1
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Kozlenkov A, Vadukapuram R, Zhou P, Fam P, Wegner M, Dracheva S. Novel method of isolating nuclei of human oligodendrocyte precursor cells reveals substantial developmental changes in gene expression and H3K27ac histone modification. Glia 2024; 72:69-89. [PMID: 37712493 PMCID: PMC10697634 DOI: 10.1002/glia.24462] [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] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Oligodendrocyte precursor cells (OPCs) generate differentiated mature oligodendrocytes (MOs) during development. In adult brain, OPCs replenish MOs in adaptive plasticity, neurodegenerative disorders, and after trauma. The ability of OPCs to differentiate to MOs decreases with age and is compromised in disease. Here we explored the cell specific and age-dependent differences in gene expression and H3K27ac histone mark in these two cell types. H3K27ac is indicative of active promoters and enhancers. We developed a novel flow-cytometry-based approach to isolate OPC and MO nuclei from human postmortem brain and profiled gene expression and H3K27ac in adult and infant OPCs and MOs genome-wide. In adult brain, we detected extensive H3K27ac differences between the two cell types with high concordance between gene expression and epigenetic changes. Notably, the expression of genes that distinguish MOs from OPCs appears to be under a strong regulatory control by the H3K27ac modification in MOs but not in OPCs. Comparison of gene expression and H3K27ac between infants and adults uncovered numerous developmental changes in each cell type, which were linked to several biological processes, including cell proliferation and glutamate signaling. A striking example was a subset of histone genes that were highly active in infant samples but fully lost activity in adult brain. Our findings demonstrate a considerable rearrangement of the H3K27ac landscape that occurs during the differentiation of OPCs to MOs and during postnatal development of these cell types, which aligned with changes in gene expression. The uncovered regulatory changes justify further in-depth epigenetic studies of OPCs and MOs in development and disease.
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Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ramu Vadukapuram
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ping Zhou
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Fam
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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2
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Li J, Jaiswal MK, Chien JF, Kozlenkov A, Jung J, Zhou P, Gardashli M, Pregent LJ, Engelberg-Cook E, Dickson DW, Belzil VV, Mukamel EA, Dracheva S. Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation. Nat Commun 2023; 14:5714. [PMID: 37714849 PMCID: PMC10504300 DOI: 10.1038/s41467-023-41033-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/16/2022] [Accepted: 08/21/2023] [Indexed: 09/17/2023] Open
Abstract
A repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we investigate single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem motor and frontal cortices from C9-ALS, C9-FTD, and control donors. C9-ALS donors present pervasive alterations of gene expression with concordant changes in chromatin accessibility and histone modifications. The greatest alterations occur in upper and deep layer excitatory neurons, as well as in astrocytes. In neurons, the changes imply an increase in proteostasis, metabolism, and protein expression pathways, alongside a decrease in neuronal function. In astrocytes, the alterations suggest activation and structural remodeling. Conversely, C9-FTD donors have fewer high-quality neuronal nuclei in the frontal cortex and numerous gene expression changes in glial cells. These findings highlight a context-dependent molecular disruption in C9-ALS and C9-FTD, indicating unique effects across cell types, brain regions, and diseases.
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Affiliation(s)
- Junhao Li
- Department of Cognitive Science, University of California San Diego, La Jolla, CA, 92037, US
| | - Manoj K Jaiswal
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | - Jo-Fan Chien
- Department of Physics, University of California San Diego, La Jolla, CA, 92037, US
| | - Alexey Kozlenkov
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | - Jinyoung Jung
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | - Ping Zhou
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | | | - Luc J Pregent
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, US
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, US
| | | | - Eran A Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, CA, 92037, US.
| | - Stella Dracheva
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US.
- Research & Development and VISN2 MIREC, James J, Peters VA Medical Center, Bronx, NY, 10468, US.
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3
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Girdhar K, Hoffman GE, Bendl J, Rahman S, Dong P, Liao W, Hauberg ME, Sloofman L, Brown L, Devillers O, Kassim BS, Wiseman JR, Park R, Zharovsky E, Jacobov R, Flatow E, Kozlenkov A, Gilgenast T, Johnson JS, Couto L, Peters MA, Phillips-Cremins JE, Hahn CG, Gur RE, Tamminga CA, Lewis DA, Haroutunian V, Dracheva S, Lipska BK, Marenco S, Kundakovic M, Fullard JF, Jiang Y, Roussos P, Akbarian S. Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains. Nat Neurosci 2022; 25:474-483. [PMID: 35332326 PMCID: PMC8989650 DOI: 10.1038/s41593-022-01032-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 06/02/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022]
Abstract
Chromosomal organization, scaling from the 147 base pair nucleosome to
megabase-ranging domains encompassing multiple transcriptional units including
heritability loci for psychiatric traits, remains largely unexplored in the
human brain. Here, we construct promoter and enhancer enriched nucleosomal
histone modification landscapes for adult prefrontal cortex (PFC) from H3-lysine
27 acetylation and H3-lysine 4 trimethylation profiles, generated from (n=739)
388 controls and 351 subjects diagnosed with schizophrenia (SCZ) or bipolar
disorder (BD). We mapped thousands of cis-regulatory domains (CRDs), revealing
fine-grained, 104-106 bp chromosomal organization, firmly
integrated into Hi-C topologically associating domain (TAD) stratification by
open/repressive chromosomal environments and nuclear topography. Large clusters
of hyperacetylated CRDs were enriched for SCZ heritability, with prominent
representation of regulatory sequences governing fetal development and
glutamatergic neuron signaling. Therefore, SCZ and BD brains show coordinated
dysregulation of risk-associated regulatory sequences assembled into kilo- to
megabase-scaling chromosomal domains.
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Affiliation(s)
- Kiran Girdhar
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gabriel E Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jaroslav Bendl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, 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 Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samir Rahman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, 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 Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pengfei Dong
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, 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 Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Will Liao
- New York Genome Center, New York, NY, USA
| | - Mads E Hauberg
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, 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 Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanne Brown
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia Devillers
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bibi S Kassim
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer R Wiseman
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Royce Park
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth Zharovsky
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rivky Jacobov
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elie Flatow
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Gilgenast
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica S Johnson
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lizette Couto
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jennifer E Phillips-Cremins
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Chang-Gyu Hahn
- Department of Psychiatry, Vickie and Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Carol A Tamminga
- Department of Psychiatry, The University of Texas Southwestern Medical School, Dallas, TX, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vahram Haroutunian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, 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.,Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Stella Dracheva
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Barbara K Lipska
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD, USA
| | - Marija Kundakovic
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, 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 Biological Sciences, Fordham University, Bronx, NY, USA
| | - John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, 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 Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Jiang
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, 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.,Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Science, 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 Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA. .,Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA.
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Psychiatry, 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.
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4
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Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, Kozlenkov A, Crowley CA, Pochareddy S, Li Y, Dracheva S, Sestan N, Akbarian S, Geschwind DH. Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders. Nat Commun 2021; 12:3968. [PMID: 34172755 PMCID: PMC8233376 DOI: 10.1038/s41467-021-24243-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 04/29/2020] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Cellular heterogeneity in the human brain obscures the identification of robust cellular regulatory networks, which is necessary to understand the function of non-coding elements and the impact of non-coding genetic variation. Here we integrate genome-wide chromosome conformation data from purified neurons and glia with transcriptomic and enhancer profiles, to characterize the gene regulatory landscape of two major cell classes in the human brain. We then leverage cell-type-specific regulatory landscapes to gain insight into the cellular etiology of several brain disorders. We find that Alzheimer's disease (AD)-associated epigenetic dysregulation is linked to neurons and oligodendrocytes, whereas genetic risk factors for AD highlighted microglia, suggesting that different cell types may contribute to disease risk, via different mechanisms. Moreover, integration of glutamatergic and GABAergic regulatory maps with genetic risk factors for schizophrenia (SCZ) and bipolar disorder (BD) identifies shared (parvalbumin-expressing interneurons) and distinct cellular etiologies (upper layer neurons for BD, and deeper layer projection neurons for SCZ). Collectively, these findings shed new light on cell-type-specific gene regulatory networks in brain disorders.
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Affiliation(s)
- Benxia Hu
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Hyejung Won
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Won Mah
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Royce B. Park
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Bibi Kassim
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Keeley Spiess
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA
| | - Alexey Kozlenkov
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.274295.f0000 0004 0420 1184James J. Peters VA Medical Center, Bronx, NY USA
| | - Cheynna A. Crowley
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Sirisha Pochareddy
- grid.47100.320000000419368710Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT USA
| | | | - Yun Li
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Biostatistics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Computer Science, University of North Carolina, Chapel Hill, NC USA
| | - Stella Dracheva
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.274295.f0000 0004 0420 1184James J. Peters VA Medical Center, Bronx, NY USA
| | - Nenad Sestan
- grid.47100.320000000419368710Department of Psychiatry, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Department of Comparative Medicine, Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT USA
| | - Schahram Akbarian
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel H. Geschwind
- grid.19006.3e0000 0000 9632 6718Neurogenetics Program, Department of Neurology, David Geffen School of Medicine University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, CA USA
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5
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Kozlenkov A, Vermunt MW, Apontes P, Li J, Hao K, Sherwood CC, Hof PR, Ely JJ, Wegner M, Mukamel EA, Creyghton MP, Koonin EV, Dracheva S. Evolution of regulatory signatures in primate cortical neurons at cell-type resolution. Proc Natl Acad Sci U S A 2020; 117:28422-28432. [PMID: 33109720 PMCID: PMC7668098 DOI: 10.1073/pnas.2011884117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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] [Indexed: 12/27/2022] Open
Abstract
The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type-specific regulatory landscapes in the cortex remain largely unexplored. Here we report epigenomic and transcriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome-wide profiling of the H3K27ac histone modification, we identify neuron-subtype-specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regulatory changes are uncovered in multiple genes, including those associated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a substantial fraction of pan-neuronal regulatory elements undergoes subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell-type-dependent gene-expression programs, and provides a resource for further exploration of human brain evolution and function.
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Affiliation(s)
- Alexey Kozlenkov
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Marit W Vermunt
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Pasha Apontes
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468
| | - Junhao Li
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, Alamogordo, NM 88330
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Eran A Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037
| | - Menno P Creyghton
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands;
- Department of Developmental Biology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Stella Dracheva
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468;
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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6
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Hauberg ME, Creus-Muncunill J, Bendl J, Kozlenkov A, Zeng B, Corwin C, Chowdhury S, Kranz H, Hurd YL, Wegner M, Børglum AD, Dracheva S, Ehrlich ME, Fullard JF, Roussos P. Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons. Nat Commun 2020; 11:5581. [PMID: 33149216 PMCID: PMC7643171 DOI: 10.1038/s41467-020-19319-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 02/26/2020] [Accepted: 10/08/2020] [Indexed: 01/04/2023] Open
Abstract
The chromatin landscape of human brain cells encompasses key information to understanding brain function. Here we use ATAC-seq to profile the chromatin structure in four distinct populations of cells (glutamatergic neurons, GABAergic neurons, oligodendrocytes, and microglia/astrocytes) from three different brain regions (anterior cingulate cortex, dorsolateral prefrontal cortex, and primary visual cortex) in human postmortem brain samples. We find that chromatin accessibility varies greatly by cell type and, more moderately, by brain region, with glutamatergic neurons showing the largest regional variability. Transcription factor footprinting implicates cell-specific transcriptional regulators and infers cell-specific regulation of protein-coding genes, long intergenic noncoding RNAs and microRNAs. In vivo transgenic mouse experiments validate the cell type specificity of several of these human-derived regulatory sequences. We find that open chromatin regions in glutamatergic neurons are enriched for neuropsychiatric risk variants, particularly those associated with schizophrenia. Integration of cell-specific chromatin data with a bulk tissue study of schizophrenia brains increases statistical power and confirms that glutamatergic neurons are most affected. These findings illustrate the utility of studying the cell-type-specific epigenome in complex tissues like the human brain, and the potential of such approaches to better understand the genetic basis of human brain function.
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Affiliation(s)
- Mads E Hauberg
- 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
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Jordi Creus-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaroslav Bendl
- 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
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Biao Zeng
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chuhyon Corwin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Chowdhury
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harald Kranz
- Gene Bridges, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Yasmin L Hurd
- 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
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Stella Dracheva
- 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
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- 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
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- 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.
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
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7
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Factor DC, Barbeau AM, Allan KC, Hu LR, Madhavan M, Hoang AT, Hazel KEA, Hall PA, Nisraiyya S, Najm FJ, Miller TE, Nevin ZS, Karl RT, Lima BR, Song Y, Sibert AG, Dhillon GK, Volsko C, Bartels CF, Adams DJ, Dutta R, Gallagher MD, Phu W, Kozlenkov A, Dracheva S, Scacheri PC, Tesar PJ, Corradin O. Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS. Cell 2020; 181:382-395.e21. [PMID: 32246942 PMCID: PMC7426147 DOI: 10.1016/j.cell.2020.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 08/26/2019] [Revised: 12/18/2019] [Accepted: 03/03/2020] [Indexed: 02/08/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterized by attack on oligodendrocytes within the central nervous system (CNS). Despite widespread use of immunomodulatory therapies, patients may still face progressive disability because of failure of myelin regeneration and loss of neurons, suggesting additional cellular pathologies. Here, we describe a general approach for identifying specific cell types in which a disease allele exerts a pathogenic effect. Applying this approach to MS risk loci, we pinpoint likely pathogenic cell types for 70%. In addition to T cell loci, we unexpectedly identified myeloid- and CNS-specific risk loci, including two sites that dysregulate transcriptional pause release in oligodendrocytes. Functional studies demonstrated inhibition of transcriptional elongation is a dominant pathway blocking oligodendrocyte maturation. Furthermore, pause release factors are frequently dysregulated in MS brain tissue. These data implicate cell-intrinsic aberrations outside of the immune system and suggest new avenues for therapeutic development. VIDEO ABSTRACT.
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Affiliation(s)
- Daniel C Factor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Anna M Barbeau
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Lucille R Hu
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mayur Madhavan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - An T Hoang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kathryn E A Hazel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Parker A Hall
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sagar Nisraiyya
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fadi J Najm
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Tyler E Miller
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zachary S Nevin
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Robert T Karl
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Bruna R Lima
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yanwei Song
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Gursimran K Dhillon
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Christina Volsko
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ranjan Dutta
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - William Phu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Olivia Corradin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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8
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Abstract
Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.
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Affiliation(s)
- Gabor Egervari
- Department of Psychiatry, 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
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, 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.
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA.
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9
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Kozlenkov A, Li J, Apontes P, Hurd YL, Byne WM, Koonin EV, Wegner M, Mukamel EA, Dracheva S. A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons. Sci Adv 2018; 4:eaau6190. [PMID: 30263963 PMCID: PMC6157969 DOI: 10.1126/sciadv.aau6190] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/22/2018] [Indexed: 05/18/2023]
Abstract
Brain function depends on interaction of diverse cell types whose gene expression and identity are defined, in part, by epigenetic mechanisms. Neuronal DNA contains two major epigenetic modifications, methylcytosine (mC) and hydroxymethylcytosine (hmC), yet their cell type-specific landscapes and relationship with gene expression are poorly understood. We report high-resolution (h)mC analyses, together with transcriptome and histone modification profiling, in three major cell types in human prefrontal cortex: glutamatergic excitatory neurons, medial ganglionic eminence-derived γ-aminobutyric acid (GABA)ergic inhibitory neurons, and oligodendrocytes. We detected a unique association between hmC and gene expression in inhibitory neurons that differed significantly from the pattern in excitatory neurons and oligodendrocytes. We also found that risk loci associated with neuropsychiatric diseases were enriched near regions of reduced hmC in excitatory neurons and reduced mC in inhibitory neurons. Our findings indicate differential roles for mC and hmC in regulation of gene expression in different brain cell types, with implications for the etiology of human brain diseases.
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Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, San Diego, CA 92037, USA
| | - Pasha Apontes
- James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Yasmin L. Hurd
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - William M. Byne
- James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Eran A. Mukamel
- Department of Cognitive Science, University of California, San Diego, San Diego, CA 92037, USA
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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10
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Gómez S, Garrido-Garcia A, Garcia-Gerique L, Lemos I, Suñol M, de Torres C, Kulis M, Pérez-Jaume S, Carcaboso ÁM, Luu B, Kieran MW, Jabado N, Kozlenkov A, Dracheva S, Ramaswamy V, Hovestadt V, Johann P, Jones DTW, Pfister SM, Morales La Madrid A, Cruz O, Taylor MD, Martin-Subero JI, Mora J, Lavarino C. A Novel Method for Rapid Molecular Subgrouping of Medulloblastoma. Clin Cancer Res 2018; 24:1355-1363. [PMID: 29351917 DOI: 10.1158/1078-0432.ccr-17-2243] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/15/2017] [Accepted: 01/10/2018] [Indexed: 11/16/2022]
Abstract
Purpose: The classification of medulloblastoma into WNT, SHH, group 3, and group 4 subgroups has become of critical importance for patient risk stratification and subgroup-tailored clinical trials. Here, we aimed to develop a simplified, clinically applicable classification approach that can be implemented in the majority of centers treating patients with medulloblastoma.Experimental Design: We analyzed 1,577 samples comprising previously published DNA methylation microarray data (913 medulloblastomas, 457 non-medulloblastoma tumors, 85 normal tissues), and 122 frozen and formalin-fixed paraffin-embedded medulloblastoma samples. Biomarkers were identified applying stringent selection filters and Linear Discriminant Analysis (LDA) method, and validated using DNA methylation microarray data, bisulfite pyrosequencing, and direct-bisulfite sequencing.Results: Using a LDA-based approach, we developed and validated a prediction method (EpiWNT-SHH classifier) based on six epigenetic biomarkers that allowed for rapid classification of medulloblastoma into the clinically relevant subgroups WNT, SHH, and non-WNT/non-SHH with excellent concordance (>99%) with current gold-standard methods, DNA methylation microarray, and gene signature profiling analysis. The EpiWNT-SHH classifier showed high prediction capacity using both frozen and formalin-fixed material, as well as diverse DNA methylation detection methods. Similarly, we developed a classifier specific for group 3 and group 4 tumors, based on five biomarkers (EpiG3-G4) with good discriminatory capacity, allowing for correct assignment of more than 92% of tumors. EpiWNT-SHH and EpiG3-G4 methylation profiles remained stable across tumor primary, metastasis, and relapse samples.Conclusions: The EpiWNT-SHH and EpiG3-G4 classifiers represent a new simplified approach for accurate, rapid, and cost-effective molecular classification of single medulloblastoma DNA samples, using clinically applicable DNA methylation detection methods. Clin Cancer Res; 24(6); 1355-63. ©2018 AACR.
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Affiliation(s)
- Soledad Gómez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain
| | - Alícia Garrido-Garcia
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain
| | - Laura Garcia-Gerique
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain
| | - Isadora Lemos
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain.,Department of Haematology and Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Marta Kulis
- Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | - Sara Pérez-Jaume
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain
| | - Ángel M Carcaboso
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain
| | - Betty Luu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mark W Kieran
- The Pediatric Brain Tumor Centre, Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Centre, Boston, Massachusetts
| | - Nada Jabado
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, New York.,The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, New York.,The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health and Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pascal Johann
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Centre at the NCT Heidelberg, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Centre at the NCT Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Immunology, Haematology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Ofelia Cruz
- Department of Haematology and Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Michael D Taylor
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jose-Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain.,Department of Haematology and Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Sant Joan de Déu, Barcelona, Spain.
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11
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Kozlenkov A, Jaffe AE, Timashpolsky A, Apontes P, Rudchenko S, Barbu M, Byne W, Hurd YL, Horvath S, Dracheva S. DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age. Genes (Basel) 2017; 8:genes8060152. [PMID: 28556790 PMCID: PMC5485516 DOI: 10.3390/genes8060152] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/21/2017] [Accepted: 05/25/2017] [Indexed: 12/30/2022] Open
Abstract
We employed Illumina 450 K Infinium microarrays to profile DNA methylation (DNAm) in neuronal nuclei separated by fluorescence-activated sorting from the postmortem orbitofrontal cortex (OFC) of heroin users who died from heroin overdose (N = 37), suicide completers (N = 22) with no evidence of heroin use and from control subjects who did not abuse illicit drugs and died of non-suicide causes (N = 28). We identified 1298 differentially methylated CpG sites (DMSs) between heroin users and controls, and 454 DMSs between suicide completers and controls (p < 0.001). DMSs and corresponding genes (DMGs) in heroin users showed significant differences in the preferential context of hyper and hypo DM. HyperDMSs were enriched in gene bodies and exons but depleted in promoters, whereas hypoDMSs were enriched in promoters and enhancers. In addition, hyperDMGs showed preference for genes expressed specifically by glutamatergic as opposed to GABAergic neurons and enrichment for axonogenesis- and synaptic-related gene ontology categories, whereas hypoDMGs were enriched for transcription factor activity- and gene expression regulation-related terms. Finally, we found that the DNAm-based “epigenetic age” of neurons from heroin users was younger than that in controls. Suicide-related results were more difficult to interpret. Collectively, these findings suggest that the observed DNAm differences could represent functionally significant marks of heroin-associated plasticity in the OFC.
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Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.
- Department of Biostatistics and Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | | | - Pasha Apontes
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
| | | | - Mihaela Barbu
- Hospital for Special Surgery, New York, NY 10021, USA.
| | - William Byne
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Yasmin L Hurd
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
- Department of Biostatistics, School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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12
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Bernal Sierra YA, Haseleu J, Kozlenkov A, Bégay V, Lewin GR. Genetic Tracing of Ca v3.2 T-Type Calcium Channel Expression in the Peripheral Nervous System. Front Mol Neurosci 2017; 10:70. [PMID: 28360836 PMCID: PMC5350092 DOI: 10.3389/fnmol.2017.00070] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/01/2017] [Indexed: 02/01/2023] Open
Abstract
Characterizing the distinct functions of the T-type ion channel subunits Cav3.1, 3.2 or 3.3 has proven difficult due to their highly conserved amino-acid sequences and the lack of pharmacological blockers specific for each subunit. To precisely determine the expression pattern of the Cav3.2 channel in the nervous system we generated two knock-in mouse strains that express EGFP or Cre recombinase under the control of the Cav3.2 gene promoter. We show that in the brains of these animals, the Cav3.2 channel is predominantly expressed in the dentate gyrus of the hippocampus. In the peripheral nervous system, the activation of the promoter starts at E9.5 in neural crest cells that will give rise to dorsal root ganglia (DRG) neurons, but not sympathetic neurons. As development progresses the number of DRG cells expressing the Cav3.2 channel reaches around 7% of the DRG at E16.5, and remains constant until E18.5. Characterization of sensory neuron subpopulations at E18.5 showed that EGFP+ cells are a heterogeneous population consisting mainly of TrkB+ and TrkC+ cells, while only a small percentage of DRG cells were TrkA+. Genetic tracing of the sensory nerve end-organ innervation of the skin showed that the activity of the Cav3.2 channel promoter in sensory progenitors marks many mechanoreceptor and nociceptor endings, but spares slowly adapting mechanoreceptors with endings associated with Merkel cells. Our genetic analysis reveals for the first time that progenitors that express the Cav3.2 T-type calcium channel, defines a sensory specific lineage that populates a large proportion of the DRG. Using our Cav3.2-Cre mice together with AAV viruses containing a conditional fluorescent reporter (tdTomato) we could also show that Cre expression is largely restricted to two functionally distinct sensory neuron types in the adult ganglia. Cav3.2 positive neurons innervating the skin were found to only form lanceolate endings on hair follicles and are probably identical to D-hair receptors. A second population of nociceptive sensory neurons expressing the Cav3.2 gene was found to be positive for the calcitonin-gene related peptide but these neurons are deep tissue nociceptors that do not innervate the skin.
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Affiliation(s)
- Yinth A Bernal Sierra
- Department of Neuroscience, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Julia Haseleu
- Department of Neuroscience, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Alexey Kozlenkov
- Department of Neuroscience, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Valérie Bégay
- Department of Neuroscience, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Gary R Lewin
- Department of Neuroscience, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin Berlin, Germany
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Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FCP, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CCY, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nat Neurosci 2016; 18:1707-12. [PMID: 26605881 DOI: 10.1038/nn.4156] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Chunyu Liu
- University of Illinois at Chicago, Chicago, Illinois, USA
| | - James A Knowles
- University of Southern California, Los Angeles, California, USA
| | | | - Peggy J Farnham
- University of Southern California, Los Angeles, California, USA
| | | | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Dalila Pinto
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stella Dracheva
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jonathan Mill
- King's College London, London, and University of Exeter, Devon, UK
| | | | | | | | | | | | | | | | - Zhiping Weng
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | | | | | | | - Chris Armoskus
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | - Nancy Francoeur
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Menachem Fromer
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Gao
- University of Southern California, Los Angeles, California, USA
| | - Kay Grennan
- University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - David H Kavanagh
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nikolay A Ivanov
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Yan Jiang
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Alexey Kozlenkov
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Mingfeng Li
- Yale University, New Haven, Connecticut, USA
| | - Zhen Li
- Yale University, New Haven, Connecticut, USA
| | - Shuang Liu
- Yale University, New Haven, Connecticut, USA
| | | | - Eugenio Mattei
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | | | - Nicole North
- National Institute of Mental Health, Bethesda, Maryland, USA
| | | | | | | | | | - Amanda J Price
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Michael Purcaro
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Robert Sebra
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Annie W Shieh
- University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - Wenjie Sun
- Genome Institute of Singapore, Singapore
| | - Vivek Swarup
- University of California, Los Angeles, California, USA
| | - Amber Thomas
- The University of Chicago, Chicago, Illinois, USA
| | - Junko Tsuji
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Yongjun Wang
- University of Illinois at Chicago, Chicago, Illinois, USA
| | - Kai Wang
- University of Southern California, Los Angeles, California, USA
| | | | | | - Heather Witt
- University of Southern California, Los Angeles, California, USA
| | - Hyejung Won
- University of California, Los Angeles, California, USA
| | - Chloe C Y Wong
- King's College London, London, and University of Exeter, Devon, UK
| | | | - Emily Y Wu
- University of California, Los Angeles, California, USA
| | - Xuming Xu
- Yale University, New Haven, Connecticut, USA
| | - Lijing Yao
- University of Southern California, Los Angeles, California, USA
| | - Geetha Senthil
- National Institute of Mental Health, Bethesda, Maryland, USA
| | - Thomas Lehner
- National Institute of Mental Health, Bethesda, Maryland, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
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14
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Halene TB, Kozlenkov A, Jiang Y, Mitchell A, Javidfar B, Dincer A, Park R, Wiseman J, Croxson P, Giannaris EL, Hof PR, Roussos P, Dracheva S, Hemby SE, Akbarian S. NeuN+ neuronal nuclei in non-human primate prefrontal cortex and subcortical white matter after clozapine exposure. Schizophr Res 2016; 170:235-44. [PMID: 26776227 PMCID: PMC4740223 DOI: 10.1016/j.schres.2015.12.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/24/2015] [Accepted: 12/28/2015] [Indexed: 12/01/2022]
Abstract
Increased neuronal densities in subcortical white matter have been reported for some cases with schizophrenia. The underlying cellular and molecular mechanisms remain unresolved. We exposed 26 young adult macaque monkeys for 6 months to either clozapine, haloperidol or placebo and measured by structural MRI frontal gray and white matter volumes before and after treatment, followed by observer-independent, flow-cytometry-based quantification of neuronal and non-neuronal nuclei and molecular fingerprinting of cell-type specific transcripts. After clozapine exposure, the proportion of nuclei expressing the neuronal marker NeuN increased by approximately 50% in subcortical white matter, in conjunction with a more subtle and non-significant increase in overlying gray matter. Numbers and proportions of nuclei expressing the oligodendrocyte lineage marker, OLIG2, and cell-type specific RNA expression patterns, were maintained after antipsychotic drug exposure. Frontal lobe gray and white matter volumes remained indistinguishable between antipsychotic-drug-exposed and control groups. Chronic clozapine exposure increases the proportion of NeuN+ nuclei in frontal subcortical white matter, without alterations in frontal lobe volumes or cell type-specific gene expression. Further exploration of neurochemical plasticity in non-human primate brain exposed to antipsychotic drugs is warranted.
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Affiliation(s)
- Tobias B. Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Corresponding author: Tobias B. Halene, MD PhD, Icahn School of Medicine at Mount Sinai, Department of Psychiatry, 1470 Madison Ave, Hess 9-105, New York, NY 10029, Tel: 646 627 5529, Fax: 646-537-9583,
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aslihan Dincer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Royce Park
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer Wiseman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paula Croxson
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eustathia Lela Giannaris
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Patrick R. Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott E. Hemby
- Department of Physiology and Pharmacology, Wake Forest University, Winston-Salem, NC, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Moreno JL, Miranda-Azpiazu P, García-Bea A, Younkin J, Cui M, Kozlenkov A, Ben-Ezra A, Voloudakis G, Fakira AK, Baki L, Ge Y, Georgakopoulos A, Morón JA, Milligan G, López-Giménez JF, Robakis NK, Logothetis DE, Meana JJ, González-Maeso J. Allosteric signaling through an mGlu2 and 5-HT2A heteromeric receptor complex and its potential contribution to schizophrenia. Sci Signal 2016; 9:ra5. [PMID: 26758213 DOI: 10.1126/scisignal.aab0467] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) can form multiprotein complexes (heteromers), which can alter the pharmacology and functions of the constituent receptors. Previous findings demonstrated that the Gq/11-coupled serotonin 5-HT2A receptor and the Gi/o-coupled metabotropic glutamate 2 (mGlu2) receptor-GPCRs that are involved in signaling alterations associated with psychosis-assemble into a heteromeric complex in the mammalian brain. In single-cell experiments with various mutant versions of the mGlu2 receptor, we showed that stimulation of cells expressing mGlu2-5-HT2A heteromers with an mGlu2 agonist led to activation of Gq/11 proteins by the 5-HT2A receptors. For this crosstalk to occur, one of the mGlu2 subunits had to couple to Gi/o proteins, and we determined the relative location of the Gi/o-contacting subunit within the mGlu2 homodimer of the heteromeric complex. Additionally, mGlu2-dependent activation of Gq/11, but not Gi/o, was reduced in the frontal cortex of 5-HT2A knockout mice and was reduced in the frontal cortex of postmortem brains from schizophrenic patients. These findings offer structural insights into this important target in molecular psychiatry.
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Affiliation(s)
- José L Moreno
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA. Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patricia Miranda-Azpiazu
- Department of Pharmacology, University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain. Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain
| | - Aintzane García-Bea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Pharmacology, University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain. Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain
| | - Jason Younkin
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Meng Cui
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariel Ben-Ezra
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amanda K Fakira
- Department of Anesthesiology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lia Baki
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - José A Morón
- Department of Anesthesiology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Graeme Milligan
- Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Juan F López-Giménez
- Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK. Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC-CSIC-UC), E-39011 Santander, Cantabria, Spain
| | - Nikolaos K Robakis
- 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
| | - Diomedes E Logothetis
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - J Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain. Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain. BioCruces Health Research Institute, E-48903 Barakaldo, Bizkaia, Spain.
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA. Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Neurology, 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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16
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Kozlenkov A, Wang M, Roussos P, Rudchenko S, Barbu M, Bibikova M, Klotzle B, Dwork AJ, Zhang B, Hurd YL, Koonin EV, Wegner M, Dracheva S. Substantial DNA methylation differences between two major neuronal subtypes in human brain. Nucleic Acids Res 2015; 44:2593-612. [PMID: 26612861 PMCID: PMC4824074 DOI: 10.1093/nar/gkv1304] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [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: 09/10/2015] [Accepted: 11/09/2015] [Indexed: 12/29/2022] Open
Abstract
The brain is built from a large number of cell types which have been historically classified using location, morphology and molecular markers. Recent research suggests an important role of epigenetics in shaping and maintaining cell identity in the brain. To elucidate the role of DNA methylation in neuronal differentiation, we developed a new protocol for separation of nuclei from the two major populations of human prefrontal cortex neurons—GABAergic interneurons and glutamatergic (GLU) projection neurons. Major differences between the neuronal subtypes were revealed in CpG, non-CpG and hydroxymethylation (hCpG). A dramatically greater number of undermethylated CpG sites in GLU versus GABA neurons were identified. These differences did not directly translate into differences in gene expression and did not stem from the differences in hCpG methylation, as more hCpG methylation was detected in GLU versus GABA neurons. Notably, a comparable number of undermethylated non-CpG sites were identified in GLU and GABA neurons, and non-CpG methylation was a better predictor of subtype-specific gene expression compared to CpG methylation. Regions that are differentially methylated in GABA and GLU neurons were significantly enriched for schizophrenia risk loci. Collectively, our findings suggest that functional differences between neuronal subtypes are linked to their epigenetic specification.
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Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- James J. Peters VA Medical Center, Bronx, NY 10468, USA The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Mihaela Barbu
- Hospital for Special Surgery, New York, NY 10021, USA
| | | | | | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yasmin L Hurd
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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17
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Di Narzo AF, Kozlenkov A, Roussos P, Hao K, Hurd Y, Lewis DA, Sibille E, Siever LJ, Koonin E, Dracheva S. A unique gene expression signature associated with serotonin 2C receptor RNA editing in the prefrontal cortex and altered in suicide. Hum Mol Genet 2014; 23:4801-13. [PMID: 24781207 DOI: 10.1093/hmg/ddu195] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Editing of the pre-mRNA for the serotonin receptor 2C (5-HT2CR) by site-specific adenosine deamination (A-to-I pre-mRNA editing) substantially increases the functional plasticity of this key neurotransmitter receptor and is thought to contribute to homeostatic mechanisms in neurons. 5-HT2CR mRNA editing generates up to 24 different receptor isoforms. The extent of editing correlates with 5-HT2CR functional activity: more highly edited isoforms exhibit the least function. Altered 5-HT2CR editing has been reported in postmortem brains of suicide victims. We report a comparative analysis of the connections among 5-HT2CR editing, genome-wide gene expression and DNA methylation in suicide victims, individuals with major depressive disorder and non-psychiatric controls. The results confirm previous findings of an overrepresentation of highly edited mRNA variants (which encode hypoactive 5-HT2CR receptors) in the brains of suicide victims. A large set of genes for which the expression level is associated with editing was detected. This signature set of editing-associated genes is significantly enriched for genes that are involved in synaptic transmission, genes that are preferentially expressed in neurons, and genes whose expression is correlated with the level of DNA methylation. Notably, we report that the link between 5-HT2CR editing and gene expression is disrupted in suicide victims. The results suggest that the postulated homeostatic function of 5-HT2CR editing is dysregulated in individuals who committed suicide.
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Affiliation(s)
| | - Alexey Kozlenkov
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences and Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences and
| | - Yasmin Hurd
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A Lewis
- Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Etienne Sibille
- Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Larry J Siever
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stella Dracheva
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
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18
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Kozlenkov A, Roussos P, Timashpolsky A, Barbu M, Rudchenko S, Bibikova M, Klotzle B, Byne W, Lyddon R, Di Narzo AF, Hurd YL, Koonin EV, Dracheva S. Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites. Nucleic Acids Res 2014; 42:109-27. [PMID: 24057217 PMCID: PMC3874157 DOI: 10.1093/nar/gkt838] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 12/18/2022] Open
Abstract
We applied Illumina Human Methylation450K array to perform a genomic-scale single-site resolution DNA methylation analysis in neuronal and nonneuronal (primarily glial) nuclei separated from the orbitofrontal cortex of postmortem human brain. The findings were validated using enhanced reduced representation bisulfite sequencing. We identified thousands of sites differentially methylated (DM) between neuronal and nonneuronal cells. The DM sites were depleted within CpG-island-containing promoters but enriched in predicted enhancers. Classification of the DM sites into those undermethylated in neurons (neuronal type) and those undermethylated in nonneuronal cells (glial type), combined with findings of others that methylation within control elements typically negatively correlates with gene expression, yielded large sets of predicted neuron-specific and non-neuron-specific genes. These sets of predicted genes were in excellent agreement with the available direct measurements of gene expression in human and mouse. We also found a distinct set of DNA methylation patterns that were unique for neuronal cells. In particular, neuronal-type differential methylation was overrepresented in CpG island shores, enriched within gene bodies but not in intergenic regions, and preferentially harbored binding motifs for a distinct set of transcription factors, including neuron-specific activity-dependent factors. Finally, non-CpG methylation was substantially more prevalent in neurons than in nonneuronal cells.
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Affiliation(s)
- Alexey Kozlenkov
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Panos Roussos
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Alisa Timashpolsky
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mihaela Barbu
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sergei Rudchenko
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Marina Bibikova
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Brandy Klotzle
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - William Byne
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca Lyddon
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Antonio Fabio Di Narzo
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Yasmin L. Hurd
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V. Koonin
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stella Dracheva
- VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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19
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Abstract
There are five mammalian stomatin-domain genes, all of which encode peripheral membrane proteins that can modulate ion channel function. Here we examined the ability of stomatin-like protein 1 (STOML1) to modulate the proton-sensitive members of the acid-sensing ion channel (ASIC) family. STOML1 profoundly inhibits ASIC1a, but has no effect on the splice variant ASIC1b. The inactivation time constant of ASIC3 is also accelerated by STOML1. We examined STOML1 null mutant mice with a β-galactosidase-neomycin cassette gene-trap reporter driven from the STOML1 gene locus, which indicated that STOML1 is expressed in at least 50% of dorsal root ganglion (DRG) neurones. Patch clamp recordings from mouse DRG neurones identified a trend for larger proton-gated currents in neurones lacking STOML1, which was due to a contribution of effects upon both transient and sustained currents, at different pH, a finding consistent with an endogenous inhibitory function for STOML1.
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Affiliation(s)
- Alexey Kozlenkov
- Department of Neuroscience, Growth Factor & Regeneration Group, Max-Delbrueck Center for Molecular Medicine, Robert-Roessle Strasse 10, D-13092 Berlin, Germany. or
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20
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Gatch MB, Kozlenkov A, Huang RQ, Yang W, Nguyen JD, González-Maeso J, Rice KC, France CP, Dillon GH, Forster MJ, Schetz JA. The HIV antiretroviral drug efavirenz has LSD-like properties. Neuropsychopharmacology 2013; 38:2373-84. [PMID: 23702798 PMCID: PMC3799056 DOI: 10.1038/npp.2013.135] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 01/19/2023]
Abstract
Anecdotal reports have surfaced concerning misuse of the HIV antiretroviral medication efavirenz ((4S)-6-chloro-4-(2-cyclopropylethynyl)-4-(trifluoromethyl)-2,4-dihydro-1H-3,1-benzoxazin-2-one) by HIV patients and non-infected teens who crush the pills and smoke the powder for its psychoactive effects. Molecular profiling of the receptor pharmacology of efavirenz pinpointed interactions with multiple established sites of action for other known drugs of abuse including catecholamine and indolamine transporters, and GABAA and 5-HT(2A) receptors. In rodents, interaction with the 5-HT(2A) receptor, a primary site of action of lysergic acid diethylamine (LSD), appears to dominate efavirenz's behavioral profile. Both LSD and efavirenz reduce ambulation in a novel open-field environment. Efavirenz occasions drug-lever responding in rats discriminating LSD from saline, and this effect is abolished by selective blockade of the 5-HT(2A) receptor. Similar to LSD, efavirenz induces head-twitch responses in wild-type, but not in 5-HT(2A)-knockout, mice. Despite having GABAA-potentiating effects (like benzodiazepines and barbiturates), and interactions with dopamine transporter, serotonin transporter, and vesicular monoamine transporter 2 (like cocaine and methamphetamine), efavirenz fails to maintain responding in rats that self-administer cocaine, and it fails to produce a conditioned place preference. Although its molecular pharmacology is multifarious, efavirenz's prevailing behavioral effect in rodents is consistent with LSD-like activity mediated via the 5-HT(2A) receptor. This finding correlates, in part, with the subjective experiences in humans who abuse efavirenz and with specific dose-dependent adverse neuropsychiatric events, such as hallucinations and night terrors, reported by HIV patients taking it as a medication.
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Affiliation(s)
- Michael B Gatch
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Alexey Kozlenkov
- Department of Psychiatry and Neurology, Mount Sinai School of Medicine, New York, NY, USA
| | - Ren-Qi Huang
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Wenjuan Yang
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jacques D Nguyen
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Javier González-Maeso
- Department of Psychiatry and Neurology, Mount Sinai School of Medicine, New York, NY, USA
| | - Kenner C Rice
- Drug Design and Synthesis Section, Chemical Biology Research Branch, National Institute on Drug Abuse and National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Charles P France
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Glenn H Dillon
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA,Institute for Aging and Alzheimer's Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Michael J Forster
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA,Institute for Aging and Alzheimer's Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - John A Schetz
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA,Institute for Aging and Alzheimer's Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA,Department of Psychiatry, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA,Department of Health Management and Policy, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX, USA,Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA, Tel: +1 817 735 2064, Fax: +1 817 735 0408, E-mail:
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21
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Lapatsina L, Jira JA, Smith ESJ, Poole K, Kozlenkov A, Bilbao D, Lewin GR, Heppenstall PA. Regulation of ASIC channels by a stomatin/STOML3 complex located in a mobile vesicle pool in sensory neurons. Open Biol 2013; 2:120096. [PMID: 22773952 PMCID: PMC3390797 DOI: 10.1098/rsob.120096] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [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: 05/22/2012] [Accepted: 06/01/2012] [Indexed: 01/21/2023] Open
Abstract
A complex of stomatin-family proteins and acid-sensing (proton-gated) ion channel (ASIC) family members participate in sensory transduction in invertebrates and vertebrates. Here, we have examined the role of the stomatin-family protein stomatin-like protein-3 (STOML3) in this process. We demonstrate that STOML3 interacts with stomatin and ASIC subunits and that this occurs in a highly mobile vesicle pool in dorsal root ganglia (DRG) neurons and Chinese hamster ovary cells. We identify a hydrophobic region in the N-terminus of STOML3 that is required for vesicular localization of STOML3 and regulates physical and functional interaction with ASICs. We further characterize STOML3-containing vesicles in DRG neurons and show that they are Rab11-positive, but not part of the early-endosomal, lysosomal or Rab14-dependent biosynthetic compartment. Moreover, uncoupling of vesicles from microtubules leads to incorporation of STOML3 into the plasma membrane and increased acid-gated currents. Thus, STOML3 defines a vesicle pool in which it associates with molecules that have critical roles in sensory transduction. We suggest that the molecular features of this vesicular pool may be characteristic of a ‘transducosome’ in sensory neurons.
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Affiliation(s)
- Liudmila Lapatsina
- Department of Neuroscience, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin-Buch, Germany
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22
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Kurita M, Moreno JL, Holloway T, Kozlenkov A, Mocci G, García-Bea A, Hanks JB, Neve R, Nestler EJ, Russo SJ, González-Maeso J. Repressive epigenetic changes at the mGlu2 promoter in frontal cortex of 5-HT2A knockout mice. Mol Pharmacol 2013; 83:1166-75. [PMID: 23508685 DOI: 10.1124/mol.112.084582] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Serotonin 5-HT(2A) and metabotropic glutamate 2 (mGlu2) are G protein-coupled receptors suspected in the pathophysiology of psychiatric disorders, such as schizophrenia, depression, and suicide. Previous findings demonstrate that mGlu2 mRNA expression is down-regulated in brain cortical regions of 5-HT2A knockout (KO) mice. However, the molecular mechanism responsible for this alteration remains unknown. We show here repressive epigenetic changes at the promoter region of the mGlu2 gene in frontal cortex of 5-HT(2A)-KO mice. Disruption of 5-HT(2A) receptor-dependent signaling in mice was associated with decreased acetylation of histone H3 (H3ac) and H4 (H4ac) and increased tri-methylation of histone H3 at lysine 27 (H3K27me3) at the mGlu2 promoter, epigenetic changes that correlate with transcriptional repression. Neither methylation of histone H3 at lysine 4 (H3K4me1/2/3) nor tri-methylation of histone H3 at lysine 9 (H3K9me3) was affected. We found that Egr1, a transcription factor in which promoter activity was positively regulated by the 5-HT(2A) receptor agonist 4-bromo-3,6-dimethoxybenzocyclobuten-1-yl)methylamine hydrobromide, binds less to the mGlu2 promoter in frontal cortex of 5-HT(2A)-KO, compared with wild-type mice. Furthermore, expression of mGlu2 was increased by viral-mediated gene transfer of FLAG-tagged Egr1 in mouse frontal cortex. Together, these observations suggest that 5-HT(2A) receptor-dependent signaling epigenetically affects mGlu2 transcription in mouse frontal cortex.
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Affiliation(s)
- Mitsumasa Kurita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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23
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Williams AA, Ingram WM, Levine S, Resnik J, Kamel CM, Lish JR, Elizalde DI, Janowski SA, Shoker J, Kozlenkov A, González-Maeso J, Gallitano AL. Reduced levels of serotonin 2A receptors underlie resistance of Egr3-deficient mice to locomotor suppression by clozapine. Neuropsychopharmacology 2012; 37:2285-98. [PMID: 22692564 PMCID: PMC3422493 DOI: 10.1038/npp.2012.81] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 04/06/2012] [Accepted: 04/26/2012] [Indexed: 02/06/2023]
Abstract
The immediate-early gene early growth response 3 (Egr3) is associated with schizophrenia and expressed at reduced levels in postmortem patients' brains. We have previously reported that Egr3-deficient (Egr3(-/-)) mice display reduced sensitivity to the sedating effects of clozapine compared with wild-type (WT) littermates, paralleling the heightened tolerance of schizophrenia patients to antipsychotic side effects. In this study, we have used a pharmacological dissection approach to identify a neurotransmitter receptor defect in Egr3(-/-) mice that may mediate their resistance to the locomotor suppressive effects of clozapine. We report that this response is specific to second-generation antipsychotic agents (SGAs), as first-generation medications suppress the locomotor activity of Egr3(-/-) and WT mice to a similar degree. Further, in contrast to the leading theory that sedation by clozapine results from anti-histaminergic effects, we show that H1 histamine receptors are not responsible for this effect in C57BL/6 mice. Instead, selective serotonin 2A receptor (5HT(2A)R) antagonists ketanserin and MDL-11939 replicate the effect of SGAs, repressing the activity in WT mice at a dosage that fails to suppress the activity of Egr3(-/-) mice. Radioligand binding revealed nearly 70% reduction in 5HT(2A)R expression in the prefrontal cortex of Egr3(-/-) mice compared with controls. Egr3(-/-) mice also exhibit a decreased head-twitch response to 5HT(2A)R agonist 1-(2,5-dimethoxy 4-iodophenyl)-2-amino propane (DOI). These findings provide a mechanism to explain the reduced sensitivity of Egr3(-/-) mice to the locomotor suppressive effects of SGAs, and suggest that 5HT(2A)Rs may also contribute to the sedating properties of these medications in humans. Moreover, as the deficit in cortical 5HT(2A)R in Egr3(-/-) mice aligns with numerous studies reporting decreased 5HT(2A)R levels in the brains of schizophrenia patients, and the gene encoding the 5HT(2A)R is itself a leading schizophrenia candidate gene, these findings suggest a potential mechanism by which putative dysfunction in EGR3 in humans may influence risk for schizophrenia.
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Affiliation(s)
| | - Wendy M Ingram
- Department of Molecular and Cell Biology, Life Sciences Addition, University of California, Berkeley, CA, USA
| | - Sarah Levine
- University of Arizona College of Medicine—Tucson, Tucson, AZ, USA
| | - Jack Resnik
- Department of Basic Medical Sciences and Psychiatry, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, USA
| | - Christy M Kamel
- Department of Basic Medical Sciences and Psychiatry, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, USA
| | - James R Lish
- Department of Basic Medical Sciences and Psychiatry, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, USA
| | - Diana I Elizalde
- Department of Basic Medical Sciences and Psychiatry, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, USA
| | - Scott A Janowski
- University of Arizona College of Medicine—Tucson, Tucson, AZ, USA
| | - Joseph Shoker
- Department of Basic Medical Sciences and Psychiatry, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - Javier González-Maeso
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
- Department of Neurology, Mount Sinai School of Medicine, New York, NY, USA
| | - Amelia L Gallitano
- Department of Basic Medical Sciences and Psychiatry, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, USA
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24
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Kurita M, Holloway T, García-Bea A, Kozlenkov A, Friedman AK, Moreno JL, Heshmati M, Golden SA, Kennedy PJ, Takahashi N, Dietz DM, Mocci G, Gabilondo AM, Hanks J, Umali A, Callado LF, Gallitano AL, Neve RL, Shen L, Buxbaum JD, Han MH, Nestler EJ, Meana JJ, Russo SJ, González-Maeso J. HDAC2 regulates atypical antipsychotic responses through the modulation of mGlu2 promoter activity. Nat Neurosci 2012; 15:1245-54. [PMID: 22864611 PMCID: PMC3431440 DOI: 10.1038/nn.3181] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/05/2012] [Indexed: 02/08/2023]
Abstract
Histone deacetylases (HDACs) compact chromatin structure and repress gene transcription. In schizophrenia, clinical studies demonstrate that HDAC inhibitors are efficacious when given in combination with atypical antipsychotics. However, the molecular mechanism that integrates a better response to antipsychotics with changes in chromatin structure remains unknown. Here we found that chronic atypical antipsychotics downregulated the transcription of metabotropic glutamate 2 receptor (mGlu2, also known as Grm2), an effect that was associated with decreased histone acetylation at its promoter in mouse and human frontal cortex. This epigenetic change occurred in concert with a serotonin 5-HT(2A) receptor-dependent upregulation and increased binding of HDAC2 to the mGlu2 promoter. Virally mediated overexpression of HDAC2 in frontal cortex decreased mGlu2 transcription and its electrophysiological properties, thereby increasing psychosis-like behavior. Conversely, HDAC inhibitors prevented the repressive histone modifications induced at the mGlu2 promoter by atypical antipsychotics, and augmented their therapeutic-like effects. These observations support the view of HDAC2 as a promising new target for schizophrenia treatment.
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Affiliation(s)
- Mitsumasa Kurita
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
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25
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Brand J, Smith ESJ, Schwefel D, Lapatsina L, Poole K, Omerbašić D, Kozlenkov A, Behlke J, Lewin GR, Daumke O. A stomatin dimer modulates the activity of acid-sensing ion channels. EMBO J 2012; 31:3635-46. [PMID: 22850675 PMCID: PMC3433786 DOI: 10.1038/emboj.2012.203] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [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: 01/06/2012] [Accepted: 07/06/2012] [Indexed: 12/14/2022] Open
Abstract
Stomatins govern membrane trafficking and ion channel activity. The banana-shaped stomatin-domain dimmers oligomerize into a cylindrical structure. A dynamic hydrophobic pocket at the concave side of the dimer mediates repression of acid-sensing ion channel 3 (ASIC3) activity. Stomatin proteins oligomerize at membranes and have been implicated in ion channel regulation and membrane trafficking. To obtain mechanistic insights into their function, we determined three crystal structures of the conserved stomatin domain of mouse stomatin that assembles into a banana-shaped dimer. We show that dimerization is crucial for the repression of acid-sensing ion channel 3 (ASIC3) activity. A hydrophobic pocket at the inside of the concave surface is open in the presence of an internal peptide ligand and closes in the absence of this ligand, and we demonstrate a function of this pocket in the inhibition of ASIC3 activity. In one crystal form, stomatin assembles via two conserved surfaces into a cylindrical oligomer, and these oligomerization surfaces are also essential for the inhibition of ASIC3-mediated currents. The assembly mode of stomatin uncovered in this study might serve as a model to understand oligomerization processes of related membrane-remodelling proteins, such as flotillin and prohibitin.
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Affiliation(s)
- Janko Brand
- Max-Delbrück Center for Molecular Medicine, Crystallography Department, Berlin, Germany
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26
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Wetzel C, Hu J, Riethmacher D, Benckendorff A, Harder L, Eilers A, Moshourab R, Kozlenkov A, Labuz D, Caspani O, Erdmann B, Machelska H, Heppenstall PA, Lewin GR. A stomatin-domain protein essential for touch sensation in the mouse. Nature 2006; 445:206-9. [PMID: 17167420 DOI: 10.1038/nature05394] [Citation(s) in RCA: 188] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 10/30/2006] [Indexed: 11/09/2022]
Abstract
Touch and mechanical pain are first detected at our largest sensory surface, the skin. The cell bodies of sensory neurons that detect such stimuli are located in the dorsal root ganglia, and subtypes of these neurons are specialized to detect specific modalities of mechanical stimuli. Molecules have been identified that are necessary for mechanosensation in invertebrates but so far not in mammals. In Caenorhabditis elegans, mec-2 is one of several genes identified in a screen for touch insensitivity and encodes an integral membrane protein with a stomatin homology domain. Here we show that about 35% of skin mechanoreceptors do not respond to mechanical stimuli in mice with a mutation in stomatin-like protein 3 (SLP3, also called Stoml3), a mammalian mec-2 homologue that is expressed in sensory neurons. In addition, mechanosensitive ion channels found in many sensory neurons do not function without SLP3. Tactile-driven behaviours are also impaired in SLP3 mutant mice, including touch-evoked pain caused by neuropathic injury. SLP3 is therefore indispensable for the function of a subset of cutaneous mechanoreceptors, and our data support the idea that this protein is an essential subunit of a mammalian mechanotransducer.
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Affiliation(s)
- Christiane Wetzel
- Department of Neuroscience, Max-Delbrück Center for Molecular Medicine and Charité Universitätsmedizin Berlin, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany
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27
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Kozlenkov A, Le Du MH, Cuniasse P, Ny T, Hoylaerts MF, Millán JL. Residues determining the binding specificity of uncompetitive inhibitors to tissue-nonspecific alkaline phosphatase. J Bone Miner Res 2004; 19:1862-72. [PMID: 15476587 DOI: 10.1359/jbmr.040608] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 04/01/2004] [Accepted: 06/28/2004] [Indexed: 11/18/2022]
Abstract
UNLABELLED Recent data have pointed to TNALP as a therapeutic target for soft-tissue ossification abnormalities. Here, we used mutagenesis, kinetic analysis, and computer modeling to identify the residues important for the binding of known ALP inhibitors to the TNALP active site. These data will enable drug design efforts aimed at developing improved specific TNALP inhibitors for therapeutic use. INTRODUCTION We have shown previously that the genetic ablation of tissue-nonspecific alkaline phosphatase (TNALP) function leads to amelioration of soft-tissue ossification in mouse models of osteoarthritis and ankylosis (i.e., Enpp1-/- and ank/ank mutant mice). We surmise that the pharmacologic inhibition of TNALP activity represents a viable therapeutic approach for these diseases. As a first step toward developing suitable TNALP therapeutics, we have now clarified the residues involved in binding well-known uncompetitive inhibitors to the TNALP active site. MATERIALS AND METHODS We compared the modeled 3D structure of TNALP with the 3D structure of human placental alkaline phosphatase (PLALP) and identified the residues that differ between these isozymes within a 12 A radius of the active site, because these isozymes differ significantly in inhibitor specificity. We then used site-directed mutagenesis to substitute TNALP residues to their respective homolog in PLALP. In addition, we mutagenized most of these residues in TNALP to Ala and the corresponding residues in PLALP to their TNALP homolog. All mutants were characterized for their sensitivity toward the uncompetitive inhibitors l-homoarginine (L-hArg), levamisole, theophylline, and l-phenylalanine. RESULTS AND CONCLUSIONS We found that the identity of residue 108 in TNALP largely determines the specificity of inhibition by L-hArg. The conserved Tyr-371 is also necessary for binding of L-hArg. In contrast, the binding of levamisole to TNALP is mostly dependent on His-434 and Tyr-371, but not on residues 108 or 109. The main determinant of sensitivity to theophylline is His-434. Thus, we have clarified the location of the binding sites for all three TNALP inhibitors, and we have also been able to exchange inhibitor specificities between TNALP and PLALP. These data will enable drug design efforts aimed at developing improved, selective, and drug-like TNALP inhibitors for therapeutic use.
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Affiliation(s)
- Alexey Kozlenkov
- Department of Medical Biosciences, Medical Genetics, Umeå University, Umeå, Sweden
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28
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Di Mauro S, Manes T, Hessle L, Kozlenkov A, Pizauro JMJ, Hoylaerts MF, Millán JL. Kinetic characterization of hypophosphatasia mutations with physiological substrates. J Bone Miner Res 2002; 17:1383-91. [PMID: 12162492 DOI: 10.1359/jbmr.2002.17.8.1383] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have analyzed 16 missense mutations of the tissue-nonspecific AP (TNAP) gene found in patients with hypophosphatasia. These mutations span the phenotypic spectrum of the disease, from the lethal perinatal/ infantile forms to the less severe adult and odontohypophosphatasia. Site-directed mutagenesis was used to introduce a sequence tag into the TNAP cDNA and eliminate the glycosylphosphatidylinositol (GPI)-anchor recognition sequence to produce a secreted epitope-tagged TNAP (setTNAP). The properties of GPI-anchored TNAP (gpiTNAP) and setTNAP were found comparable. After introducing each single hypophosphatasia mutation, the setTNAP and mutant TNAP cDNAs were expressed in COS-1 cells and the recombinant flagged enzymes were affinity purified. We characterized the kinetic behavior, inhibition, and heat stability properties of each mutant using the artificial substrate p-nitrophenylphosphate (pNPP) at pH 9.8. We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. Six of the mutant enzymes were completely devoid of catalytic activity (R54C, R54P, A94T, R206W, G317D, and V365I), and 10 others (A16V, A115V, A160T, A162T, E174K, E174G, D277A, E281K, D361V, and G439R) showed various levels of residual activity. The A160T substitution was found to decrease the catalytic efficiency of the mutant enzyme toward pNPP to retain normal activity toward PPi and to display increased activity toward PLP. The A162T substitution caused a considerable reduction in the pNPPase, PPiase, and PLPase activities of the mutant enzyme. The D277A mutant was found to maintain high catalytic efficiency toward pNPP as substrate but not against PLP or PPi. Three mutations ( E174G, E174K, and E281K) were found to retain normal or slightly subnormal catalytic efficiency toward pNPP and PPi but not against PLP. Because abnormalities in PLP metabolism have been shown to cause epileptic seizures in mice null for the TNAP gene, these kinetic data help explain the variable expressivity of epileptic seizures in hypophosphatasia patients.
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Abstract
We have probed the structural/functional relationship of key residues in human placental alkaline phosphatase (PLAP) and compared their properties with those of the corresponding residues in Escherichia coli alkaline phosphatase (ECAP). Mutations were introduced in wild-type PLAP, i.e. [E429]PLAP, and in some instances also in [G429]PLAP, which displays properties characteristic of the human germ cell alkaline phosphatase isozyme. All active site metal ligands, as well as residues in their vicinity, were substituted to alanines or to the homologous residues present in ECAP. We found that mutations at Zn2 or Mg sites had similar effects in PLAP and ECAP but that the environment of the Zn1 ion in PLAP is less affected by substitutions than that in ECAP. Substitutions of the Mg and Zn1 neighboring residues His-317 and His-153 increased k(cat) and increased K(m) when compared with wild-type PLAP, contrary to what was predicted by the reciprocal substitutions in ECAP. All mammalian alkaline phosphatases (APs) have five cysteine residues (Cys-101, Cys-121, Cys-183, Cys-467, and Cys-474) per subunit, not homologous to any of the four cysteines in ECAP. By substituting each PLAP Cys by Ser, we found that disrupting the disulfide bond between Cys-121 and Cys-183 completely prevents the formation of the active enzyme, whereas the carboxyl-terminally located Cys-467-Cys-474 bond plays a lesser structural role. The substitution of the free Cys-101 did not significantly affect the properties of the enzyme. A distinguishing feature found in all mammalian APs, but not in ECAP, is the Tyr-367 residue involved in subunit contact and located close to the active site of the opposite subunit. We studied the A367 and F367 mutants of PLAP, as well as the corresponding double mutants containing G429. The mutations led to a 2-fold decrease in k(cat), a significant decrease in heat stability, and a significant disruption of inhibition by the uncompetitive inhibitors l-Phe and l-Leu. Our mutagenesis data, computer modeling, and docking predictions indicate that this residue contributes to the formation of the hydrophobic pocket that accommodates and stabilizes the side chain of the inhibitor during uncompetitive inhibition of mammalian APs.
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Affiliation(s)
- Alexey Kozlenkov
- Department of Medical Biosciences, Umeå University, S-901 85 Umeå, Sweden
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Wennberg C, Kozlenkov A, Di Mauro S, Fröhlander N, Beckman L, Hoylaerts MF, Millán JL. Structure, genomic DNA typing, and kinetic characterization of the D allozyme of placental alkaline phosphatase (PLAP/ALPP). Hum Mutat 2002; 19:258-67. [PMID: 11857742 DOI: 10.1002/humu.10052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The D allozyme of placental alkaline phosphatase (PLAP) displays enzymatic properties at variance with those of the common PLAP allozymes. We have deduced the amino acid sequence of the PLAP D allele by PCR cloning of its gene, ALPP. Two coding substitutions were found in comparison with the cDNA of the common PLAP F allele, i.e., 692C>G and 1352A>G, which translate into a P209R and E429G substitution. A single nucleotide primer extension (SNuPE) assay was developed using PCR primers that enable the amplification of a 1.9 kb PLAP fragment. Extension primers were then used on this PCR fragment to detect the 692C>G and 1352A>G substitution. The SNuPE assay on these two nucleotide substitutions enabled us to distinguish the PLAP F and D alleles from the PLAP S/I alleles. Functional studies on the D allozyme were made possible by constructing and expressing a PLAP D cDNA, i.e., [Arg209, Gly429]PLAP, into wild-type Chinese hamster ovary cells. We determined the k(cat) and K(m), of the PLAP S, F, and D allozymes using the non-physiological substrate p-nitrophenylphosphate at an optimal pH (9.8) as well as two physiological substrates, i.e., pyridoxal-5-phosphate and inorganic pyrophosphate at physiological pH (7.5). We found that the biochemical properties of the D allozyme of PLAP are significantly different from those of the common PLAP allozymes. These biochemical findings suggest that a suboptimal enzymatic function by the PLAP D allozyme may be the basis for the apparent negative selective pressure of the PLAP D allele. The development of the SNuPE assay will enable us to test the hypothesis that the PLAP D allele is subjected to intrauterine selection by examining genomic DNA from statistically informative population samples.
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Affiliation(s)
- Charlotte Wennberg
- Department of Medical Biosciences, Medical Genetics, Umeå University, Umeå, Sweden
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