-Lysine-4 (H3K4me1/2/3). H3K4 methylation is predominantly described to result in transcriptional activation, with its mono- di- and trimethylated forms differentially enriched at promoters or enhancers. Recently, dominant mostly de novo variants in SETD1A have clinically been linked to developmental delay, intellectual disability (DD/ID), and schizophrenia (SCZ). Affected individuals often display both developmental and neuropsychiatric abnormalities. The primary diagnoses are mainly dependent on the age at which the individual is assessed. Investigations in mouse models of SETD1A dysfunction have been able to recapitulate key behavioral features associated with ID and SCZ. Furthermore, functional investigations suggest disrupted synaptic and neuronal network function in these mouse models. In this review, we provide an overview of pre-clinical studies on the role of SETD1A in neuronal development. A better understanding of the pathobiology underlying these disorders may provide novel opportunities for therapeutic intervention. As such, we will discuss possible strategies to move forward in elucidating the genotype-phenotype correlation in SETD1A associated disorders.
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Affiliation(s)
- Shan Wang
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Anna Bleeck
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands.,Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands.,Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, Netherlands
| | - Jon-Ruben van Rhijn
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
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32
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Ng B, Casazza W, Kim NH, Wang C, Farhadi F, Tasaki S, Bennett DA, De Jager PL, Gaiteri C, Mostafavi S. Cascading epigenomic analysis for identifying disease genes from the regulatory landscape of GWAS variants. PLoS Genet 2021; 17:e1009918. [PMID: 34807913 PMCID: PMC8648125 DOI: 10.1371/journal.pgen.1009918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 12/06/2021] [Accepted: 10/30/2021] [Indexed: 12/14/2022] Open
Abstract
The majority of genetic variants detected in genome wide association studies (GWAS) exert their effects on phenotypes through gene regulation. Motivated by this observation, we propose a multi-omic integration method that models the cascading effects of genetic variants from epigenome to transcriptome and eventually to the phenome in identifying target genes influenced by risk alleles. This cascading epigenomic analysis for GWAS, which we refer to as CEWAS, comprises two types of models: one for linking cis genetic effects to epigenomic variation and another for linking cis epigenomic variation to gene expression. Applying these models in cascade to GWAS summary statistics generates gene level statistics that reflect genetically-driven epigenomic effects. We show on sixteen brain-related GWAS that CEWAS provides higher gene detection rate than related methods, and finds disease relevant genes and gene sets that point toward less explored biological processes. CEWAS thus presents a novel means for exploring the regulatory landscape of GWAS variants in uncovering disease mechanisms. The majority of genetic variants detected in genome wide association studies (GWAS) exert their effects on phenotypes through gene regulation. Motivated by this observation, we propose a multi-omic integration method that models the cascading effects of genetic variants from epigenome to transcriptome and eventually to the phenome in identifying target genes influenced by risk alleles. This cascading epigenomic analysis for GWAS, which we refer to as CEWAS, combines the effect of genetic variants on DNA methylation as well as gene expression. We show on sixteen brain-related GWAS that CEWAS provides higher gene detection rate than related methods, and finds disease relevant genes and gene sets that point toward less explored biological processes.
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Affiliation(s)
- Bernard Ng
- Department of Statistics and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - William Casazza
- Department of Statistics and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Nam Hee Kim
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chendi Wang
- Department of Statistics and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Farnush Farhadi
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Shinya Tasaki
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Christopher Gaiteri
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Sara Mostafavi
- Department of Statistics and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Paul G. Allen School for Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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33
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Faust TE, Gunner G, Schafer DP. Mechanisms governing activity-dependent synaptic pruning in the developing mammalian CNS. Nat Rev Neurosci 2021; 22:657-673. [PMID: 34545240 PMCID: PMC8541743 DOI: 10.1038/s41583-021-00507-y] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Almost 60 years have passed since the initial discovery by Hubel and Wiesel that changes in neuronal activity can elicit developmental rewiring of the central nervous system (CNS). Over this period, we have gained a more comprehensive picture of how both spontaneous neural activity and sensory experience-induced changes in neuronal activity guide CNS circuit development. Here we review activity-dependent synaptic pruning in the mammalian CNS, which we define as the removal of a subset of synapses, while others are maintained, in response to changes in neural activity in the developing nervous system. We discuss the mounting evidence that immune and cell-death molecules are important mechanistic links by which changes in neural activity guide the pruning of specific synapses, emphasizing the role of glial cells in this process. Finally, we discuss how these developmental pruning programmes may go awry in neurodevelopmental disorders of the human CNS, focusing on autism spectrum disorder and schizophrenia. Together, our aim is to give an overview of how the field of activity-dependent pruning research has evolved, led to exciting new questions and guided the identification of new, therapeutically relevant mechanisms that result in aberrant circuit development in neurodevelopmental disorders.
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Affiliation(s)
- Travis E Faust
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Georgia Gunner
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dorothy P Schafer
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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34
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Nagahama K, Fujino S, Watanabe T, Uesaka N, Kano M. Combining electrophysiology and optogenetics for functional screening of pyramidal neurons in the mouse prefrontal cortex. STAR Protoc 2021; 2:100469. [PMID: 33937875 PMCID: PMC8079664 DOI: 10.1016/j.xpro.2021.100469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Here, we present a comprehensive protocol to analyze the roles of disease-related genes in synaptic transmission. We have developed a pipeline of electrophysiological techniques and combined these with optogenetics in the medial prefrontal cortex of mice. This methodology provides a cost-effective, faster, and easier screening approach to elucidate functional aspects of single genes in several regions in the mouse brain such as a specific layer of the mPFC. For complete details on the use and execution of this protocol, please refer to Nagahama et al. (2020) and Sacai et al. (2020).
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Affiliation(s)
- Kenichiro Nagahama
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo 113-0033, Japan
| | - Shuhei Fujino
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takaki Watanabe
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo 113-0033, Japan
| | - Naofumi Uesaka
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo 113-0033, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo 113-0033, Japan
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35
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MIYAZAKI T, ABE H, UCHIDA H, TAKAHASHI T. Translational medicine of the glutamate AMPA receptor. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:1-21. [PMID: 33431723 PMCID: PMC7859086 DOI: 10.2183/pjab.97.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/30/2020] [Indexed: 05/05/2023]
Abstract
Psychiatric and neurological disorders severely hamper patient's quality of life. Despite their high unmet needs, the development of diagnostics and therapeutics has only made slow progress. This is due to limited evidence on the biological basis of these disorders in humans. Synapses are essential structural units of neurotransmission, and neuropsychiatric disorders are considered as "synapse diseases". Thus, a translational approach with synaptic physiology is crucial to tackle these disorders. Among a variety of synapses, excitatory glutamatergic synapses play central roles in neuronal functions. The glutamate α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor (AMPAR) is a principal component of glutamatergic neurotransmission; therefore, it is considered to be a promising translational target. Here, we review the limitations of current diagnostics and therapeutics of neuropsychiatric disorders and advocate the urgent need for the promotion of translational medicine based on the synaptic physiology of AMPAR. Furthermore, we introduce our recent translational approach to these disorders by targeting at AMPARs.
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Affiliation(s)
- Tomoyuki MIYAZAKI
- Yokohama City University Graduate School of Medicine, Department of Physiology, Yokohama, Kanagawa, Japan
| | - Hiroki ABE
- Yokohama City University Graduate School of Medicine, Department of Physiology, Yokohama, Kanagawa, Japan
| | - Hiroyuki UCHIDA
- Keio University School of Medicine, Department of Neuropsychiatry, Tokyo, Japan
| | - Takuya TAKAHASHI
- Yokohama City University Graduate School of Medicine, Department of Physiology, Yokohama, Kanagawa, Japan
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