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Ma Y, Bendl J, Hartley BJ, Fullard JF, Abdelaal R, Ho SM, Kosoy R, Gochman P, Rapoport J, Hoffman GE, Brennand KJ, Roussos P. Activity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders. Biol Psychiatry 2024; 95:187-198. [PMID: 37454787 PMCID: PMC10787819 DOI: 10.1016/j.biopsych.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 06/07/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Converging evidence from large-scale genetic and postmortem studies highlights the role of aberrant neurotransmission and genetic regulation in brain-related disorders. However, identifying neuronal activity-regulated transcriptional programs in the human brain and understanding how changes contribute to disease remain challenging. METHODS To better understand how the activity-dependent regulome contributes to risk for brain-related disorders, we profiled the transcriptomic and epigenomic changes following neuronal depolarization in human induced pluripotent stem cell-derived glutamatergic neurons (NGN2) from 6 patients with schizophrenia and 5 control participants. RESULTS Multiomic data integration associated global patterns of chromatin accessibility with gene expression and identified enhancer-promoter interactions in glutamatergic neurons. Within 1 hour of potassium chloride-induced depolarization, independent of diagnosis, glutamatergic neurons displayed substantial activity-dependent changes in the expression of genes regulating synaptic function. Depolarization-induced changes in the regulome revealed significant heritability enrichment for schizophrenia and Parkinson's disease, adding to mounting evidence that sequence variation within activation-dependent regulatory elements contributes to the genetic risk for brain-related disorders. Gene coexpression network analysis elucidated interactions among activity-dependent and disease-associated genes and pointed to a key driver (NAV3) that interacted with multiple genes involved in axon guidance. CONCLUSIONS Overall, we demonstrated that deciphering the activity-dependent regulome in glutamatergic neurons reveals novel targets for advanced diagnosis and therapy.
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Affiliation(s)
- Yixuan Ma
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brigham J Hartley
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rawan Abdelaal
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York
| | - Seok-Man Ho
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York
| | - Roman Kosoy
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Judith Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristen J Brennand
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York.
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, New York; Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, New York.
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2
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Chang A, Botteri E, Gillis RD, Löfling L, Le CP, Ziegler AI, Chung NC, Rowe MC, Fabb SA, Hartley BJ, Nowell CJ, Kurozumi S, Gandini S, Munzone E, Montagna E, Eikelis N, Phillips SE, Honda C, Masuda K, Katayama A, Oyama T, Cole SW, Lambert GW, Walker AK, Sloan EK. Beta-blockade enhances anthracycline control of metastasis in triple-negative breast cancer. Sci Transl Med 2023; 15:eadf1147. [PMID: 37099632 DOI: 10.1126/scitranslmed.adf1147] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Beta-adrenergic blockade has been associated with improved cancer survival in patients with triple-negative breast cancer (TNBC), but the mechanisms of these effects remain unclear. In clinical epidemiological analyses, we identified a relationship between beta-blocker use and anthracycline chemotherapy in protecting against TNBC progression, disease recurrence, and mortality. We recapitulated the effect of beta-blockade on anthracycline efficacy in xenograft mouse models of TNBC. In metastatic 4T1.2 and MDA-MB-231 mouse models of TNBC, beta-blockade improved the efficacy of the anthracycline doxorubicin by reducing metastatic development. We found that anthracycline chemotherapy alone, in the absence of beta-blockade, increased sympathetic nerve fiber activity and norepinephrine concentration in mammary tumors through the induction of nerve growth factor (NGF) by tumor cells. Moreover, using preclinical models and clinical samples, we found that anthracycline chemotherapy up-regulated β2-adrenoceptor expression and amplified receptor signaling in tumor cells. Neurotoxin inhibition of sympathetic neural signaling in mammary tumors using 6-hydroxydopamine or genetic deletion of NGF or β2-adrenoceptor in tumor cells enhanced the therapeutic effect of anthracycline chemotherapy by reducing metastasis in xenograft mouse models. These findings reveal a neuromodulatory effect of anthracycline chemotherapy that undermines its potential therapeutic impact, which can be overcome by inhibiting β2-adrenergic signaling in the tumor microenvironment. Supplementing anthracycline chemotherapy with adjunctive β2-adrenergic antagonists represents a potential therapeutic strategy for enhancing the clinical management of TNBC.
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Affiliation(s)
- Aeson Chang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Edoardo Botteri
- Department of Research, Cancer Registry of Norway, Oslo 0379, Norway
| | - Ryan D Gillis
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Lukas Löfling
- Department of Research, Cancer Registry of Norway, Oslo 0379, Norway
| | - Caroline P Le
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
- Jreissati Pancreatic Centre, Epworth HealthCare, Richmond, VIC 3121, Australia
| | - Alexandra I Ziegler
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Ni-Chun Chung
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Matthew C Rowe
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Stewart A Fabb
- Drug Delivery, Disposition, and Dynamics Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | | | - Cameron J Nowell
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sasagu Kurozumi
- Department of Breast Surgery, International University of Health and Welfare, Narita, Chiba 286-8520, Japan
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Sara Gandini
- Molecular and Pharmaco-Epidemiology Unit, Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Elisabetta Munzone
- Division of Medical Senology, European Institute of Oncology IRCCS, Milan, Italy
| | - Emilia Montagna
- Division of Medical Senology, European Institute of Oncology IRCCS, Milan, Italy
| | - Nina Eikelis
- Iverson Health Innovation Research Institute and School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Human Neurotransmitters Laboratory, Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Sarah E Phillips
- Iverson Health Innovation Research Institute and School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Human Neurotransmitters Laboratory, Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Chikako Honda
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Kei Masuda
- Department of Diagnostic Pathology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Ayaka Katayama
- Department of Diagnostic Pathology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Tetsunari Oyama
- Department of Diagnostic Pathology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Steve W Cole
- Departments of Psychiatry and Biobehavioral Sciences and Medicine, Division of Hematology-Oncology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, and the Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Gavin W Lambert
- Iverson Health Innovation Research Institute and School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Human Neurotransmitters Laboratory, Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Adam K Walker
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW 2031, Australia
- Discipline of Psychiatry and Mental Health, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Erica K Sloan
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, and the Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA
- Division of Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
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3
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Hafez AK, Zimmerman AJ, Papageorgiou G, Chandrasekaran J, Amoah SK, Lin R, Lozano E, Pierotti C, Dell'Orco M, Hartley BJ, Alural B, Lalonde J, Esposito JM, Berretta S, Squassina A, Chillotti C, Voloudakis G, Shao Z, Fullard JF, Brennand KJ, Turecki G, Roussos P, Perlis RH, Haggarty SJ, Perrone-Bizzozero N, Brigman JL, Mellios N. A bidirectional competitive interaction between circHomer1 and Homer1b within the orbitofrontal cortex regulates reversal learning. Cell Rep 2022; 38:110282. [PMID: 35045295 PMCID: PMC8809079 DOI: 10.1016/j.celrep.2021.110282] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/28/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
Abstract
Although circular RNAs (circRNAs) are enriched in the brain, their relevance for brain function and psychiatric disorders is poorly understood. Here, we show that circHomer1 is inversely associated with relative HOMER1B mRNA isoform levels in both the orbitofrontal cortex (OFC) and stem-cell-derived neuronal cultures of subjects with psychiatric disorders. We further demonstrate that in vivo circHomer1 knockdown (KD) within the OFC can inhibit the synaptic expression of Homer1b mRNA. Furthermore, we show that circHomer1 directly binds to Homer1b mRNA and that Homer1b-specific KD increases synaptic circHomer1 levels and improves OFC-mediated behavioral flexibility. Importantly, double circHomer1 and Homer1b in vivo co-KD results in a complete rescue in circHomer1-associated alterations in both chance reversal learning and synaptic gene expression. Lastly, we uncover an RNA-binding protein that can directly bind to circHomer1 and promote its biogenesis. Taken together, our data provide mechanistic insights into the importance of circRNAs in brain function and disease.
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Affiliation(s)
- Alexander K Hafez
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA; Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Amber J Zimmerman
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Grigorios Papageorgiou
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | - Stephen K Amoah
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA; Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rixing Lin
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Evelyn Lozano
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Caroline Pierotti
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Michela Dell'Orco
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Brigham J Hartley
- Pamela Sklar Division of Psychiatric Genomics, Friedman Brain Institute, Departments of Genetics and Genomic Sciences, Neuroscience, and Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Begüm Alural
- Center for Genomic Medicine, Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jasmin Lalonde
- Center for Genomic Medicine, Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Sabina Berretta
- Translational Neuroscience Laboratory, Mclean Hospital, Belmont, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Caterina Chillotti
- Unit of Clinical Pharmacology, University Hospital Agency of Cagliari, Cagliari, Italy
| | - Georgios Voloudakis
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhiping Shao
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Friedman Brain Institute, Departments of Genetics and Genomic Sciences, Neuroscience, and Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Roy H Perlis
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA; Center for Experimental Drugs and Diagnostics, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen J Haggarty
- Center for Genomic Medicine, Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Jonathan L Brigman
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Nikolaos Mellios
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA; Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
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4
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Fischbacher B, Hedaya S, Hartley BJ, Wang Z, Lallos G, Hutson D, Zimmer M, Brammer J, Paull D. Modular deep learning enables automated identification of monoclonal cell lines. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00354-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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5
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Issler O, van der Zee YY, Ramakrishnan A, Wang J, Tan C, Loh YHE, Purushothaman I, Walker DM, Lorsch ZS, Hamilton PJ, Peña CJ, Flaherty E, Hartley BJ, Torres-Berrío A, Parise EM, Kronman H, Duffy JE, Estill MS, Calipari ES, Labonté B, Neve RL, Tamminga CA, Brennand KJ, Dong Y, Shen L, Nestler EJ. Sex-Specific Role for the Long Non-coding RNA LINC00473 in Depression. Neuron 2020; 106:912-926.e5. [PMID: 32304628 PMCID: PMC7305959 DOI: 10.1016/j.neuron.2020.03.023] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/27/2020] [Accepted: 03/23/2020] [Indexed: 12/26/2022]
Abstract
Depression is a common disorder that affects women at twice the rate of men. Here, we report that long non-coding RNAs (lncRNAs), a recently discovered class of regulatory transcripts, represent about one-third of the differentially expressed genes in the brains of depressed humans and display complex region- and sex-specific patterns of regulation. We identified the primate-specific, neuronal-enriched gene LINC00473 as downregulated in prefrontal cortex (PFC) of depressed females but not males. Using viral-mediated gene transfer to express LINC00473 in adult mouse PFC neurons, we mirrored the human sex-specific phenotype by inducing stress resilience solely in female mice. This sex-specific phenotype was accompanied by changes in synaptic function and gene expression selectively in female mice and, along with studies of human neuron-like cells in culture, implicates LINC00473 as a CREB effector. Together, our studies identify LINC00473 as a female-specific driver of stress resilience that is aberrant in female depression.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Behavior, Animal
- Depression/genetics
- Depression/metabolism
- Depressive Disorder, Major/genetics
- Depressive Disorder, Major/metabolism
- Down-Regulation
- Female
- Humans
- Male
- Mice
- Mice, Transgenic
- Middle Aged
- Neurons/metabolism
- Prefrontal Cortex/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA-Seq
- Resilience, Psychological
- Sex Factors
- Stress, Psychological/genetics
- Stress, Psychological/metabolism
- Young Adult
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Affiliation(s)
- Orna Issler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yentl Y van der Zee
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University, 6229 ER, Maastricht, the Netherlands
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Junshi Wang
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Chunfeng Tan
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yong-Hwee E Loh
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Immanuel Purushothaman
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deena M Walker
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zachary S Lorsch
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter J Hamilton
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine J Peña
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erin Flaherty
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brigham J Hartley
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angélica Torres-Berrío
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric M Parise
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hope Kronman
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia E Duffy
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Molly S Estill
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erin S Calipari
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benoit Labonté
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rachael L Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, MA 02139, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Dong
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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6
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Zimmerman AJ, Hafez AK, Amoah SK, Rodriguez BA, Dell’Orco M, Lozano E, Hartley BJ, Alural B, Lalonde J, Chander P, Webster MJ, Perlis RH, Brennand KJ, Haggarty SJ, Weick J, Perrone-Bizzozero N, Brigman JL, Mellios N. A psychiatric disease-related circular RNA controls synaptic gene expression and cognition. Mol Psychiatry 2020; 25:2712-2727. [PMID: 31988434 PMCID: PMC7577899 DOI: 10.1038/s41380-020-0653-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/17/2019] [Accepted: 01/16/2020] [Indexed: 02/06/2023]
Abstract
Although circular RNAs (circRNAs) are enriched in the mammalian brain, very little is known about their potential involvement in brain function and psychiatric disease. Here, we show that circHomer1a, a neuronal-enriched circRNA abundantly expressed in the frontal cortex, derived from Homer protein homolog 1 (HOMER1), is significantly reduced in both the prefrontal cortex (PFC) and induced pluripotent stem cell-derived neuronal cultures from patients with schizophrenia (SCZ) and bipolar disorder (BD). Moreover, alterations in circHomer1a were positively associated with the age of onset of SCZ in both the dorsolateral prefrontal cortex (DLPFC) and orbitofrontal cortex (OFC). No correlations between the age of onset of SCZ and linear HOMER1 mRNA were observed, whose expression was mostly unaltered in BD and SCZ postmortem brain. Using in vivo circRNA-specific knockdown of circHomer1a in mouse PFC, we show that it modulates the expression of numerous alternative mRNA transcripts from genes involved in synaptic plasticity and psychiatric disease. Intriguingly, in vivo circHomer1a knockdown in mouse OFC resulted in specific deficits in OFC-mediated cognitive flexibility. Lastly, we demonstrate that the neuronal RNA-binding protein HuD binds to circHomer1a and can influence its synaptic expression in the frontal cortex. Collectively, our data uncover a novel psychiatric disease-associated circRNA that regulates synaptic gene expression and cognitive flexibility.
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Affiliation(s)
- Amber J. Zimmerman
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Alexander K. Hafez
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Stephen K. Amoah
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA ,Autophagy inflammation and metabolism (AIM) center, Albuquerque, NM USA
| | - Brian A. Rodriguez
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Michela Dell’Orco
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Evelyn Lozano
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Brigham J. Hartley
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Begüm Alural
- grid.32224.350000 0004 0386 9924Departments of Neurology and Psychiatry, Center for Genomic Medicine, Chemical Neurobiology Laboratory, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Jasmin Lalonde
- grid.32224.350000 0004 0386 9924Departments of Neurology and Psychiatry, Center for Genomic Medicine, Chemical Neurobiology Laboratory, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA ,grid.34429.380000 0004 1936 8198Present Address: Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada
| | - Praveen Chander
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Maree J. Webster
- grid.453353.70000 0004 0473 2858Laboratory of Brain Research, Stanley Medical Research Institute, Chevy Chase, MD USA
| | - Roy H. Perlis
- grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA ,grid.32224.350000 0004 0386 9924Center for Experimental Drugs and Diagnostics, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA USA
| | - Kristen J. Brennand
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Stephen J. Haggarty
- grid.32224.350000 0004 0386 9924Departments of Neurology and Psychiatry, Center for Genomic Medicine, Chemical Neurobiology Laboratory, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Jason Weick
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Nora Perrone-Bizzozero
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Jonathan L. Brigman
- grid.266832.b0000 0001 2188 8502Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM USA
| | - Nikolaos Mellios
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA. .,Autophagy inflammation and metabolism (AIM) center, Albuquerque, NM, USA.
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7
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Readhead B, Hartley BJ, Eastwood BJ, Collier DA, Evans D, Farias R, He C, Hoffman G, Sklar P, Dudley JT, Schadt EE, Savić R, Brennand KJ. Author Correction: Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nat Commun 2018; 9:4926. [PMID: 30451900 PMCID: PMC6242834 DOI: 10.1038/s41467-018-07326-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Benjamin Readhead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Brigham J Hartley
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - David A Collier
- Eli Lilly and Company Ltd, Erl Wood Manor, Surrey, UK.,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - David Evans
- Eli Lilly and Company Ltd, Erl Wood Manor, Surrey, UK
| | - Richard Farias
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ching He
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriel Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, Connecticut, USA.
| | - Radoslav Savić
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, Connecticut, USA.
| | - Kristen J Brennand
- Department of Genetics and Genomic Sciences, 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. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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8
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Readhead B, Hartley BJ, Eastwood BJ, Collier DA, Evans D, Farias R, He C, Hoffman G, Sklar P, Dudley JT, Schadt EE, Savić R, Brennand KJ. Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nat Commun 2018; 9:4412. [PMID: 30356048 PMCID: PMC6200740 DOI: 10.1038/s41467-018-06515-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/07/2018] [Indexed: 12/11/2022] Open
Abstract
A lack of biologically relevant screening models hinders the discovery of better treatments for schizophrenia (SZ) and other neuropsychiatric disorders. Here we compare the transcriptional responses of 8 commonly used cancer cell lines (CCLs) directly with that of human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells (NPCs) from 12 individuals with SZ and 12 controls across 135 drugs, generating 4320 unique drug-response transcriptional signatures. We identify those drugs that reverse post-mortem SZ-associated transcriptomic signatures, several of which also differentially regulate neuropsychiatric disease-associated genes in a cell type (hiPSC NPC vs. CCL) and/or a diagnosis (SZ vs. control)-dependent manner. Overall, we describe a proof-of-concept application of transcriptomic drug screening to hiPSC-based models, demonstrating that the drug-induced gene expression differences observed with patient-derived hiPSC NPCs are enriched for SZ biology, thereby revealing a major advantage of incorporating cell type and patient-specific platforms in drug discovery. Unbiased large scale screening of small molecules for drug discovery in psychiatric disease is technically challenging and financially costly. Here, Readhead and colleagues integrate in silico and in vitro approaches to design and conduct transcriptomic drug screening in schizophrenia patient-derived neural cells, in order to survey novel pathologies and points of intervention.
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Affiliation(s)
- Benjamin Readhead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Brigham J Hartley
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - David A Collier
- Eli Lilly and Company Ltd, Erl Wood Manor, Surrey, UK.,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - David Evans
- Eli Lilly and Company Ltd, Erl Wood Manor, Surrey, UK
| | - Richard Farias
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ching He
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriel Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, Connecticut, USA.
| | - Radoslav Savić
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, Connecticut, USA.
| | - Kristen J Brennand
- Department of Genetics and Genomic Sciences, 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. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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9
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Xu J, Hartley BJ, Kurup P, Phillips A, Topol A, Xu M, Ononenyi C, Foscue E, Ho SM, Baguley TD, Carty N, Barros CS, Müller U, Gupta S, Gochman P, Rapoport J, Ellman JA, Pittenger C, Aronow B, Nairn AC, Nestor MW, Lombroso PJ, Brennand KJ. Inhibition of STEP 61 ameliorates deficits in mouse and hiPSC-based schizophrenia models. Mol Psychiatry 2018; 23:271-281. [PMID: 27752082 PMCID: PMC5395367 DOI: 10.1038/mp.2016.163] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/13/2016] [Accepted: 08/11/2016] [Indexed: 02/03/2023]
Abstract
The brain-specific tyrosine phosphatase, STEP (STriatal-Enriched protein tyrosine Phosphatase) is an important regulator of synaptic function. STEP normally opposes synaptic strengthening by increasing N-methyl D-aspartate glutamate receptor (NMDAR) internalization through dephosphorylation of GluN2B and inactivation of the kinases extracellular signal-regulated kinase 1/2 and Fyn. Here we show that STEP61 is elevated in the cortex in the Nrg1+/- knockout mouse model of schizophrenia (SZ). Genetic reduction or pharmacological inhibition of STEP prevents the loss of NMDARs from synaptic membranes and reverses behavioral deficits in Nrg1+/- mice. STEP61 protein is also increased in cortical lysates from the central nervous system-specific ErbB2/4 mouse model of SZ, as well as in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons and Ngn2-induced excitatory neurons, from two independent SZ patient cohorts. In these selected SZ models, increased STEP61 protein levels likely reflect reduced ubiquitination and degradation. These convergent findings from mouse and hiPSC SZ models provide evidence for STEP61 dysfunction in SZ.
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Affiliation(s)
- J Xu
- Child Study Center, Yale University, New Haven, CT, USA
| | - B J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Kurup
- Child Study Center, Yale University, New Haven, CT, USA
| | - A Phillips
- Hussman Institute for Autism, Baltimore, MD, USA
| | - A Topol
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Xu
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - C Ononenyi
- Child Study Center, Yale University, New Haven, CT, USA
| | - E Foscue
- Child Study Center, Yale University, New Haven, CT, USA
| | - S-M Ho
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Developmental and Stem Cell Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T D Baguley
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - N Carty
- Child Study Center, Yale University, New Haven, CT, USA
| | - C S Barros
- Dorris Neuroscience Center, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA,Plymouth University School of Medicine, Plymouth UK
| | - U Müller
- Dorris Neuroscience Center, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - S Gupta
- UC Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - P Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J A Ellman
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - C Pittenger
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - B Aronow
- UC Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - A C Nairn
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - M W Nestor
- Hussman Institute for Autism, Baltimore, MD, USA
| | - P J Lombroso
- Child Study Center, Yale University, New Haven, CT, USA,Department of Psychiatry, Yale University, New Haven, CT, USA,Department of Neurobiology, Yale University, New Haven, CT, USA,Department of Psychiatry, Yale University, New Haven, CT, USA E-mail:
| | - K J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA. E-mail:
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10
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Hoffman GE, Hartley BJ, Flaherty E, Ladran I, Gochman P, Ruderfer DM, Stahl EA, Rapoport J, Sklar P, Brennand KJ. Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains. Nat Commun 2017; 8:2225. [PMID: 29263384 PMCID: PMC5738408 DOI: 10.1038/s41467-017-02330-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/20/2017] [Indexed: 12/20/2022] Open
Abstract
The power of human induced pluripotent stem cell (hiPSC)-based studies to resolve the smaller effects of common variants within the size of cohorts that can be realistically assembled remains uncertain. We identified and accounted for a variety of technical and biological sources of variation in a large case/control schizophrenia (SZ) hiPSC-derived cohort of neural progenitor cells and neurons. Reducing the stochastic effects of the differentiation process by correcting for cell type composition boosted the SZ signal and increased the concordance with post-mortem data sets. We predict a growing convergence between hiPSC and post-mortem studies as both approaches expand to larger cohort sizes. For studies of complex genetic disorders, to maximize the power of hiPSC cohorts currently feasible, in most cases and whenever possible, we recommend expanding the number of individuals even at the expense of the number of replicate hiPSC clones.
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Affiliation(s)
- Gabriel E Hoffman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Brigham J Hartley
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erin Flaherty
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ian Ladran
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peter Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Douglas M Ruderfer
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Division of Genetic Medicine, Departments of Medicine, Psychiatry and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Eli A Stahl
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judith Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pamela Sklar
- Department of Genetics and Genomics, 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.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kristen J Brennand
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute of Genomics and Multiscale Biology, 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. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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11
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Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Tran N, Rittenhouse CA, Simone A, Ruderfer DM, Johnson J, Readhead B, Hadas Y, Gochman PA, Wang YC, Shah H, Cagney G, Rapoport J, Gage FH, Dudley JT, Sklar P, Mattheisen M, Cotter D, Fang G, Brennand KJ. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Rep 2017; 20:2525. [PMID: 28877483 DOI: 10.1016/j.celrep.2017.08.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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12
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Zhou T, Tan L, Cederquist GY, Fan Y, Hartley BJ, Mukherjee S, Tomishima M, Brennand KJ, Zhang Q, Schwartz RE, Evans T, Studer L, Chen S. High-Content Screening in hPSC-Neural Progenitors Identifies Drug Candidates that Inhibit Zika Virus Infection in Fetal-like Organoids and Adult Brain. Cell Stem Cell 2017; 21:274-283.e5. [PMID: 28736217 PMCID: PMC5553280 DOI: 10.1016/j.stem.2017.06.017] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 05/02/2017] [Accepted: 06/28/2017] [Indexed: 12/21/2022]
Abstract
Zika virus (ZIKV) infects fetal and adult human brain and is associated with serious neurological complications. To date, no therapeutic treatment is available to treat ZIKV-infected patients. We performed a high-content chemical screen using human pluripotent stem cell-derived cortical neural progenitor cells (hNPCs) and found that hippeastrine hydrobromide (HH) and amodiaquine dihydrochloride dihydrate (AQ) can inhibit ZIKV infection in hNPCs. Further validation showed that HH also rescues ZIKV-induced growth and differentiation defects in hNPCs and human fetal-like forebrain organoids. Finally, HH and AQ inhibit ZIKV infection in adult mouse brain in vivo. Strikingly, HH suppresses viral propagation when administered to adult mice with active ZIKV infection, highlighting its therapeutic potential. Our approach highlights the power of stem cell-based screens and validation in human forebrain organoids and mouse models in identifying drug candidates for treating ZIKV infection and related neurological complications in fetal and adult patients.
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Affiliation(s)
- Ting Zhou
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lei Tan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Gustav Y Cederquist
- The Center for Stem Cell Biology, New York, NY 10065, USA; Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Yujie Fan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Brigham J Hartley
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Suranjit Mukherjee
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Mark Tomishima
- The Center for Stem Cell Biology, New York, NY 10065, USA; Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Kristen J Brennand
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Qisheng Zhang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Physiology Biophysics and Systems Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, New York, NY 10065, USA; Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA.
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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13
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Tcw J, Wang M, Pimenova AA, Bowles KR, Hartley BJ, Lacin E, Machlovi SI, Abdelaal R, Karch CM, Phatnani H, Slesinger PA, Zhang B, Goate AM, Brennand KJ. An Efficient Platform for Astrocyte Differentiation from Human Induced Pluripotent Stem Cells. Stem Cell Reports 2017; 9:600-614. [PMID: 28757165 PMCID: PMC5550034 DOI: 10.1016/j.stemcr.2017.06.018] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 11/24/2022] Open
Abstract
Growing evidence implicates the importance of glia, particularly astrocytes, in neurological and psychiatric diseases. Here, we describe a rapid and robust method for the differentiation of highly pure populations of replicative astrocytes from human induced pluripotent stem cells (hiPSCs), via a neural progenitor cell (NPC) intermediate. We evaluated this protocol across 42 NPC lines (derived from 30 individuals). Transcriptomic analysis demonstrated that hiPSC-astrocytes from four individuals are highly similar to primary human fetal astrocytes and characteristic of a non-reactive state. hiPSC-astrocytes respond to inflammatory stimulants, display phagocytic capacity, and enhance microglial phagocytosis. hiPSC-astrocytes also possess spontaneous calcium transient activity. Our protocol is a reproducible, straightforward (single medium), and rapid (<30 days) method to generate populations of hiPSC-astrocytes that can be used for neuron-astrocyte and microglia-astrocyte co-cultures for the study of neuropsychiatric disorders.
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Affiliation(s)
- Julia Tcw
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Anna A Pimenova
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Kathryn R Bowles
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Brigham J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Emre Lacin
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Saima I Machlovi
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Rawan Abdelaal
- New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hemali Phatnani
- New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Paul A Slesinger
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Alison M Goate
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA.
| | - Kristen J Brennand
- Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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14
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Ho SM, Hartley BJ, Flaherty E, Rajarajan P, Abdelaal R, Obiorah I, Barretto N, Muhammad H, Phatnani HP, Akbarian S, Brennand KJ. Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes. Stem Cell Reports 2017; 9:615-628. [PMID: 28757163 PMCID: PMC5550013 DOI: 10.1016/j.stemcr.2017.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 12/11/2022] Open
Abstract
Modulation of transcription, either synthetic activation or repression, via dCas9-fusion proteins is a relatively new methodology with the potential to facilitate high-throughput up- or downregulation studies of gene function. Genetic studies of neurodevelopmental disorders have identified a growing list of risk variants, including both common single-nucleotide variants and rare copy-number variations, many of which are associated with genes having limited functional annotations. By applying a CRISPR-mediated gene-activation/repression platform to populations of human-induced pluripotent stem cell-derived neural progenitor cells, neurons, and astrocytes, we demonstrate that it is possible to manipulate endogenous expression levels of candidate neuropsychiatric risk genes across these three cell types. Although proof-of-concept studies using catalytically inactive Cas9-fusion proteins to modulate transcription have been reported, here we present a detailed survey of the reproducibility of gRNA positional effects across a variety of neurodevelopmental disorder-relevant risk genes, donors, neural cell types, and dCas9 effectors. The efficacy of CRISPR-mediated transcript modulation varies between genes gRNAs should be re-validated for each individual, cell type, and dCas9-effector
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Affiliation(s)
- Seok-Man Ho
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brigham J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erin Flaherty
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Prashanth Rajarajan
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rawan Abdelaal
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Ifeanyi Obiorah
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Natalie Barretto
- 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; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hamza Muhammad
- 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; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hemali P Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, 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; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- 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 Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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15
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Jiang Y, Loh YHE, Rajarajan P, Hirayama T, Liao W, Kassim BS, Javidfar B, Hartley BJ, Kleofas L, Park RB, Labonte B, Ho SM, Chandrasekaran S, Do C, Ramirez BR, Peter CJ, C W JT, Safaie BM, Morishita H, Roussos P, Nestler EJ, Schaefer A, Tycko B, Brennand KJ, Yagi T, Shen L, Akbarian S. The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. Nat Genet 2017; 49:1239-1250. [PMID: 28671686 PMCID: PMC5560095 DOI: 10.1038/ng.3906] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
We report locus-specific disintegration of megabase-scale chromosomal conformations in brain after neuronal ablation of Kmt1e/Setdb1 histone H3-lysine 9 methyltransferase, including a large topologically associated 1.2Mb domain conserved in human and mouse and encompassing >70 genes at the clustered Protocadherin (cPcdh) locus. TADcPcdh in mutant neurons showed abnormal accumulations of CTCF transcriptional regulator and 3D genome organizer at cryptic binding sites, converted into permissive state with DNA cytosine hypomethylation and histone hyperacetylation. Broadly upregulated expression across cPcdh included defective S-type Protocadherin single-cell stochastic constraint. Setdb1-dependent loop formations, bypassing 0.2–1Mb of linear genome, radiated from TADPcdh fringes towards cPcdh cis-regulatory sequences, counterbalanced shorter-range facilitative promoter-enhancer contacts and carried loop-bound polymorphisms associated with genetic risk for schizophrenia. We show that KRAB-zinc finger Setdb1 repressor complex, shielding neuronal 3D genomes from excess CTCF binding, is critically required for structural maintenance of TADcPcdh.
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Affiliation(s)
- Yan Jiang
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yong-Hwee Eddie Loh
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Prashanth Rajarajan
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Teruyoshi Hirayama
- Kokoro-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Will Liao
- New York Genome Center, New York, New York, USA
| | - Bibi S Kassim
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brigham J Hartley
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Kleofas
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Royce B Park
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benoit Labonte
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Seok-Man Ho
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sandhya Chandrasekaran
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Catherine Do
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Brianna R Ramirez
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Cyril J Peter
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Julia T C W
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brian M Safaie
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hirofumi Morishita
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Panos Roussos
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Mental Illness Research, Education and Clinical Center, James J. Peters Virginia Medical Center, New York, New York, USA
| | - Eric J Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anne Schaefer
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Kristen J Brennand
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Takeshi Yagi
- Kokoro-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Li Shen
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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16
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Chatterton Z, Hartley BJ, Seok MH, Mendelev N, Chen S, Milekic M, Rosoklija G, Stankov A, Trencevsja-Ivanovska I, Brennand K, Ge Y, Dwork AJ, Haghighi F. In utero exposure to maternal smoking is associated with DNA methylation alterations and reduced neuronal content in the developing fetal brain. Epigenetics Chromatin 2017; 10:4. [PMID: 28149327 PMCID: PMC5270321 DOI: 10.1186/s13072-017-0111-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Intrauterine exposure to maternal smoking is linked to impaired executive function and behavioral problems in the offspring. Maternal smoking is associated with reduced fetal brain growth and smaller volume of cortical gray matter in childhood, indicating that prenatal exposure to tobacco may impact cortical development and manifest as behavioral problems. Cellular development is mediated by changes in epigenetic modifications such as DNA methylation, which can be affected by exposure to tobacco. Results In this study, we sought to ascertain how maternal smoking during pregnancy affects global DNA methylation profiles of the developing dorsolateral prefrontal cortex (DLPFC) during the second trimester of gestation. When DLPFC methylation profiles (assayed via Illumina, HM450) of smoking-exposed and unexposed fetuses were compared, no differentially methylated regions (DMRs) passed the false discovery correction (FDR ≤ 0.05). However, the most significant DMRs were hypomethylated CpG Islands within the promoter regions of GNA15 and SDHAP3 of smoking-exposed fetuses. Interestingly, the developmental up-regulation of SDHAP3 mRNA was delayed in smoking-exposed fetuses. Interaction analysis between gestational age and smoking exposure identified significant DMRs annotated to SYCE3, C21orf56/LSS, SPAG1 and RNU12/POLDIP3 that passed FDR. Furthermore, utilizing established methods to estimate cell proportions by DNA methylation, we found that exposed DLPFC samples contained a lower proportion of neurons in samples from fetuses exposed to maternal smoking. We also show through in vitro experiments that nicotine impedes the differentiation of neurons independent of cell death. Conclusions We found evidence that intrauterine smoking exposure alters the developmental patterning of DNA methylation and gene expression and is associated with reduced mature neuronal content, effects that are likely driven by nicotine. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0111-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zac Chatterton
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Brigham J Hartley
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Man-Ho Seok
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Natalia Mendelev
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Sean Chen
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Maria Milekic
- Department of Psychiatry, Columbia University, New York, NY 10032 USA
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University, New York, NY 10032 USA.,Macedonian Academy of Sciences and Arts, Skopje, Macedonia.,School of Medicine, Skopje, Macedonia
| | | | | | - Kristen Brennand
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY 10032 USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY 10032 USA.,Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Fatemeh Haghighi
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
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17
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Hartley BJ, Brennand KJ. Neural organoids for disease phenotyping, drug screening and developmental biology studies. Neurochem Int 2016; 106:85-93. [PMID: 27744003 DOI: 10.1016/j.neuint.2016.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 02/01/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) can theoretically yield limitless supplies of cells fated to any cell type that comprise the human organism, making them a new tool by which to potentially overcome caveats in current biomedical research. In vitro derivation of central nervous system (CNS) cell types has the potential to provide material for drug discovery and validation, safety and toxicity assays, cell replacement therapy and the elucidation of previously unknown disease mechanisms. However, current two-dimensional (2D) CNS differentiation protocols do not faithfully recapitulate the spatial organization of heterogeneous tissue, nor the cell-cell interactions, cell-extracellular matrix interactions, or specific physiological functions generated within complex tissue such as the brain. In an effort to overcome 2D protocol limitations, there have been advancements in deriving highly complicated 3D neural organoid structures. Herein we provide a synopsis of the derivation and application of neural organoids and discuss recent advancements and remaining challenges on the full potential of this novel technological platform.
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Affiliation(s)
- Brigham J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States.
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18
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Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Tran N, Rittenhouse CA, Simone A, Ruderfer DM, Johnson J, Readhead B, Hadas Y, Gochman PA, Wang YC, Shah H, Cagney G, Rapoport J, Gage FH, Dudley JT, Sklar P, Mattheisen M, Cotter D, Fang G, Brennand KJ. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Rep 2016; 15:1024-1036. [PMID: 27117414 PMCID: PMC4856588 DOI: 10.1016/j.celrep.2016.03.090] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/02/2016] [Accepted: 03/27/2016] [Indexed: 01/19/2023] Open
Abstract
Converging evidence indicates that microRNAs (miRNAs) may contribute to disease risk for schizophrenia (SZ). We show that microRNA-9 (miR-9) is abundantly expressed in control neural progenitor cells (NPCs) but also significantly downregulated in a subset of SZ NPCs. We observed a strong correlation between miR-9 expression and miR-9 regulatory activity in NPCs as well as between miR-9 levels/activity, neural migration, and diagnosis. Overexpression of miR-9 was sufficient to ameliorate a previously reported neural migration deficit in SZ NPCs, whereas knockdown partially phenocopied aberrant migration in control NPCs. Unexpectedly, proteomic- and RNA sequencing (RNA-seq)-based analysis revealed that these effects were mediated primarily by small changes in expression of indirect miR-9 targets rather than large changes in direct miR-9 targets; these indirect targets are enriched for migration-associated genes. Together, these data indicate that aberrant levels and activity of miR-9 may be one of the many factors that contribute to SZ risk, at least in a subset of patients.
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Affiliation(s)
- Aaron Topol
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Shijia Zhu
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Brigham J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Jane English
- Department of Psychiatry, Royal College of Surgeons in Ireland, Beaumont Hospital, Beaumont, Dublin 9, Ireland
| | - Mads E Hauberg
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark
| | - Ngoc Tran
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Chelsea Ann Rittenhouse
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Anthony Simone
- Laboratory of Genetics, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Douglas M Ruderfer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Jessica Johnson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Ben Readhead
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Yoav Hadas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Peter A Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Judith Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Pamela Sklar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Manuel Mattheisen
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark
| | - David Cotter
- Department of Psychiatry, Royal College of Surgeons in Ireland, Beaumont Hospital, Beaumont, Dublin 9, Ireland
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA.
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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19
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Lee IS, Carvalho CMB, Douvaras P, Ho SM, Hartley BJ, Zuccherato LW, Ladran IG, Siegel AJ, McCarthy S, Malhotra D, Sebat J, Rapoport J, Fossati V, Lupski JR, Levy DL, Brennand KJ. Characterization of molecular and cellular phenotypes associated with a heterozygous CNTNAP2 deletion using patient-derived hiPSC neural cells. NPJ Schizophr 2015; 1. [PMID: 26985448 PMCID: PMC4789165 DOI: 10.1038/npjschz.2015.19] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Neurodevelopmental disorders, such as autism spectrum disorders and schizophrenia, are complex disorders with a high degree of heritability. Genetic studies have identified several candidate genes associated with these disorders, including contactin-associated protein-like 2 (CNTNAP2). Traditionally, in animal models or in vitro, CNTNAP2 has been studied by genetic deletion or transcriptional knockdown, which reduces the expression of the entire gene; however, it remains unclear whether the mutations identified in clinical settings are sufficient to alter CNTNAP2 expression in human neurons. Here, using human induced pluripotent stem cells (hiPSCs) derived from two individuals with a large (289 kb) heterozygous deletion in CNTNAP2 (affecting exons 14–15) and discordant clinical outcomes, we have characterized CNTNAP2 expression patterns in hiPSC neural progenitor cells, two independent populations of hiPSC-derived neurons and hiPSC-derived oligodendrocyte precursor cells. First, we observed exon-specific changes in CNTNAP2 expression in both carriers; although the expression of exons 14–15 is significantly decreased, the expression of other exons is upregulated. Second, we observed significant differences in patterns of allele-specific expression in CNTNAP2 carriers that were consistent with the clinical outcome. Third, we observed a robust neural migration phenotype that correlated with diagnosis and exon- and allele-specific CNTNAP2 expression patterns, but not with genotype. In all, our data highlight the importance of considering the nature, location, and regulation of mutated alleles when attempting to connect genome wide association studies to gene function.
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Affiliation(s)
- Inkyu S Lee
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Claudia M B Carvalho
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030
| | | | - Seok-Man Ho
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Brigham J Hartley
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Luciana W Zuccherato
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030
| | - Ian G Ladran
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Arthur J Siegel
- Internal Medicine Department, McLean Hospital, Belmont, Massachusetts 02478, USA
| | - Shane McCarthy
- Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, NY 11724
| | | | - Jonathan Sebat
- University of California San Diego, Department of Psychiatry and Department of Cellular and Molecular Medicine, University Of California, San Diego, La Jolla, CA 92093
| | - Judith Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | | | - James R Lupski
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Baylor College of Medicine, Department of Pediatrics, Houston, Texas 77030, USA
| | - Deborah L Levy
- Psychology Research Laboratory, McLean Hospital, Belmont, Massachusetts 02478, USA
| | - Kristen J Brennand
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
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20
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Affiliation(s)
- Brigham J. Hartley
- Departments of Psychiatry and Neuroscience, Mount Sinai School of
Medicine, 1425 Madison Avenue, New York, NY 10029
| | - Ngoc Tran
- Departments of Psychiatry and Neuroscience, Mount Sinai School of
Medicine, 1425 Madison Avenue, New York, NY 10029
| | - Ian Ladran
- Departments of Psychiatry and Neuroscience, Mount Sinai School of
Medicine, 1425 Madison Avenue, New York, NY 10029
| | - Kathryn Reggio
- Departments of Psychiatry and Neuroscience, Mount Sinai School of
Medicine, 1425 Madison Avenue, New York, NY 10029
| | - Kristen J. Brennand
- Departments of Psychiatry and Neuroscience, Mount Sinai School of
Medicine, 1425 Madison Avenue, New York, NY 10029
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21
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Watmuff B, Hartley BJ, Hunt CPJ, Fabb SA, Pouton CW, Haynes JM. Human pluripotent stem cell derived midbrain PITX3(eGFP/w) neurons: a versatile tool for pharmacological screening and neurodegenerative modeling. Front Cell Neurosci 2015; 9:104. [PMID: 25873861 PMCID: PMC4379917 DOI: 10.3389/fncel.2015.00104] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 03/09/2015] [Indexed: 11/21/2022] Open
Abstract
PITX3 expression is confined to adult midbrain dopaminergic (mDA) neurons. In this study we describe the generation and basic functional characteristics of mDA neurons derived from a human pluripotent stem cell (hPSC) line expressing eGFP under the control of the PITX3 promoter. Flow cytometry showed that eGFP was evident in 15% of the neuron population at day 12 of differentiation and this level was maintained until at least day 80. From days 20 to 80 of differentiation intracellular chloride decreased and throughout this period around ∼20% of PITX3eGFP/w neurons exhibited spontaneous Ca2+ transients (from 3.3 ± 0.3 to 5.0 ± 0.1 min-1, respectively). These neurons also responded to any of ATP, glutamate, acetylcholine, or noradrenaline with elevations of intracellular calcium. As neuronal cultures matured more dopamine was released and single PITX3eGFP/w neurons began to respond to more than one neurotransmitter. MPP+ and tumor necrosis factor (TNF), but not prostaglandin E2, caused death of the ∼50% of PITX3eGFP/w neurons (day 80). Tracking eGFP using time lapse confocal microscopy over 24 h demonstrated significant TNF-mediated neurite retraction over time. This work now shows that these PITX3eGFP/w neurons are amenable to flow cytometry, release dopamine and respond to multiple neurotransmitters with elevations of intracellular calcium, we believe that they represent a versatile system for neuropharmacological and neurotoxicological studies.
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Affiliation(s)
- Bradley Watmuff
- Stem Cell Biology Group, Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University Parkville, VIC, Australia
| | - Brigham J Hartley
- Stem Cell Biology Group, Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University Parkville, VIC, Australia
| | - Cameron P J Hunt
- Stem Cell Biology Group, Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University Parkville, VIC, Australia
| | - Stewart A Fabb
- Stem Cell Biology Group, Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University Parkville, VIC, Australia
| | - Colin W Pouton
- Stem Cell Biology Group, Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University Parkville, VIC, Australia
| | - John M Haynes
- Stem Cell Biology Group, Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University Parkville, VIC, Australia
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22
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Hartley BJ, Fabb SA, Finnin BAL, Haynes JM, Pouton CW. Zinc-finger nuclease enhanced gene targeting in human embryonic stem cells. J Vis Exp 2014:e51764. [PMID: 25177806 DOI: 10.3791/51764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
One major limitation with current human embryonic stem cell (ESC) differentiation protocols is the generation of heterogeneous cell populations. These cultures contain the cells of interest, but are also contaminated with undifferentiated ESCs, non-neural derivatives and other neuronal subtypes. This limits their use in in vitro and in vivo applications, such as in vitro modeling for drug discovery or cell replacement therapy. To help overcome this, reporter cell lines, which offer a means to visualize, track and isolate cells of interest, can be engineered. However, to achieve this in human embryonic stem cells via conventional homologous recombination is extremely inefficient. This protocol describes targeting of the Pituitary homeobox 3 (PITX3) locus in human embryonic stem cells using custom designed zinc-finger nucleases, which introduce site-specific double-strand DNA breaks, together with a PITX3-EGFP-specific DNA donor vector. Following the generation of the PITX3 reporter cell line, it can then be differentiated using published protocols for use in studies such as in vitro Parkinson's disease modeling or cell replacement therapy.
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Affiliation(s)
- Brigham J Hartley
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University
| | - Stewart A Fabb
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University
| | - Ben A L Finnin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University
| | - John M Haynes
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University
| | - Colin W Pouton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University;
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23
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Nefzger CM, Su CT, Fabb SA, Hartley BJ, Beh SJ, Zeng WR, Haynes JM, Pouton CW. Lmx1a Allows Context-Specific Isolation of Progenitors of GABAergic or Dopaminergic Neurons During Neural Differentiation of Embryonic Stem Cells. Stem Cells 2012; 30:1349-61. [DOI: 10.1002/stem.1105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Hartley BJ, Scott DJ, Callander GE, Wilkinson TN, Ganella DE, Kong CK, Layfield S, Ferraro T, Petrie EJ, Bathgate RAD. Resolving the Unconventional Mechanisms Underlying RXFP1 and RXFP2 Receptor Function. Ann N Y Acad Sci 2009; 1160:67-73. [DOI: 10.1111/j.1749-6632.2009.03949.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Panesar J, Vadgama B, Rogers G, Ramsay AD, Hartley BJ. Juvenile angiofibroma of the maxillary sinus. Rhinology 2004; 42:171-4. [PMID: 15521673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Primary extra-nasopharyngeal sites of angiofibromas are extremely unusual. We describe a rare case of extra-nasopharyngeal angiofibroma in a one year old child arising from the left maxilla and indirectly involving the lacrimal system. The initial presentation was of a swelling in the region of the left medial canthus. Only four cases of extra-nasopharyngeal angiofibromas in children below the age of two have been described. We review the literature on what is known about extra-nasopharyngeal angiofibromas.
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Affiliation(s)
- J Panesar
- Department of Otolaryngology, Great Ormand Street Hospital for Children, London, WC1N 3JH, United Kingdom.
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