2
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Powell SK, Liao W, O’Shea C, Kammourh S, Ghorbani S, Rigat R, Elahi R, Deans PJM, Le DJ, Agarwal P, Seow WQ, Wang KC, Akbarian S, Brennand KJ. Schizophrenia Risk Mapping and Functional Engineering of the 3D Genome in Three Neuronal Subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549339. [PMID: 37502907 PMCID: PMC10370055 DOI: 10.1101/2023.07.17.549339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Common variants associated with schizophrenia are concentrated in non-coding regulatory sequences, but their precise target genes are context-dependent and impacted by cell-type-specific three-dimensional spatial chromatin organization. Here, we map long-range chromosomal conformations in isogenic human dopaminergic, GABAergic, and glutamatergic neurons to track developmentally programmed shifts in the regulatory activity of schizophrenia risk loci. Massive repressive compartmentalization, concomitant with the emergence of hundreds of neuron-specific multi-valent chromatin architectural stripes, occurs during neuronal differentiation, with genes interconnected to genetic risk loci through these long-range chromatin structures differing in their biological roles from genes more proximal to sequences conferring heritable risk. Chemically induced CRISPR-guided chromosomal loop-engineering for the proximal risk gene SNAP91 and distal risk gene BHLHE22 profoundly alters synaptic development and functional activity. Our findings highlight the large-scale cell-type-specific reorganization of chromosomal conformations at schizophrenia risk loci during neurodevelopment and establish a causal link between risk-associated gene-regulatory loop structures and neuronal function.
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Affiliation(s)
- Samuel K. Powell
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Will Liao
- New York Genome Center, New York, NY, 10029
| | - Callan O’Shea
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Sarah Kammourh
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Sadaf Ghorbani
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Raymond Rigat
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Rahat Elahi
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - PJ Michael Deans
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Derek J. Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Poonam Agarwal
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
| | - Wei Qiang Seow
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
| | - Kevin C. Wang
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, 94305, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, California, 94304, USA
| | - Schahram Akbarian
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
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3
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Hong Y, Yang Q, Song H, Ming GL. Opportunities and limitations for studying neuropsychiatric disorders using patient-derived induced pluripotent stem cells. Mol Psychiatry 2023; 28:1430-1439. [PMID: 36782062 PMCID: PMC10213114 DOI: 10.1038/s41380-023-01990-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Neuropsychiatric disorders affect a large proportion of the global population and there is an urgent need to understand the pathogenesis and to develop novel and improved treatments of these devastating disorders. However, the diverse symptomatology combined with complex polygenic etiology, and the limited access to disorder-relevant cell types in human brains represent a major obstacle for mechanistic disease research. Conventional animal models, such as rodents, are limited by inherent species differences in brain development, architecture, and function. Advances in human induced pluripotent stem cells (hiPSCs) technologies have provided platforms for new discoveries in neuropsychiatric disorders. First, hiPSC-based disease models enable unprecedented investigation of psychiatric disorders at the molecular, cellular, and structural levels. Second, hiPSCs derived from patients with known genetics, symptoms, and drug response profiles offer an opportunity to recapitulate pathogenesis in relevant cell types and provide novel approaches for understanding disease mechanisms and for developing effective treatments. Third, genome-editing technologies have extended the potential of hiPSCs for generating models to elucidate the genetic basis of rare monogenetic and complex polygenic psychiatric disorders and to establish the causality between genotype and phenotype. Here we review opportunities and limitations for studying psychiatric disorders using various hiPSC-derived model systems.
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Affiliation(s)
- Yan Hong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qian Yang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Plaza-Jennings A, Valada A, Akbarian S. 3D Genome Plasticity in Normal and Diseased Neurodevelopment. Genes (Basel) 2022; 13:1999. [PMID: 36360237 PMCID: PMC9690570 DOI: 10.3390/genes13111999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 10/17/2023] Open
Abstract
Non-random spatial organization of the chromosomal material inside the nuclei of brain cells emerges as an important regulatory layer of genome organization and function in health and disease. Here, we discuss how integrative approaches assessing chromatin in context of the 3D genome is providing new insights into normal and diseased neurodevelopment. Studies in primate (incl. human) and rodent brain have confirmed that chromosomal organization in neurons and glia undergoes highly dynamic changes during pre- and early postnatal development, with potential for plasticity across a much wider age window. For example, neuronal 3D genomes from juvenile and adult cerebral cortex and hippocampus undergo chromosomal conformation changes at hundreds of loci in the context of learning and environmental enrichment, viral infection, and neuroinflammation. Furthermore, locus-specific structural DNA variations, such as micro-deletions, duplications, repeat expansions, and retroelement insertions carry the potential to disrupt the broader epigenomic and transcriptional landscape far beyond the boundaries of the site-specific variation, highlighting the critical importance of long-range intra- and inter-chromosomal contacts for neuronal and glial function.
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Affiliation(s)
- Amara Plaza-Jennings
- Graduate School of Biomedical Sciences, Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aditi Valada
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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7
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Colizzi M, Bortoletto R, Costa R, Bhattacharyya S, Balestrieri M. The Autism-Psychosis Continuum Conundrum: Exploring the Role of the Endocannabinoid System. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5616. [PMID: 35565034 PMCID: PMC9105053 DOI: 10.3390/ijerph19095616] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
Evidence indicates shared physiopathological mechanisms between autism and psychosis. In this regard, the endocannabinoid system has been suggested to modulate neural circuits during the early stage of neurodevelopment, with implications for both autism and psychosis. Nevertheless, such potential common markers of disease have been investigated in both autism and psychosis spectrum disorders, without considering the conundrum of differentiating the two groups of conditions in terms of diagnosis and treatment. Here, we systematically review all human and animal studies examining the endocannabinoid system and its biobehavioral correlates in the association between autism and psychosis. Studies indicate overlapping biobehavioral aberrancies between autism and schizophrenia, subject to correction by modulation of the endocannabinoid system. In addition, common cannabinoid-based pharmacological strategies have been identified, exerting epigenetic effects across genes controlling neural mechanisms shared between autism and schizophrenia. Interestingly, a developmental and transgenerational trajectory between autism and schizophrenia is supported by evidence that exogenous alteration of the endocannabinoid system promotes progression to inheritable psychosis phenotypes in the context of biobehavioral autism vulnerability. However, evidence for a diametral association between autism and psychosis is scant. Several clinical implications follow from evidence of a developmental continuum between autism and psychosis as a function of the endocannabinoid system dysregulation.
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Affiliation(s)
- Marco Colizzi
- Unit of Psychiatry, Department of Medicine (DAME), University of Udine, 33100 Udine, Italy;
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK;
| | - Riccardo Bortoletto
- Child and Adolescent Neuropsychiatry Unit, Maternal-Child Integrated Care Department, Integrated University Hospital of Verona, 37126 Verona, Italy;
| | - Rosalia Costa
- Community Mental Health Team, Friuli Centrale University Health Service (ASUFC), 33057 Palmanova, Italy;
| | - Sagnik Bhattacharyya
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK;
| | - Matteo Balestrieri
- Unit of Psychiatry, Department of Medicine (DAME), University of Udine, 33100 Udine, Italy;
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8
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Nishimura K, Nitta T, Doi K, Takata K. Rapid conversion of human induced pluripotent stem cells into dopaminergic neurons by inducible expression of two transcription factors. Stem Cells Dev 2022; 31:269-277. [PMID: 35420042 DOI: 10.1089/scd.2021.0363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) including human embryonic stem cells and human induced pluripotent stem cells (hiPSCs) provide promising sources for regenerative therapy, disease modeling, and drug screening. Relevant efforts have been invested in establishing robust induction protocols for PSC-derived dopaminergic (DA) neuron generation by mimicking brain development-related signaling pathways. However, these protocols require fully trained techniques and a long time to yield mature DA neurons. In this study, to accelerate the entire process, we generated a hiPSC line differentiating into DA neurons by the inducible force expression of two transcription factors ASCL1 and LMX1A. Using this hiPSC line, we established a rapid and simple induction protocol to generate mature DA neurons in 28 days. The induced DA neurons were characterized by gene expression and immunohistochemical analyses of fundamental DA neuronal markers. Moreover, the cell functional properties were analyzed by a multielectrode array system on day 28. This resource offers future applications for high-throughput screening, such as drug development and toxicology that require highly validated DA neurons.
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Affiliation(s)
- Kaneyasu Nishimura
- Kyoto Pharmaceutical University, 12916, Kyoto, Japan.,Doshisha University, 12757, Kyoto, Kyoto, Japan;
| | - Tatsumi Nitta
- Kyoto Pharmaceutical University, 12916, Kyoto, Kyoto, Japan;
| | - Keisuke Doi
- Kyoto Pharmaceutical University, 12916, Kyoto, Kyoto, Japan;
| | - Kazuyuki Takata
- Kyoto Pharmaceutical University, 12916, Kyoto, Kyoto, Japan;
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