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Hong Y, Hu J, Zhang S, Liu J, Yan F, Yang H, Hu H. Integrative analysis identifies region- and sex-specific gene networks and Mef2c as a mediator of anxiety-like behavior. Cell Rep 2024; 43:114455. [PMID: 38990717 DOI: 10.1016/j.celrep.2024.114455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/20/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The molecular mechanisms underlying multi-brain region origins and sexual dimorphism of anxiety remain unclear. Here, we leverage large-scale transcriptomics from seven brain regions in mouse models of anxiety and extensive experiments to dissect brain-region- and sex-specific gene networks. We identify 4,840 genes with sex-specific expression alterations across seven brain regions, organized into ten network modules with sex-biased expression patterns. Modular analysis prioritizes 86 sex-specific mediators of anxiety susceptibility, including myocyte-specific enhancer factor 2c (Mef2c) in the CA3 region of male mice. Mef2c expression is decreased in the pyramidal neurons (PyNs) of susceptible male mice. Up-regulating Mef2c in CA3 PyNs significantly alleviates anxiety-like behavior, whereas down-regulating Mef2c induces anxiety-like behavior in male mice. The anxiolytic effect of Mef2c up-regulation is associated with enhanced neuronal excitability and synaptic transmission. In summary, this study uncovers brain-region- and sex-specific networks and identifies Mef2c in CA3 PyNs as a critical mediator of anxiety in male mice.
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Affiliation(s)
- Yizhou Hong
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Jiameng Hu
- School of Life Science and Technology, Chongqing Innovation Institute of China Pharmaceutical University, China Pharmaceutical University, Nanjing, China
| | - Shiya Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; College of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jiaxin Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; College of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangrong Yan
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hua Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
| | - Haiyang Hu
- School of Life Science and Technology, Chongqing Innovation Institute of China Pharmaceutical University, China Pharmaceutical University, Nanjing, China; Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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2
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Serafini RA, Farzinpour Z, Patel V, Kelley AM, Estill M, Pryce KD, Sakloth F, Teague CD, Torres-Berrio A, Nestler EJ, Shen L, Akbarian S, Karkhanis AN, Blitzer RD, Zachariou V. Nucleus accumbens myocyte enhancer factor 2C mediates the maintenance of peripheral nerve injury-induced physiological and behavioral maladaptations. Pain 2024:00006396-990000000-00648. [PMID: 38985454 DOI: 10.1097/j.pain.0000000000003316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 04/18/2024] [Indexed: 07/11/2024]
Abstract
ABSTRACT Preclinical and clinical work has demonstrated altered plasticity and activity in the nucleus accumbens (NAc) under chronic pain states, highlighting critical therapeutic avenues for the management of chronic pain conditions. In this study, we demonstrate that myocyte enhancer factor 2C (MEF2C), a master regulator of neuronal activity and plasticity, is repressed in NAc neurons after prolonged spared nerve injury (SNI). Viral-mediated overexpression of Mef2c in NAc neurons partially ameliorated sensory hypersensitivity and emotional behaviors in mice with SNI, while also altering transcriptional pathways associated with synaptic signaling. Mef2c overexpression also reversed SNI-induced potentiation of phasic dopamine release and neuronal hyperexcitability in the NAc. Transcriptional changes induced by Mef2c overexpression were different than those observed after desipramine treatment, suggesting a mechanism of action different from antidepressants. Overall, we show that interventions in MEF2C-regulated mechanisms in the NAc are sufficient to disrupt the maintenance of chronic pain states, providing potential new treatment avenues for neuropathic pain.
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Affiliation(s)
- Randal A Serafini
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
- Department of Pharmacology, Physiology, & Biophysics, Chobanian and Avedisian School of Medicine at Boston University, Boston, MA, United states
| | - Zahra Farzinpour
- Department of Pharmacology, Physiology, & Biophysics, Chobanian and Avedisian School of Medicine at Boston University, Boston, MA, United states
| | - Vishwendra Patel
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Abigail M Kelley
- Department of Psychology, Binghamton University-SUNY, Binghamton, NY, United states
| | - Molly Estill
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Kerri D Pryce
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Farhana Sakloth
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Collin D Teague
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Angelica Torres-Berrio
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Schahram Akbarian
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Anushree N Karkhanis
- Department of Psychology, Binghamton University-SUNY, Binghamton, NY, United states
| | - Robert D Blitzer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United states
| | - Venetia Zachariou
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United states
- Department of Pharmacology, Physiology, & Biophysics, Chobanian and Avedisian School of Medicine at Boston University, Boston, MA, United states
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Cordeiro A, Gomes C, Bicker J, Fortuna A. Aging and cognitive resilience: Molecular mechanisms as new potential therapeutic targets. Drug Discov Today 2024; 29:104093. [PMID: 38992420 DOI: 10.1016/j.drudis.2024.104093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/25/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
As the global population ages, the need to prolong lifespan and healthspan becomes increasingly imperative. Understanding the molecular determinants underlying cognitive resilience, together with changes during aging and the (epi)genetic factors that predispose an individual to decreased cognitive resilience, open avenues for researching novel therapies. This review provides a critical and timely appraisal of the molecular mechanisms underlying cognitive resilience, framed within a critical analysis of emerging therapeutic strategies to mitigate age-related cognitive decline. Significant insights from both animals and human subjects are discussed herein, directed either toward active pharmaceutical ingredients (drug repositioning or macromolecules), or, alternatively, advanced cellular therapies.
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Affiliation(s)
- Ana Cordeiro
- Laboratory of Pharmacology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Catarina Gomes
- Laboratory of Pharmacology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Coimbra, Portugal
| | - Joana Bicker
- Laboratory of Pharmacology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Coimbra, Portugal
| | - Ana Fortuna
- Laboratory of Pharmacology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Coimbra, Portugal.
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4
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Haikonen J, Szrinivasan R, Ojanen S, Rhee JK, Ryazantseva M, Sulku J, Zumaraite G, Lauri SE. GluK1 kainate receptors are necessary for functional maturation of parvalbumin interneurons regulating amygdala circuit function. Mol Psychiatry 2024:10.1038/s41380-024-02641-2. [PMID: 38942774 DOI: 10.1038/s41380-024-02641-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Parvalbumin expressing interneurons (PV INs) are key players in the local inhibitory circuits and their developmental maturation coincides with the onset of adult-type network dynamics in the brain. Glutamatergic signaling regulates emergence of the unique PV IN phenotype, yet the receptor mechanisms involved are not fully understood. Here we show that GluK1 subunit containing kainate receptors (KARs) are necessary for development and maintenance of the neurochemical and functional properties of PV INs in the lateral and basal amygdala (BLA). Ablation of GluK1 expression specifically from PV INs resulted in low parvalbumin expression and loss of characteristic high firing rate throughout development. In addition, we observed reduced spontaneous excitatory synaptic activity at adult GluK1 lacking PV INs. Intriguingly, inactivation of GluK1 expression in adult PV INs was sufficient to abolish their high firing rate and to reduce PV expression levels, suggesting a role for GluK1 in dynamic regulation of PV IN maturation state. The PV IN dysfunction in the absence of GluK1 perturbed the balance between evoked excitatory vs. inhibitory synaptic inputs and long-term potentiation (LTP) in LA principal neurons, and resulted in aberrant development of the resting-state functional connectivity between mPFC and BLA. Behaviorally, the absence of GluK1 from PV INs associated with hyperactivity and increased fear of novelty. These results indicate a critical role for GluK1 KARs in regulation of PV IN function across development and suggest GluK1 as a potential therapeutic target for pathologies involving PV IN malfunction.
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Affiliation(s)
- Joni Haikonen
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Rakenduvadhana Szrinivasan
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Simo Ojanen
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Jun Kyu Rhee
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Maria Ryazantseva
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Janne Sulku
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Gabija Zumaraite
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Sari E Lauri
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland.
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Lim Y, Akula SK, Myers AK, Chen C, Rafael KA, Walsh CA, Golden JA, Cho G. ARX regulates cortical interneuron differentiation and migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578282. [PMID: 38895467 PMCID: PMC11185560 DOI: 10.1101/2024.01.31.578282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Mutations in aristaless-related homeobox ( ARX ) are associated with neurodevelopmental disorders including developmental epilepsies, intellectual disabilities, and autism spectrum disorders, with or without brain malformations. Aspects of these disorders have been linked to abnormal cortical interneuron (cIN) development and function. To further understand ARX's role in cIN development, multiple Arx mutant mouse lines were interrogated. We found that ARX is critical for controlling cIN numbers and distribution, especially, in the developing marginal zone (MZ). Single cell transcriptomics and ChIP-seq, combined with functional studies, revealed ARX directly or indirectly regulates genes involved in proliferation and the cell cycle (e.g., Bub3 , Cspr3 ), fate specification (e.g., Nkx2.1 , Maf , Mef2c ), and migration (e.g., Nkx2.1 , Lmo1 , Cxcr4 , Nrg1 , ErbB4 ). Our data suggest that the MZ stream defects primarily result from disordered cell-cell communication. Together our findings provide new insights into the mechanisms underlying cIN development and migration and how they are disrupted in several disorders.
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Ward C, Nasrallah K, Tran D, Sabri E, Vazquez A, Sjulson L, Castillo PE, Batista-Brito R. Developmental Disruption of Mef2c in Medial Ganglionic Eminence-Derived Cortical Inhibitory Interneurons Impairs Cellular and Circuit Function. Biol Psychiatry 2024:S0006-3223(24)01360-X. [PMID: 38848814 DOI: 10.1016/j.biopsych.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/25/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND MEF2C is strongly linked to various neurodevelopmental disorders including autism, intellectual disability, schizophrenia, and attention-deficit/hyperactivity disorder. Mice that constitutively lack 1 copy of Mef2c or selectively lack both copies of Mef2c in cortical excitatory neurons display a variety of behavioral phenotypes associated with neurodevelopmental disorders. The MEF2C protein is a transcription factor necessary for cellular development and synaptic modulation of excitatory neurons. MEF2C is also expressed in a subset of cortical GABAergic (gamma-aminobutyric acidergic) inhibitory neurons, but its function in those cell types remains largely unknown. METHODS Using conditional deletions of the Mef2c gene in mice, we investigated the role of MEF2C in parvalbumin-expressing interneurons (PV-INs), the largest subpopulation of cortical GABAergic cells, at 2 developmental time points. We performed slice electrophysiology, in vivo recordings, and behavior assays to test how embryonic and late postnatal loss of MEF2C from GABAergic INs impacts their survival and maturation and alters brain function and behavior. RESULTS Loss of MEF2C from PV-INs during embryonic, but not late postnatal, development resulted in reduced PV-IN number and failure of PV-INs to molecularly and synaptically mature. In association with these deficits, early loss of MEF2C in GABAergic INs led to abnormal cortical network activity, hyperactive and stereotypic behavior, and impaired cognitive and social behavior. CONCLUSIONS MEF2C expression is critical for the development of cortical GABAergic INs, particularly PV-INs. Embryonic loss of function of MEF2C mediates dysfunction of GABAergic INs, leading to altered in vivo patterns of cortical activity and behavioral phenotypes associated with neurodevelopmental disorders.
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Affiliation(s)
- Claire Ward
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Kaoutsar Nasrallah
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York; Department of Biological Sciences, Fordham University, Bronx, New York
| | - Duy Tran
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Ehsan Sabri
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Arenski Vazquez
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Lucas Sjulson
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York
| | - Renata Batista-Brito
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York; Department of Genetics, Albert Einstein College of Medicine, Bronx, New York.
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Wu R, Sun Y, Zhou Z, Dong Z, Liu Y, Liu M, Gao H. MEF2C contributes to axonal branching by regulating Kif2c transcription. Eur J Neurosci 2024; 59:3389-3402. [PMID: 38663879 DOI: 10.1111/ejn.16344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 06/15/2024]
Abstract
Neurons are post-mitotic cells, with microtubules playing crucial roles in axonal transport and growth. Kinesin family member 2c (KIF2C), a member of the Kinesin-13 family, possesses the ability to depolymerize microtubules and is involved in remodelling the microtubule lattice. Myocyte enhancer factor 2c (MEF2C) was initially identified as a regulator of muscle differentiation but has recently been associated with neurological abnormalities such as severe cognitive impairment, stereotyping, epilepsy and brain malformations when mutated or deleted. However, further investigation is required to determine which target genes MEF2C acts upon to influence neuronal function as a transcription regulator. Our data demonstrate that knockdown of both Mef2c and Kif2c significantly impacts spinal motor neuron development and behaviour in zebrafish. Luciferase reporter assays and chromosome immunoprecipitation assays, along with down/upregulated expression analysis, revealed that MFE2C functions as a novel transcription regulator for the Kif2c gene. Additionally, the knockdown of either Mef2c or Kif2c expression in E18 cortical neurons substantially reduces the number of primary neurites and axonal branches during neuronal development in vitro without affecting neurite length. Finally, depletion of Kif2c eliminated the effects of overexpression of Mef2c on the neurite branching. Based on these findings, we provided novel evidence demonstrating that MEF2C regulates the transcription of the Kif2c gene thereby influencing the axonal branching.
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Affiliation(s)
- Ronghua Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Ying Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Zhihao Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Zhangji Dong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Yan Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Mei Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Huasong Gao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
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Ward C, Nasrallah K, Tran D, Sabri E, Vazquez A, Sjulson L, Castillo PE, Batista-Brito R. Developmental disruption of Mef2c in Medial Ganglionic Eminence-derived cortical inhibitory interneurons impairs cellular and circuit function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592084. [PMID: 38746148 PMCID: PMC11092645 DOI: 10.1101/2024.05.01.592084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
MEF2C is strongly linked to various neurodevelopmental disorders (NDDs) including autism, intellectual disability, schizophrenia, and attention-deficit/hyperactivity. Mice constitutively lacking one copy of Mef2c , or selectively lacking both copies of Mef2c in cortical excitatory neurons, display a variety of behavioral phenotypes associated with NDDs. The MEF2C protein is a transcription factor necessary for cellular development and synaptic modulation of excitatory neurons. MEF2C is also expressed in a subset of cortical GABAergic inhibitory neurons, but its function in those cell types remains largely unknown. Using conditional deletions of the Mef2c gene in mice, we investigated the role of MEF2C in Parvalbumin-expressing Interneurons (PV-INs), the largest subpopulation of cortical GABAergic cells, at two developmental timepoints. We performed slice electrophysiology, in vivo recordings, and behavior assays to test how embryonic and late postnatal loss of MEF2C from GABAergic interneurons impacts their survival and maturation, and alters brain function and behavior. We found that loss of MEF2C from PV-INs during embryonic, but not late postnatal, development resulted in reduced PV-IN number and failure of PV-INs to molecularly and synaptically mature. In association with these deficits, early loss of MEF2C in GABAergic interneurons lead to abnormal cortical network activity, hyperactive and stereotypic behavior, and impaired cognitive and social behavior. Our findings indicate that MEF2C expression is critical for the development of cortical GABAergic interneurons, particularly PV-INs. Embryonic loss of function of MEF2C mediates dysfunction of GABAergic interneurons, leading to altered in vivo patterns of cortical activity and behavioral phenotypes associated with neurodevelopmental disorders.
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Vogt K, Kulkarni A, Pandey R, Dehnad M, Konopka G, Greene R. Sleep need driven oscillation of glutamate synaptic phenotype. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578985. [PMID: 38370691 PMCID: PMC10871195 DOI: 10.1101/2024.02.05.578985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Sleep loss increases AMPA-synaptic strength and number in the neocortex. However, this is only part of the synaptic sleep loss response. We report increased AMPA/NMDA EPSC ratio in frontal-cortical pyramidal neurons of layers 2-3. Silent synapses are absent, decreasing the plastic potential to convert silent NMDA to active AMPA synapses. These sleep loss changes are recovered by sleep. Sleep genes are enriched for synaptic shaping cellular components controlling glutamate synapse phenotype, overlap with autism risk genes and are primarily observed in excitatory pyramidal neurons projecting intra-telencephalically. These genes are enriched with genes controlled by the transcription factor, MEF2c and its repressor, HDAC4. Thus, sleep genes under the influence of MEF2c and HDAC4, can provide a framework within which motor learning and training occurs mediated by sleep-dependent oscillation of glutamate-synaptic phenotypes.
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Affiliation(s)
- K.E. Vogt
- International Institute of Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - A. Kulkarni
- Department of Neuroscience, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - R. Pandey
- Department of Psychiatry, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - M. Dehnad
- Department of Psychiatry, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - G. Konopka
- Department of Neuroscience, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - R.W. Greene
- International Institute of Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
- Department of Neuroscience, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Psychiatry, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
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Cho JY, Rumschlag JA, Tsvetkov E, Proper DS, Lang H, Berto S, Assali A, Cowan CW. MEF2C Hypofunction in GABAergic Cells Alters Sociability and Prefrontal Cortex Inhibitory Synaptic Transmission in a Sex-Dependent Manner. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100289. [PMID: 38390348 PMCID: PMC10881314 DOI: 10.1016/j.bpsgos.2024.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 02/24/2024] Open
Abstract
Background Heterozygous mutations or deletions of MEF2C cause a neurodevelopmental disorder termed MEF2C haploinsufficiency syndrome (MCHS), characterized by autism spectrum disorder and neurological symptoms. In mice, global Mef2c heterozygosity has produced multiple MCHS-like phenotypes. MEF2C is highly expressed in multiple cell types of the developing brain, including GABAergic (gamma-aminobutyric acidergic) inhibitory neurons, but the influence of MEF2C hypofunction in GABAergic neurons on MCHS-like phenotypes remains unclear. Methods We employed GABAergic cell type-specific manipulations to study mouse Mef2c heterozygosity in a battery of MCHS-like behaviors. We also performed electroencephalography, single-cell transcriptomics, and patch-clamp electrophysiology and optogenetics to assess the impact of Mef2c haploinsufficiency on gene expression and prefrontal cortex microcircuits. Results Mef2c heterozygosity in developing GABAergic cells produced female-specific deficits in social preference and altered approach-avoidance behavior. In female, but not male, mice, we observed that Mef2c heterozygosity in developing GABAergic cells produced 1) differentially expressed genes in multiple cell types, including parvalbumin-expressing GABAergic neurons, 2) baseline and social-related frontocortical network activity alterations, and 3) reductions in parvalbumin cell intrinsic excitability and inhibitory synaptic transmission onto deep-layer pyramidal neurons. Conclusions MEF2C hypofunction in female, but not male, developing GABAergic cells is important for typical sociability and approach-avoidance behaviors and normal parvalbumin inhibitory neuron function in the prefrontal cortex of mice. While there is no apparent sex bias in autism spectrum disorder symptoms of MCHS, our findings suggest that GABAergic cell-specific dysfunction in females with MCHS may contribute disproportionately to sociability symptoms.
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Affiliation(s)
- Jennifer Y. Cho
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
- Medical Scientist Training Program, Medical University of South Carolina, Charleston, South Carolina
| | - Jeffrey A. Rumschlag
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Evgeny Tsvetkov
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Divya S. Proper
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Hainan Lang
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Ahlem Assali
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Christopher W. Cowan
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
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Faraone SV, Bellgrove MA, Brikell I, Cortese S, Hartman CA, Hollis C, Newcorn JH, Philipsen A, Polanczyk GV, Rubia K, Sibley MH, Buitelaar JK. Attention-deficit/hyperactivity disorder. Nat Rev Dis Primers 2024; 10:11. [PMID: 38388701 DOI: 10.1038/s41572-024-00495-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Attention-deficit/hyperactivity disorder (ADHD; also known as hyperkinetic disorder) is a common neurodevelopmental condition that affects children and adults worldwide. ADHD has a predominantly genetic aetiology that involves common and rare genetic variants. Some environmental correlates of the disorder have been discovered but causation has been difficult to establish. The heterogeneity of the condition is evident in the diverse presentation of symptoms and levels of impairment, the numerous co-occurring mental and physical conditions, the various domains of neurocognitive impairment, and extensive minor structural and functional brain differences. The diagnosis of ADHD is reliable and valid when evaluated with standard diagnostic criteria. Curative treatments for ADHD do not exist but evidence-based treatments substantially reduce symptoms and/or functional impairment. Medications are effective for core symptoms and are usually well tolerated. Some non-pharmacological treatments are valuable, especially for improving adaptive functioning. Clinical and neurobiological research is ongoing and could lead to the creation of personalized diagnostic and therapeutic approaches for this disorder.
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Affiliation(s)
- Stephen V Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Mark A Bellgrove
- School of Psychological Sciences, Turner Institute for Brain and Mental Health, Monash University, Melbourne, Victoria, Australia
| | - Isabell Brikell
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Samuele Cortese
- Centre for Innovation in Mental Health, School of Psychology, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences (CNS and Psychiatry), Faculty of Medicine, University of Southampton, Southampton, UK
- Solent NHS Trust, Southampton, UK
- Hassenfeld Children's Hospital at NYU Langone, New York University Child Study Center, New York City, NY, USA
- DiMePRe-J-Department of Precision and Rigenerative Medicine-Jonic Area, University of Bari "Aldo Moro", Bari, Italy
| | - Catharina A Hartman
- Interdisciplinary Center Psychopathology and Emotion regulation (ICPE), Department of Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Chris Hollis
- National Institute for Health and Care Research (NIHR) MindTech MedTech Co-operative and NIHR Nottingham Biomedical Research Centre, Institute of Mental Health, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jeffrey H Newcorn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Philipsen
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Guilherme V Polanczyk
- Department of Psychiatry, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Katya Rubia
- Department of Child & Adolescent Psychiatry, Institute of Psychiatry, Psychology & Neurosciences, King's College London, London, UK
- Department of Child & Adolescent Psychiatry, Transcampus Professor KCL-Dresden, Technical University, Dresden, Germany
| | | | - Jan K Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
- Karakter Child and Adolescent Psychiatry University Center, Nijmegen, Netherlands
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12
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Wahl N, Espeso-Gil S, Chietera P, Nagel A, Laighneach A, Morris DW, Rajarajan P, Akbarian S, Dechant G, Apostolova G. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol Cell 2024; 84:621-639.e9. [PMID: 38244545 PMCID: PMC10923151 DOI: 10.1016/j.molcel.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.
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Affiliation(s)
- Nico Wahl
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Sergio Espeso-Gil
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria; Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paola Chietera
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Amelie Nagel
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Prashanth Rajarajan
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
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13
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Rexrode LE, Hartley J, Showmaker KC, Challagundla L, Vandewege MW, Martin BE, Blair E, Bollavarapu R, Antonyraj RB, Hilton K, Gardiner A, Valeri J, Gisabella B, Garrett MR, Theoharides TC, Pantazopoulos H. Molecular profiling of the hippocampus of children with autism spectrum disorder. Mol Psychiatry 2024:10.1038/s41380-024-02441-8. [PMID: 38355786 DOI: 10.1038/s41380-024-02441-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Several lines of evidence point to a key role of the hippocampus in Autism Spectrum Disorders (ASD). Altered hippocampal volume and deficits in memory for person and emotion related stimuli have been reported, along with enhanced ability for declarative memories. Mouse models have demonstrated a critical role of the hippocampus in social memory dysfunction, associated with ASD, together with decreased synaptic plasticity. Chondroitin sulfate proteoglycans (CSPGs), a family of extracellular matrix molecules, represent a potential key link between neurodevelopment, synaptic plasticity, and immune system signaling. There is a lack of information regarding the molecular pathology of the hippocampus in ASD. We conducted RNAseq profiling on postmortem human brain samples containing the hippocampus from male children with ASD (n = 7) and normal male children (3-14 yrs old), (n = 6) from the NIH NeuroBioBank. Gene expression profiling analysis implicated molecular pathways involved in extracellular matrix organization, neurodevelopment, synaptic regulation, and immune system signaling. qRT-PCR and Western blotting were used to confirm several of the top markers identified. The CSPG protein BCAN was examined with multiplex immunofluorescence to analyze cell-type specific expression of BCAN and astrocyte morphology. We observed decreased expression of synaptic proteins PSD95 (p < 0.02) and SYN1 (p < 0.02), increased expression of the extracellular matrix (ECM) protease MMP9 (p < 0.03), and decreased expression of MEF2C (p < 0.03). We also observed increased BCAN expression with astrocytes in children with ASD, together with altered astrocyte morphology. Our results point to alterations in immune system signaling, glia cell differentiation, and synaptic signaling in the hippocampus of children with ASD, together with alterations in extracellular matrix molecules. Furthermore, our results demonstrate altered expression of genes implicated in genetic studies of ASD including SYN1 and MEF2C.
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Affiliation(s)
- Lindsay E Rexrode
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Joshua Hartley
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | | | - Lavanya Challagundla
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | | | - Brigitte E Martin
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | - Estelle Blair
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Ratna Bollavarapu
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Rhenius B Antonyraj
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Keauna Hilton
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Alex Gardiner
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Jake Valeri
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA
| | - Barbara Gisabella
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA
| | - Michael R Garrett
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | - Theoharis C Theoharides
- Institute of Neuro-Immune Medicine, Nova Southeastern University, Clearwater, FL, USA
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | - Harry Pantazopoulos
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA.
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA.
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14
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Basu S, Ro EJ, Liu Z, Kim H, Bennett A, Kang S, Suh H. The Mef2c Gene Dose-Dependently Controls Hippocampal Neurogenesis and the Expression of Autism-Like Behaviors. J Neurosci 2024; 44:e1058232023. [PMID: 38123360 PMCID: PMC10860657 DOI: 10.1523/jneurosci.1058-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Mutations in the activity-dependent transcription factor MEF2C have been associated with several neuropsychiatric disorders. Among these, autism spectrum disorder (ASD)-related behavioral deficits are manifested. Multiple animal models that harbor mutations in Mef2c have provided compelling evidence that Mef2c is indeed an ASD gene. However, studies in mice with germline or global brain knock-out of Mef2c are limited in their ability to identify the precise neural substrates and cell types that are required for the expression of Mef2c-mediated ASD behaviors. Given the role of hippocampal neurogenesis in cognitive and social behaviors, in this study we aimed to investigate the role of Mef2c in the structure and function of newly generated dentate granule cells (DGCs) in the postnatal hippocampus and to determine whether disrupted Mef2c function is responsible for manifesting ASD behaviors. Overexpression of Mef2c (Mef2cOE ) arrested the transition of neurogenesis at progenitor stages, as indicated by sustained expression of Sox2+ in Mef2cOE DGCs. Conditional knock-out of Mef2c (Mef2ccko ) allowed neuronal commitment of Mef2ccko cells; however, Mef2ccko impaired not only dendritic arborization and spine formation but also synaptic transmission onto Mef2ccko DGCs. Moreover, the abnormal structure and function of Mef2ccko DGCs led to deficits in social interaction and social novelty recognition, which are key characteristics of ASD behaviors. Thus, our study revealed a dose-dependent requirement of Mef2c in the control of distinct steps of neurogenesis, as well as a critical cell-autonomous function of Mef2c in newborn DGCs in the expression of proper social behavior in both sexes.
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Affiliation(s)
- Sreetama Basu
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
| | - Eun Jeoung Ro
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
| | - Zhi Liu
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
| | - Hyunjung Kim
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta 30912, Georgia
| | - Aubrey Bennett
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta 30912, Georgia
| | - Seungwoo Kang
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta 30912, Georgia
| | - Hoonkyo Suh
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
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15
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Li WK, Zhang SQ, Peng WL, Shi YH, Yuan B, Yuan YT, Xue ZY, Wang JC, Han WJ, Chen ZF, Shan SF, Xue BQ, Chen JL, Zhang C, Zhu SJ, Tai YL, Cheng TL, Qiu ZL. Whole-brain in vivo base editing reverses behavioral changes in Mef2c-mutant mice. Nat Neurosci 2024; 27:116-128. [PMID: 38012399 DOI: 10.1038/s41593-023-01499-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
Whole-brain genome editing to correct single-base mutations and reduce or reverse behavioral changes in animal models of autism spectrum disorder (ASD) has not yet been achieved. We developed an apolipoprotein B messenger RNA-editing enzyme, catalytic polypeptide-embedded cytosine base editor (AeCBE) system for converting C·G to T·A base pairs. We demonstrate its effectiveness by targeting AeCBE to an ASD-associated mutation of the MEF2C gene (c.104T>C, p.L35P) in vivo in mice. We first constructed Mef2cL35P heterozygous mice. Male heterozygous mice exhibited hyperactivity, repetitive behavior and social abnormalities. We then programmed AeCBE to edit the mutated C·G base pairs of Mef2c in the mouse brain through the intravenous injection of blood-brain barrier-crossing adeno-associated virus. This treatment successfully restored Mef2c protein levels in several brain regions and reversed the behavioral abnormalities in Mef2c-mutant mice. Our work presents an in vivo base-editing paradigm that could potentially correct single-base genetic mutations in the brain.
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Affiliation(s)
- Wei-Ke Li
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shu-Qian Zhang
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Wan-Ling Peng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Han Shi
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bo Yuan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Ting Yuan
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen-Yu Xue
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin-Cheng Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Wen-Jian Han
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Fang Chen
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Shi-Fang Shan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bi-Qing Xue
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jin-Long Chen
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Cheng Zhang
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shu-Jia Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Lin Tai
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tian-Lin Cheng
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
| | - Zi-Long Qiu
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Clinical Neuroscience Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
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16
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Fahey L, Ali D, Donohoe G, Ó Broin P, Morris DW. Genes positively regulated by Mef2c in cortical neurons are enriched for common genetic variation associated with IQ and educational attainment. Hum Mol Genet 2023; 32:3194-3203. [PMID: 37672226 PMCID: PMC10630234 DOI: 10.1093/hmg/ddad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Abstract
The myocyte enhancer factor 2 C (MEF2C) gene encodes a transcription factor important for neurogenesis and synapse development and contains common variants associated with intelligence (IQ) and educational attainment (EA). Here, we took gene expression data from the mouse cortex of a Mef2c mouse model with a heterozygous DNA binding-deficient mutation of Mef2c (Mef2c-het) and combined these data with MEF2C ChIP-seq data from cortical neurons and single-cell data from the mouse brain. This enabled us to create a set of genes that were differentially regulated in Mef2c-het mice, represented direct target genes of MEF2C and had elevated in expression in cortical neurons. We found this gene-set to be enriched for genes containing common genetic variation associated with IQ and EA. Genes within this gene-set that were down-regulated, i.e. have reduced expression in Mef2c-het mice versus controls, were specifically significantly enriched for both EA and IQ associated genes. These down-regulated genes were enriched for functionality in the adenylyl cyclase signalling system, which is known to positively regulate synaptic transmission and has been linked to learning and memory. Within the adenylyl cyclase signalling system, three genes regulated by MEF2C, CRHR1, RGS6, and GABRG3, are associated at genome-wide significant levels with IQ and/or EA. Our results indicate that genetic variation in MEF2C and its direct target genes within cortical neurons contribute to variance in cognition within the general population, and the molecular mechanisms involved include the adenylyl cyclase signalling system's role in synaptic function.
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Affiliation(s)
- Laura Fahey
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
- Discipline of Bioinformatics, School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Deema Ali
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Gary Donohoe
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Pilib Ó Broin
- Discipline of Bioinformatics, School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
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17
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Whitlock JH, Soelter TM, Howton TC, Wilk EJ, Oza VH, Lasseigne BN. Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 S858R Schinzel Giedion Syndrome mice. J Cell Mol Med 2023; 27:3565-3577. [PMID: 37872881 PMCID: PMC10660642 DOI: 10.1111/jcmm.18001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Schinzel Giedion Syndrome (SGS) is an ultra-rare autosomal dominant Mendelian disease presenting with abnormalities spanning multiple organ systems. The most notable phenotypes involve severe developmental delay, progressive brain atrophy, and drug-resistant seizures. SGS is caused by spontaneous variants in SETBP1, which encodes for the epigenetic hub SETBP1 transcription factor (TF). SETBP1 variants causing classical SGS cluster at the degron, disrupting SETBP1 protein degradation and resulting in toxic accumulation, while those located outside cause milder atypical SGS. Due to the multisystem phenotype, we evaluated gene expression and regulatory programs altered in atypical SGS by snRNA-seq of the cerebral cortex and kidney of Setbp1S858R heterozygous mice (corresponds to the human likely pathogenic SETBP1S867R variant) compared to matched wild-type mice by constructing cell-type-specific regulatory networks. Setbp1 was differentially expressed in excitatory neurons, but known SETBP1 targets were differentially expressed and regulated in many cell types. Our findings suggest molecular drivers underlying neurodevelopmental phenotypes in classical SGS also drive atypical SGS, persist after birth, and are present in the kidney. Our results indicate SETBP1's role as an epigenetic hub leads to cell-type-specific differences in TF activity, gene targeting, and regulatory rewiring. This research provides a framework for investigating cell-type-specific variant impact on gene expression and regulation.
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Affiliation(s)
- Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
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18
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McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H. Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants. CELL GENOMICS 2023; 3:100404. [PMID: 37868037 PMCID: PMC10589626 DOI: 10.1016/j.xgen.2023.100404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 02/23/2023] [Accepted: 08/21/2023] [Indexed: 10/24/2023]
Abstract
Genome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel reporter assay (MPRA) on 5,173 fine-mapped schizophrenia GWAS variants in primary human neural progenitors and identified 439 variants with allelic regulatory effects (MPRA-positive variants). Transcription factor binding had modest predictive power, while fine-map posterior probability, enhancer overlap, and evolutionary conservation failed to predict MPRA-positive variants. Furthermore, 64% of MPRA-positive variants did not exhibit expressive quantitative trait loci signature, suggesting that MPRA could identify yet unexplored variants with regulatory potentials. To predict the combinatorial effect of MPRA-positive variants on gene regulation, we propose an accessibility-by-contact model that combines MPRA-measured allelic activity with neuronal chromatin architecture.
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Affiliation(s)
- Jessica C. McAfee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sool Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jiseok Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica L. Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kimberly Insigne
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marielle L. Bond
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nanxiang Zhao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P. Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Douglas H. Phanstiel
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - W. Brad Ruzicka
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02141, USA
- Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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19
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Ji C, Tang Y, Zhang Y, Huang X, Li C, Yang Y, Wu Q, Xia X, Cai Q, Qi XR, Zheng JC. Glutaminase 1 deficiency confined in forebrain neurons causes autism spectrum disorder-like behaviors. Cell Rep 2023; 42:112712. [PMID: 37384529 DOI: 10.1016/j.celrep.2023.112712] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 04/21/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
An abnormal glutamate signaling pathway has been proposed in the mechanisms of autism spectrum disorder (ASD). However, less is known about the involvement of alterations of glutaminase 1 (GLS1) in the pathophysiology of ASD. We show that the transcript level of GLS1 is significantly decreased in the postmortem frontal cortex and peripheral blood of ASD subjects. Mice lacking Gls1 in CamKIIα-positive neurons display a series of ASD-like behaviors, synaptic excitatory and inhibitory (E/I) imbalance, higher spine density, and glutamate receptor expression in the prefrontal cortex, as well as a compromised expression pattern of genes involved in synapse pruning and less engulfed synaptic puncta in microglia. A low dose of lipopolysaccharide treatment restores microglial synapse pruning, corrects synaptic neurotransmission, and rescues behavioral deficits in these mice. In summary, these findings provide mechanistic insights into Gls1 loss in ASD symptoms and identify Gls1 as a target for the treatment of ASD.
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Affiliation(s)
- Chenhui Ji
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
| | - Yalin Tang
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
| | - Yanyan Zhang
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
| | - Xiaoyan Huang
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
| | - Congcong Li
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
| | - Yuhong Yang
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
| | - Qihui Wu
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
| | - Xiaohuan Xia
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China; Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China; Shanghai Frontiers Science Center of Nanocatalytic Medicine, Tongji University, Shanghai 200331, China
| | - Qingyuan Cai
- Franklin and Marshall College, 415 Harrisburg Avenue, Lancaster, PA 17603, USA
| | - Xin-Rui Qi
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China.
| | - Jialin C Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China; Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China; Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China; Shanghai Frontiers Science Center of Nanocatalytic Medicine, Tongji University, Shanghai 200331, China.
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20
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Hatchell D, Alshareef M, Vasas T, Guglietta S, Borucki D, Guo C, Mallah K, Eskandari R, Tomlinson S. A role for P-selectin and complement in the pathological sequelae of germinal matrix hemorrhage. J Neuroinflammation 2023; 20:143. [PMID: 37322469 PMCID: PMC10273747 DOI: 10.1186/s12974-023-02828-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Germinal matrix hemorrhage is a devastating disease of pre-term infancy commonly resulting in post-hemorrhagic hydrocephalus, periventricular leukomalacia, and subsequent neurocognitive deficits. We demonstrate vascular expression of the adhesion molecule P-selectin after GMH and investigate a strategy to specifically target complement inhibition to sites of P-selectin expression to mitigate the pathological sequelae of GMH. METHODS We prepared two fusion proteins consisting of different anti-P-selectin single chain antibodies (scFv's) linked to the complement inhibitor Crry. One scFv targeting vehicle (2.12scFv) blocked the binding of P-selectin to its PSGL-1 ligand expressed on leukocytes, whereas the other targeting vehicle (2.3scFv) bound P-selectin without blocking ligand binding. Post-natal C57BL/6 J mice on day 4 (P4) were subjected to collagenase induced-intraventricular hemorrhage and treated with 2.3Psel-Crry, 2.12Psel-Crry, or vehicle. RESULTS Compared to vehicle treatment, 2.3Psel-Crry treatment after induction of GMH resulted in reduced lesion size and mortality, reduced hydrocephalus development, and improved neurological deficit measurements in adolescence. In contrast, 2.12Psel-Crry treatment resulted in worse outcomes compared to vehicle. Improved outcomes with 2.3Psel-Crry were accompanied by decreased P-selectin expression, and decreased complement activation and microgliosis. Microglia from 2.3Psel-Crry treated mice displayed a ramified morphology, similar to naïve mice, whereas microglia in vehicle treated animals displayed a more ameboid morphology that is associated with a more activated status. Consistent with these morphological characteristics, there was increased microglial internalization of complement deposits in vehicle compared to 2.3Psel-Crry treated animals, reminiscent of aberrant C3-dependent microglial phagocytosis that occurs in other (adult) types of brain injury. In addition, following systemic injection, 2.3Psel-Crry specifically targeted to the post-GMH brain. Likely accounting for the unexpected finding that 2.12Psel-Crry worsens outcome following GMH was the finding that this construct interfered with coagulation in this hemorrhagic condition, and specifically with heterotypic platelet-leukocyte aggregation, which express P-selectin and PSGL-1, respectively. CONCLUSIONS GMH induces expression of P-selectin, the targeting of which with a complement inhibitor protects against pathogenic sequelae of GMH. A dual functioning construct with both P-selectin and complement blocking activity interferes with coagulation and worsens outcomes following GMH, but has potential for treatment of conditions that incorporate pathological thrombotic events, such as ischemic stroke.
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Affiliation(s)
- Devin Hatchell
- Department of Neurological Surgery, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Mohammed Alshareef
- Department of Neurological Surgery, Children's Hospital of Colorado, Aurora, CO, USA
| | - Tyler Vasas
- College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Silvia Guglietta
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Davis Borucki
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, USA
| | - Chunfang Guo
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Khalil Mallah
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Ramin Eskandari
- Department of Neurological Surgery, Medical University of South Carolina, Charleston, SC, 29425, USA.
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, 29425, USA.
| | - Stephen Tomlinson
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, 29425, USA.
- Ralph Johnson VA Medical Center, Charleston, SC, USA.
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21
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Guo Q, Wang Y, Wang Q, Qian Y, Jiang Y, Dong X, Chen H, Chen X, Liu X, Yu S, Zhu J, Shan S, Wu B, Zhou W, Wang H. In the developing cerebral cortex: axonogenesis, synapse formation, and synaptic plasticity are regulated by SATB2 target genes. Pediatr Res 2023; 93:1519-1527. [PMID: 36028553 DOI: 10.1038/s41390-022-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/23/2022] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Special AT-rich sequence-binding protein 2 is essential for the development of cerebral cortex and key molecular node for the establishment of proper neural circuitry and function. Mutations in the SATB2 gene lead to SATB2-associated syndrome, which is characterized by abnormal development of skeleton and central nervous systems. METHODS We generated Satb2 knockout mouse model through CRISPR-Cas9 technology and performed RNA-seq and ChIP-seq of embryonic cerebral cortex. We conducted RT-qPCR, western blot, immunofluorescence staining, luciferase reporter assay and behavioral analysis for experimental verification. RESULTS We identified 1363 downstream effector genes of Satb2 and correlation analysis of Satb2-targeted genes and neurological disease genes showed that Satb2 contribute to cognitive and mental disorders from the early developmental stage. We found that Satb2 directly regulate the expression of Ntng1, Cdh13, Kitl, genes important for axon guidance, synaptic formation, neuron migration, and Satb2 directly activates the expression of Mef2c. We also showed that Satb2 heterozygous knockout mice showed impaired spatial learning and memory. CONCLUSIONS Taken together, our study supportsroles of Satb2 in the regulation of axonogenesis and synaptic formation at the early developmental stage and provides new insights into the complicated regulatory mechanism of Satb2 and new evidence to elucidate the pathogen of SATB2-associated syndrome. IMPACT 1363 downstream effector genes of Satb2 were classified into 5 clusters with different temporal expression patterns. We identified Plxnd1, Ntng1, Efnb2, Ephb1, Plxna2, Epha3, Plxna4, Unc5c, and Flrt2 as axon guidance molecules to regulate axonogenesis. 168 targeted genes of Satb2 were found to regulate synaptic formation in the early development of the cerebral cortex. Transcription factor Mef2c is positively regulated by Satb2, and 28 Mef2c-targeted genes can be directly regulated by Satb2. In the Morris water maze test, Satb2+/- mice showed impaired spatial learning and memory, further strengthening that Satb2 can regulate synaptic functions.
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Affiliation(s)
- Qiufang Guo
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
- Berry Genomics Co, 102206, Beijing, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Qing Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yinmo Jiang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiang Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiuyun Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Sha Yu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Jitao Zhu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Shifang Shan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Key Laboratory of Neonatal Diseases, Ministry of Health, 201102, Shanghai, China.
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
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22
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Medina E, Peterson S, Ford K, Singletary K, Peixoto L. Critical periods and Autism Spectrum Disorders, a role for sleep. Neurobiol Sleep Circadian Rhythms 2023; 14:100088. [PMID: 36632570 PMCID: PMC9826922 DOI: 10.1016/j.nbscr.2022.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Brain development relies on both experience and genetically defined programs. Time windows where certain brain circuits are particularly receptive to external stimuli, resulting in heightened plasticity, are referred to as "critical periods". Sleep is thought to be essential for normal brain development. Importantly, studies have shown that sleep enhances critical period plasticity and promotes experience-dependent synaptic pruning in the developing mammalian brain. Therefore, normal plasticity during critical periods depends on sleep. Problems falling and staying asleep occur at a higher rate in Autism Spectrum Disorder (ASD) relative to typical development. In this review, we explore the potential link between sleep, critical period plasticity, and ASD. First, we review the importance of critical period plasticity in typical development and the role of sleep in this process. Next, we summarize the evidence linking ASD with deficits in synaptic plasticity in rodent models of high-confidence ASD gene candidates. We then show that the high-confidence rodent models of ASD that show sleep deficits also display plasticity deficits. Given how important sleep is for critical period plasticity, it is essential to understand the connections between synaptic plasticity, sleep, and brain development in ASD. However, studies investigating sleep or plasticity during critical periods in ASD mouse models are lacking. Therefore, we highlight an urgent need to consider developmental trajectory in studies of sleep and plasticity in neurodevelopmental disorders.
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Affiliation(s)
- Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Sarah Peterson
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Kristan Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
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23
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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Qian Z, Qin J, Lai Y, Zhang C, Zhang X. Large-Scale Integration of Single-Cell RNA-Seq Data Reveals Astrocyte Diversity and Transcriptomic Modules across Six Central Nervous System Disorders. Biomolecules 2023; 13:692. [PMID: 37189441 PMCID: PMC10135484 DOI: 10.3390/biom13040692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
The dysfunction of astrocytes in response to environmental factors contributes to many neurological diseases by impacting neuroinflammation responses, glutamate and ion homeostasis, and cholesterol and sphingolipid metabolism, which calls for comprehensive and high-resolution analysis. However, single-cell transcriptome analyses of astrocytes have been hampered by the sparseness of human brain specimens. Here, we demonstrate how large-scale integration of multi-omics data, including single-cell and spatial transcriptomic and proteomic data, overcomes these limitations. We created a single-cell transcriptomic dataset of human brains by integration, consensus annotation, and analyzing 302 publicly available single-cell RNA-sequencing (scRNA-seq) datasets, highlighting the power to resolve previously unidentifiable astrocyte subpopulations. The resulting dataset includes nearly one million cells that span a wide variety of diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), multiple sclerosis (MS), epilepsy (Epi), and chronic traumatic encephalopathy (CTE). We profiled the astrocytes at three levels, subtype compositions, regulatory modules, and cell-cell communications, and comprehensively depicted the heterogeneity of pathological astrocytes. We constructed seven transcriptomic modules that are involved in the onset and progress of disease development, such as the M2 ECM and M4 stress modules. We validated that the M2 ECM module could furnish potential markers for AD early diagnosis at both the transcriptome and protein levels. In order to accomplish a high-resolution, local identification of astrocyte subtypes, we also carried out a spatial transcriptome analysis of mouse brains using the integrated dataset as a reference. We found that astrocyte subtypes are regionally heterogeneous. We identified dynamic cell-cell interactions in different disorders and found that astrocytes participate in key signaling pathways, such as NRG3-ERBB4, in epilepsy. Our work supports the utility of large-scale integration of single-cell transcriptomic data, which offers new insights into underlying multiple CNS disease mechanisms where astrocytes are involved.
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Affiliation(s)
- Zhenwei Qian
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Jinglin Qin
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Yiwen Lai
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Chen Zhang
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Beijing 102206, China
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing 210000, China
| | - Xiannian Zhang
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
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25
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Hatchell D, Alshareef M, Vasas T, Guglietta S, Borucki D, Guo C, Mallah K, Eskandari R, Tomlinson S. A Role for P-selectin and Complement in the Pathological Sequelae of Germinal Matrix Hemorrhage. RESEARCH SQUARE 2023:rs.3.rs-2617965. [PMID: 36909595 PMCID: PMC10002788 DOI: 10.21203/rs.3.rs-2617965/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Background Germinal Matrix Hemorrhage is a devastating disease of pre-term infancy commonly resulting in post-hemorrhagic hydrocephalus, periventricular leukomalacia, and subsequent neurocognitive deficits. We demonstrate vascular expression of the adhesion molecule P-selectin after GMH and investigate a strategy to specifically target complement inhibition to sites of P-selectin expression to mitigate the pathological sequelae of GMH. Methods We prepared two fusion proteins consisting of different anti-P-selectin single chain antibodies (scFv's) linked to the complement inhibitor Crry. One scFv targeting vehicle (2.12scFv) blocked the binding of P-selectin to its PSGL-1 ligand expressed on leukocytes, whereas the other targeting vehicle (2.3scFv) bound P-selectin without blocking ligand binding. Post-natal mice on day 4 (P4) were subjected to collagenase induced-intraventricular hemorrhage and treated with 2.3Psel-Crry, 2.12Psel-Crry, or vehicle. Results Compared to vehicle treatment, 2.3Psel-Crry treatment after induction of GMH resulted in reduced lesion size and mortality, reduced hydrocephalus development, and improved neurological deficit measurements in adolescence. In contrast, 2.12Psel-Crry treatment resulted in worse outcomes compared to vehicle. Improved outcomes with 2.3Psel-Crry were accompanied by decreased P-selectin expression, and decreased complement activation and microgliosis. Microglia from 2.3Psel-Crry treated mice displayed a ramified morphology, similar to naïve mice, whereas microglia in vehicle treated animals displayed a more ameboid morphology that is associated with a more activated status. Consistent with these morphological characteristics, there was increased microglial internalization of complement deposits in vehicle compared to 2.3Psel-Crry treated animals, reminiscent of aberrant C3-dependent microglial phagocytosis that occurs in other (adult) types of brain injury. Also, following systemic injection, 2.3Psel-Crry specifically targeted to the post-GMH brain. Likely accounting for the unexpected finding that 2.12Psel-Crry worsens outcome following GMH was the finding that this construct interfered with coagulation in this hemorrhagic condition, and specifically with heterotypic platelet-leukocyte aggregation, which express P-selectin and PSGL-1, respectively. Conclusion GMH induces expression of P-selectin, the targeting of which with a complement inhibitor protects against pathogenic sequelae of GMH. A dual functioning construct with both P-selectin and complement blocking activity interferes with coagulation and worsens outcomes following GMH, but has potential for treatment of conditions that incorporate pathological thrombotic events, such as ischemic stroke.
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The Role of MEF2 Transcription Factor Family in Neuronal Survival and Degeneration. Int J Mol Sci 2023; 24:ijms24043120. [PMID: 36834528 PMCID: PMC9963821 DOI: 10.3390/ijms24043120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
The family of myocyte enhancer factor 2 (MEF2) transcription factors comprises four highly conserved members that play an important role in the nervous system. They appear in precisely defined time frames in the developing brain to turn on and turn off genes affecting growth, pruning and survival of neurons. MEF2s are known to dictate neuronal development, synaptic plasticity and restrict the number of synapses in the hippocampus, thus affecting learning and memory formation. In primary neurons, negative regulation of MEF2 activity by external stimuli or stress conditions is known to induce apoptosis, albeit the pro or antiapoptotic action of MEF2 depends on the neuronal maturation stage. By contrast, enhancement of MEF2 transcriptional activity protects neurons from apoptotic death both in vitro and in preclinical models of neurodegenerative diseases. A growing body of evidence places this transcription factor in the center of many neuropathologies associated with age-dependent neuronal dysfunctions or gradual but irreversible neuron loss. In this work, we discuss how the altered function of MEF2s during development and in adulthood affecting neuronal survival may be linked to neuropsychiatric disorders.
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27
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Rodríguez-Giraldo M, González-Reyes RE, Ramírez-Guerrero S, Bonilla-Trilleras CE, Guardo-Maya S, Nava-Mesa MO. Astrocytes as a Therapeutic Target in Alzheimer's Disease-Comprehensive Review and Recent Developments. Int J Mol Sci 2022; 23:13630. [PMID: 36362415 PMCID: PMC9654484 DOI: 10.3390/ijms232113630] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 09/20/2023] Open
Abstract
Alzheimer's disease (AD) is a frequent and disabling neurodegenerative disorder, in which astrocytes participate in several pathophysiological processes including neuroinflammation, excitotoxicity, oxidative stress and lipid metabolism (along with a critical role in apolipoprotein E function). Current evidence shows that astrocytes have both neuroprotective and neurotoxic effects depending on the disease stage and microenvironmental factors. Furthermore, astrocytes appear to be affected by the presence of amyloid-beta (Aβ), with alterations in calcium levels, gliotransmission and proinflammatory activity via RAGE-NF-κB pathway. In addition, astrocytes play an important role in the metabolism of tau and clearance of Aβ through the glymphatic system. In this review, we will discuss novel pharmacological and non-pharmacological treatments focused on astrocytes as therapeutic targets for AD. These interventions include effects on anti-inflammatory/antioxidant systems, glutamate activity, lipid metabolism, neurovascular coupling and glymphatic system, calcium dysregulation, and in the release of peptides which affects glial and neuronal function. According to the AD stage, these therapies may be of benefit in either preventing or delaying the progression of the disease.
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Affiliation(s)
| | | | | | | | | | - Mauricio O. Nava-Mesa
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencias Neurovitae-UR, Instituto de Medicina Traslacional (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá 111711, Colombia
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Mohajeri K, Yadav R, D'haene E, Boone PM, Erdin S, Gao D, Moyses-Oliveira M, Bhavsar R, Currall BB, O'Keefe K, Burt ND, Lowther C, Lucente D, Salani M, Larson M, Redin C, Dudchenko O, Aiden EL, Menten B, Tai DJC, Gusella JF, Vergult S, Talkowski ME. Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models. Am J Hum Genet 2022; 109:2049-2067. [PMID: 36283406 PMCID: PMC9674968 DOI: 10.1016/j.ajhg.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 01/26/2023] Open
Abstract
Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.
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Affiliation(s)
- Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dadi Gao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mariana Moyses-Oliveira
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas D Burt
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Monica Salani
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathew Larson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Claire Redin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA; UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Derek J C Tai
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
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McChesney N, Barth JL, Rumschlag JA, Tan J, Harrington AJ, Noble KV, McClaskey CM, Elvis P, Vaena SG, Romeo MJ, Harris KC, Cowan CW, Lang H. Peripheral Auditory Nerve Impairment in a Mouse Model of Syndromic Autism. J Neurosci 2022; 42:8002-8018. [PMID: 36180228 PMCID: PMC9617620 DOI: 10.1523/jneurosci.0253-22.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/27/2022] [Accepted: 08/13/2022] [Indexed: 11/21/2022] Open
Abstract
Dysfunction of the peripheral auditory nerve (AN) contributes to dynamic changes throughout the central auditory system, resulting in abnormal auditory processing, including hypersensitivity. Altered sound sensitivity is frequently observed in autism spectrum disorder (ASD), suggesting that AN deficits and changes in auditory information processing may contribute to ASD-associated symptoms, including social communication deficits and hyperacusis. The MEF2C transcription factor is associated with risk for several neurodevelopmental disorders, and mutations or deletions of MEF2C produce a haploinsufficiency syndrome characterized by ASD, language, and cognitive deficits. A mouse model of this syndromic ASD (Mef2c-Het) recapitulates many of the MEF2C haploinsufficiency syndrome-linked behaviors, including communication deficits. We show here that Mef2c-Het mice of both sexes exhibit functional impairment of the peripheral AN and a modest reduction in hearing sensitivity. We find that MEF2C is expressed during development in multiple AN and cochlear cell types; and in Mef2c-Het mice, we observe multiple cellular and molecular alterations associated with the AN, including abnormal myelination, neuronal degeneration, neuronal mitochondria dysfunction, and increased macrophage activation and cochlear inflammation. These results reveal the importance of MEF2C function in inner ear development and function and the engagement of immune cells and other non-neuronal cells, which suggests that microglia/macrophages and other non-neuronal cells might contribute, directly or indirectly, to AN dysfunction and ASD-related phenotypes. Finally, our study establishes a comprehensive approach for characterizing AN function at the physiological, cellular, and molecular levels in mice, which can be applied to animal models with a wide range of human auditory processing impairments.SIGNIFICANCE STATEMENT This is the first report of peripheral auditory nerve (AN) impairment in a mouse model of human MEF2C haploinsufficiency syndrome that has well-characterized ASD-related behaviors, including communication deficits, hyperactivity, repetitive behavior, and social deficits. We identify multiple underlying cellular, subcellular, and molecular abnormalities that may contribute to peripheral AN impairment. Our findings also highlight the important roles of immune cells (e.g., cochlear macrophages) and other non-neuronal elements (e.g., glial cells and cells in the stria vascularis) in auditory impairment in ASD. The methodological significance of the study is the establishment of a comprehensive approach for evaluating peripheral AN function and impact of peripheral AN deficits with minimal hearing loss.
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Affiliation(s)
- Nathan McChesney
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Jeremy L Barth
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Jeffrey A Rumschlag
- Department of Otolaryngology & Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Junying Tan
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Adam J Harrington
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Kenyaria V Noble
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Carolyn M McClaskey
- Department of Otolaryngology & Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Phillip Elvis
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Silvia G Vaena
- Hollings Cancer Institute, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Martin J Romeo
- Hollings Cancer Institute, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Kelly C Harris
- Department of Otolaryngology & Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Christopher W Cowan
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Hainan Lang
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina 29425
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30
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Lynch AW, Theodoris CV, Long HW, Brown M, Liu XS, Meyer CA. MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells. Nat Methods 2022; 19:1097-1108. [PMID: 36068320 PMCID: PMC9517733 DOI: 10.1038/s41592-022-01595-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/26/2022] [Indexed: 02/06/2023]
Abstract
Rigorously comparing gene expression and chromatin accessibility in the same single cells could illuminate the logic of how coupling or decoupling of these mechanisms regulates fate commitment. Here we present MIRA, probabilistic multimodal models for integrated regulatory analysis, a comprehensive methodology that systematically contrasts transcription and accessibility to infer the regulatory circuitry driving cells along cell state trajectories. MIRA leverages topic modeling of cell states and regulatory potential modeling of individual gene loci. MIRA thereby represents cell states in an efficient and interpretable latent space, infers high-fidelity cell state trees, determines key regulators of fate decisions at branch points and exposes the variable influence of local accessibility on transcription at distinct loci. Applied to epidermal differentiation and embryonic brain development from two different multimodal platforms, MIRA revealed that early developmental genes were tightly regulated by local chromatin landscape whereas terminal fate genes were titrated without requiring extensive chromatin remodeling.
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Affiliation(s)
- Allen W Lynch
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School Genetics Training Program, Boston, MA, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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31
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Baranova A, Wang J, Cao H, Chen JH, Chen J, Chen M, Ni S, Xu X, Ke X, Xie S, Sun J, Zhang F. Shared genetics between autism spectrum disorder and attention-deficit/hyperactivity disorder and their association with extraversion. Psychiatry Res 2022; 314:114679. [PMID: 35717853 DOI: 10.1016/j.psychres.2022.114679] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/31/2022] [Accepted: 06/10/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND Deciphering the genetic relationships between autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) may uncover underlining shared pathophysiology as well as inform treatment. METHODS The summary results of genome-wide association studies on ADHD, ASD, and extraversion were utilized for the analyzes. Genetic correlations between ADHD, ASD, and extraversion were tested using linkage disequilibrium score regression. Causal relationships between ADHD, ASD, and extraversion were investigated using Mendelian randomization (MR) analysis. Novel pleiotropic genomic loci shared by ADHD and ASD were identified using a cross-trait meta-analysis. RESULTS Extraversion was positively correlated with ADHD (rg = 0.205) and negatively correlated with ASD (rg = -0.193). The MR analysis showed that ADHD confers a causal effect on ASD (OR: 1.35, 95% confidence interval (CI):1.20-1.52) and vice versa (1.46, 1.38-1.55). Extraversion exerts a causal effect on ADHD only (1.19, 1.05-1.33). The cross-trait meta-analysis identified three novel pleiotropic genomic loci for ADHD and ASD, involving two pleiotropic genes, LINC00461 and KIZ. CONCLUSIONS Our study provides new insights into the shared genetics of ADHD and ASD and their connections with extraversion.
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Affiliation(s)
- Ancha Baranova
- School of Systems Biology, George Mason University, Manassas 20110, USA; Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Jun Wang
- Department of Psychiatry, Wuxi Mental Health Center of Nanjing Medical University, Wuxi 214151, China
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Manassas 20110, USA
| | - Jiang-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Jiu Chen
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, 264 Guangzhou Road, Nanjing 210029, China
| | - Miao Chen
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Sulin Ni
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xijia Xu
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xiaoyan Ke
- Child Mental Health Research Center, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shiping Xie
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jing Sun
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Fuquan Zhang
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, 264 Guangzhou Road, Nanjing 210029, China; Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China.
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Funahashi Y, Yoshino Y, Iga JI, Ueno SI. Impact of clozapine on the expression of miR-675-3p in plasma exosomes derived from patients with schizophrenia. World J Biol Psychiatry 2022; 24:303-313. [PMID: 35904423 DOI: 10.1080/15622975.2022.2104924] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
OBJECTIVES Recently, the expression changes of microRNAs (miRNAs) in the serum exosomes (EXO) of schizophrenia (SCZ) have been reported. The aim of this study was to investigate the global expression changes of miRNA derived from the plasma EXO of patients with treatment-resistant schizophrenia (TRS) and the effects of clozapine on miRNA expression. METHODS Global miRNA expression changes in plasma EXO between TRS and controls were studied using microarray analysis. Then, miRNA expressions among TRS, non-TRS, and controls were confirmed with quantitative qPCR experiments. We also studied changes in EXO miRNA expression with in-vitro SH-SY5Y cells. RESULTS A microarray for miRNA expression analysis (nine controls vs. nine patients with TRS) revealed 13 up- and 18 downregulated miRNAs that were relevant to neuronal and brain development based on gene ontology analysis. Of those, upregulated miR-675-3p expression was successfully validated in the same cohort by qPCR experiments. Conversely, miR-675-3p expression levels were significantly decreased in the non-TRS cohort (50 controls vs. 50 patients without TRS without clozapine treatment). CONCLUSIONS We identified global miRNA changes in plasma EXO derived from patients with SCZ that were relevant to neuronal functions, among which, hsa-miR-675-3p expression was upregulated by clozapine treatment.
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Affiliation(s)
- Yu Funahashi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Japan
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Manyukhina VO, Prokofyev AO, Galuta IA, Goiaeva DE, Obukhova TS, Schneiderman JF, Altukhov DI, Stroganova TA, Orekhova EV. Globally elevated excitation-inhibition ratio in children with autism spectrum disorder and below-average intelligence. Mol Autism 2022; 13:20. [PMID: 35550191 PMCID: PMC9102291 DOI: 10.1186/s13229-022-00498-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/25/2022] [Indexed: 12/04/2022] Open
Abstract
Background Altered neuronal excitation–inhibition (E–I) balance is strongly implicated in ASD. However, it is not known whether the direction and degree of changes in the E–I ratio in individuals with ASD correlates with intellectual disability often associated with this developmental disorder. The spectral slope of the aperiodic 1/f activity reflects the E–I balance at the scale of large neuronal populations and may uncover its putative alternations in individuals with ASD with and without intellectual disability. Methods Herein, we used magnetoencephalography (MEG) to test whether the 1/f slope would differentiate ASD children with average and below–average (< 85) IQ. MEG was recorded at rest with eyes open/closed in 49 boys with ASD aged 6–15 years with IQ ranging from 54 to 128, and in 49 age-matched typically developing (TD) boys. The cortical source activity was estimated using the beamformer approach and individual brain models. We then extracted the 1/f slope by fitting a linear function to the log–log-scale power spectra in the high-frequency range. Results The global 1/f slope averaged over all cortical sources demonstrated high rank-order stability between the two conditions. Consistent with previous research, it was steeper in the eyes-closed than in the eyes-open condition and flattened with age. Regardless of condition, children with ASD and below-average IQ had flatter slopes than either TD or ASD children with average or above-average IQ. These group differences could not be explained by differences in signal-to-noise ratio or periodic (alpha and beta) activity. Limitations Further research is needed to find out whether the observed changes in E–I ratios are characteristic of children with below-average IQ of other diagnostic groups. Conclusions The atypically flattened spectral slope of aperiodic activity in children with ASD and below-average IQ suggests a shift of the global E–I balance toward hyper-excitation. The spectral slope can provide an accessible noninvasive biomarker of the E–I ratio for making objective judgments about treatment effectiveness in people with ASD and comorbid intellectual disability. Supplementary Information The online version contains supplementary material available at 10.1186/s13229-022-00498-2.
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Affiliation(s)
- Viktoriya O Manyukhina
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation.,Department of Psychology, National Research University Higher School of Economics, Moscow, Russian Federation
| | - Andrey O Prokofyev
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Ilia A Galuta
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Dzerassa E Goiaeva
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Tatiana S Obukhova
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Justin F Schneiderman
- MedTech West and the Institute of Neuroscience and Physiology, Sahlgrenska Academy, The University of Gothenburg, Gothenburg, Sweden
| | - Dmitrii I Altukhov
- Department of Psychology, National Research University Higher School of Economics, Moscow, Russian Federation
| | - Tatiana A Stroganova
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Elena V Orekhova
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation.
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Fan CC, Loughnan R, Makowski C, Pecheva D, Chen CH, Hagler DJ, Thompson WK, Parker N, van der Meer D, Frei O, Andreassen OA, Dale AM. Multivariate genome-wide association study on tissue-sensitive diffusion metrics highlights pathways that shape the human brain. Nat Commun 2022; 13:2423. [PMID: 35505052 PMCID: PMC9065144 DOI: 10.1038/s41467-022-30110-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/12/2022] [Indexed: 11/12/2022] Open
Abstract
The molecular determinants of tissue composition of the human brain remain largely unknown. Recent genome-wide association studies (GWAS) on this topic have had limited success due to methodological constraints. Here, we apply advanced whole-brain analyses on multi-shell diffusion imaging data and multivariate GWAS to two large scale imaging genetic datasets (UK Biobank and the Adolescent Brain Cognitive Development study) to identify and validate genetic association signals. We discover 503 unique genetic loci that have impact on multiple regions of human brain. Among them, more than 79% are validated in either of two large-scale independent imaging datasets. Key molecular pathways involved in axonal growth, astrocyte-mediated neuroinflammation, and synaptogenesis during development are found to significantly impact the measured variations in tissue-specific imaging features. Our results shed new light on the biological determinants of brain tissue composition and their potential overlap with the genetic basis of neuropsychiatric disorders.
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Affiliation(s)
- Chun Chieh Fan
- Population Neuroscience and Genetics Lab, University of California, San Diego, La Jolla, CA, USA. .,Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA. .,Department of Radiology, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Robert Loughnan
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Carolina Makowski
- Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Diliana Pecheva
- Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chi-Hua Chen
- Department of Radiology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Donald J Hagler
- Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wesley K Thompson
- Population Neuroscience and Genetics Lab, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nadine Parker
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dennis van der Meer
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Oleksandr Frei
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anders M Dale
- Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, USA
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35
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Noble AJ, Pearson JF, Noble AD, Boden JM, Horwood LJ, Kennedy MA, Osborne AJ. DNA methylation analysis using bisulphite-based amplicon sequencing of individuals exposed to maternal tobacco use during pregnancy, and offspring conduct problems in childhood and adolescence. Reprod Fertil Dev 2022; 34:540-548. [PMID: 35412968 DOI: 10.1071/rd21108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
Maternal tobacco smoking during pregnancy is a large driver of health inequalities and a higher prevalence of conduct problem (CP) has been observed in exposed offspring. Further, maternal tobacco use during pregnancy can also alter offspring DNA methylation. However, currently, limited molecular evidence has been found to support this observation. Thus we aim to examine the association between maternal tobacco use in pregnancy and offspring CP, to determine whether offspring CP is mediated by tobacco exposure-induced DNA methylation differences. Understanding the etiology of the association between maternal tobacco use and offspring CP will be crucial in the early identification and treatment of CP in children and adolescents. Here, a sub group of N =96 individuals was sourced from the Christchurch Health and Development Study, a longitudinal birth cohort studied for over 40 years in New Zealand. Whole blood samples underwent bisulphite-based amplicon sequencing at 10 loci known to play a role in neurodevelopment, or which had associations with CP phenotypes. We identified significant (P CYP1A1 , ASH2L and MEF2C in individuals with CP who were exposed to tobacco in utero . We conclude that environmentally-induced DNA methylation differences could play a role in the observed link between maternal tobacco use during pregnancy and childhood/adolescent CP. However, larger sample sizes are needed to produce an adequate amount of power to investigate this interaction further.
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Affiliation(s)
- Alexandra J Noble
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology and Biomedical Sciences, University of Otago, Christchurch, New Zealand
| | | | - Joseph M Boden
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - L John Horwood
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Sciences, University of Otago, Christchurch, New Zealand
| | - Amy J Osborne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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36
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Fu X, Yao T, Chen X, Li H, Wu J. MEF2C gene variations are associated with ADHD in the Chinese Han population: a case-control study. J Neural Transm (Vienna) 2022; 129:431-439. [PMID: 35357565 DOI: 10.1007/s00702-022-02490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/12/2022] [Indexed: 11/30/2022]
Abstract
Myocyte enhancer factor 2C (MEF2C) is associated with hyperactivity and might be a novel risk gene for susceptibility to attention deficit hyperactivity disorder (ADHD). Therefore, this study aimed to explore the association between MEF2C genetic variants and ADHD in the Chinese Han population. A total of 215 patients with ADHD and 233 controls were recruited for this study. The Swanson, Nolan, and Pelham version IV questionnaire was used to evaluate the clinical features of ADHD. In silico analysis was used to annotate the biological functions of the promising single nucleotide polymorphisms. Our findings indicated that MEF2C rs587490 was significantly associated with ADHD in the multiplicative model (OR = 0.640, p = 0.002). Participants with the rs587490 TT allele exhibited less hyperactivity/impulsivity than those with the rs587490 CC allele. Furthermore, the expression quantitative trait loci analysis suggested that rs587490 could regulate the gene expression of MEF2C in the hippocampus, putamen, thalamus, and frontal white matter. Our study concluded that the MEF2C rs587490 T allele is significantly associated with a reduced risk of ADHD in the Chinese Han population, which provides new insight into the genetic etiology of ADHD.
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Affiliation(s)
- Xihang Fu
- Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Ting Yao
- Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Xinzhen Chen
- Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Huiru Li
- Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Jing Wu
- Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China.
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37
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Zhang Z, Zhao Y. Progress on the roles of MEF2C in neuropsychiatric diseases. Mol Brain 2022; 15:8. [PMID: 34991657 PMCID: PMC8740500 DOI: 10.1186/s13041-021-00892-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/23/2021] [Indexed: 12/15/2022] Open
Abstract
Myocyte Enhancer Factor 2 C (MEF2C), one of the transcription factors of the MADS-BOX family, is involved in embryonic brain development, neuronal formation and differentiation, as well as in the growth and pruning of axons and dendrites. MEF2C is also involved in the development of various neuropsychiatric disorders, such as autism spectrum disorders (ASD), epilepsy, schizophrenia and Alzheimer’s disease (AD). Here, we review the relationship between MEF2C and neuropsychiatric disorders, and provide further insights into the mechanism of these diseases.
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Affiliation(s)
- Zhikun Zhang
- National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.,Department of Mental Health, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, Guangxi, China
| | - Yongxiang Zhao
- National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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38
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Ren J, Zhang S, Wang X, Deng Y, Zhao Y, Xiao Y, Liu J, Chu L, Qi X. MEF2C ameliorates learning, memory, and molecular pathological changes in Alzheimer’s disease in vivo and in vitro. Acta Biochim Biophys Sin (Shanghai) 2021; 54:77-90. [PMID: 35130621 PMCID: PMC9909301 DOI: 10.3724/abbs.2021012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Myocyte enhancer factor 2C (MEF2C) is highly expressed in the nervous system, and regulates neuro-development, synaptic plasticity, and inflammation. However, its mechanism in Alzheimer's disease (AD) is underestimated. In this study, the role and mechanism of MEF2C were investigated in the brain tissue specimens from patients with AD, APPswe/PSEN1dE9 double transgenic (APP/PS1_DT) mice, and SH-SY5Y cells treated with β-amyloid peptide (Aβ). The results indicated that the expression of MEF2C is significantly reduced, and the expression of MEF2C/Aβ in different parts of brain is negatively correlated in patients with AD. Knockdown of MEF2C promotes cell apoptosis and the level of β-amyloid precursor protein cleaving enzyme 1 (BACE) but reduces BACE2 expression. In addition, knockdown of enhances the generation and aggregation of Aβ in the cortex of APP/PS1_DT mice, reduces the expression of synaptic proteins, exacerbates the ability of learning and memory of APP/PS1_DT mice, damages the structure of mitochondria, increases the oxidative stress (OS) level, and inhibits the expression levels of members of the Nrf2-ARE signal pathway. In summary, inhibition of MEF2C exacerbates the toxic effect of Aβ and , damages synaptic plasticity, reduces the ability of learning and memory of APP/PS1 mice, and increases the level of OS via the Nrf2-ARE signal pathway.
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Affiliation(s)
- Jiamou Ren
- Key Laboratory of Endemic and Ethnic DiseasesMinistry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyang550004China,Department of Laboratory Medicinethe 4th People′s Hospital of GuiyangGuiyang550004China
| | - Shuli Zhang
- Chinese People′s Liberation ArmySecret Service Center Sanatorium of XiamenXiamen361000China
| | - Xiaoling Wang
- Key Laboratory of Endemic and Ethnic DiseasesMinistry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyang550004China
| | - Yuxin Deng
- Key Laboratory of Endemic and Ethnic DiseasesMinistry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyang550004China
| | - Yi Zhao
- Key Laboratory of Endemic and Ethnic DiseasesMinistry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyang550004China
| | - Yan Xiao
- Key Laboratory of Endemic and Ethnic DiseasesMinistry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyang550004China
| | - Jian Liu
- Department of NeurosurgeryAffiliated Hospital of Guizhou Medical UniversityGuiyang550004China
| | - Liangzhao Chu
- Department of NeurosurgeryAffiliated Hospital of Guizhou Medical UniversityGuiyang550004China,Correspondence address. Tel: +86-851-86752814; E-mail: (X.Q.) / E-mail: (L.C.)@qq.com
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic DiseasesMinistry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyang550004China,Translational Medicine Research CenterGuizhou Medical UniversityGuiyang550004China,Correspondence address. Tel: +86-851-86752814; E-mail: (X.Q.) / E-mail: (L.C.)@qq.com
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39
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Bertoni A, Schaller F, Tyzio R, Gaillard S, Santini F, Xolin M, Diabira D, Vaidyanathan R, Matarazzo V, Medina I, Hammock E, Zhang J, Chini B, Gaiarsa JL, Muscatelli F. Oxytocin administration in neonates shapes hippocampal circuitry and restores social behavior in a mouse model of autism. Mol Psychiatry 2021; 26:7582-7595. [PMID: 34290367 PMCID: PMC8872977 DOI: 10.1038/s41380-021-01227-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Oxytocin is an important regulator of the social brain. In some animal models of autism, notably in Magel2tm1.1Mus-deficient mice, peripheral administration of oxytocin in infancy improves social behaviors until adulthood. However, neither the mechanisms responsible for social deficits nor the mechanisms by which such oxytocin administration has long-term effects are known. Here, we aimed to clarify these oxytocin-dependent mechanisms, focusing on social memory performance. Using in situ hybridization (RNAscope), we have established that Magel2 and oxytocin receptor are co-expressed in the dentate gyrus and CA2/CA3 hippocampal regions involved in the circuitry underlying social memory. Then, we have shown that Magel2tm1.1Mus-deficient mice, evaluated in a three-chamber test, present a deficit in social memory. Next, in hippocampus, we conducted neuroanatomical and functional studies using immunostaining, oxytocin-binding experiments, ex vivo electrophysiological recordings, calcium imaging and biochemical studies. We demonstrated: an increase of the GABAergic activity of CA3-pyramidal cells associated with an increase in the quantity of oxytocin receptors and of somatostatin interneurons in both DG and CA2/CA3 regions. We also revealed a delay in the GABAergic development sequence in Magel2tm1.1Mus-deficient pups, linked to phosphorylation modifications of KCC2. Above all, we demonstrated the positive effects of subcutaneous administration of oxytocin in the mutant neonates, restoring hippocampal alterations and social memory at adulthood. Although clinical trials are debated, this study highlights the mechanisms by which peripheral oxytocin administration in neonates impacts the brain and demonstrates the therapeutic value of oxytocin to treat infants with autism spectrum disorders.
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Affiliation(s)
- Alessandra Bertoni
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | - Fabienne Schaller
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | - Roman Tyzio
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | | | - Francesca Santini
- Institute of Neuroscience, National Research Council (CNR), Vedano al Lambro, Italy. Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Marion Xolin
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | - Diabé Diabira
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | | | - Valery Matarazzo
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | - Igor Medina
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | | | - Jinwei Zhang
- Institute of Biomedical and Clinical Sciences, College of Medicine and Health, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - Bice Chini
- Institute of Neuroscience, National Research Council (CNR), Vedano al Lambro, Italy. NeuroMI Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Jean-Luc Gaiarsa
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France
| | - Françoise Muscatelli
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1249, Institut de Neurobiologie de la Méditerranée (INMED), Institut Marseille Maladies Rares (MarMaRa), Aix-Marseille Université, Marseille, France.
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Barker SJ, Raju RM, Milman NEP, Wang J, Davila-Velderrain J, Gunter-Rahman F, Parro CC, Bozzelli PL, Abdurrob F, Abdelaal K, Bennett DA, Kellis M, Tsai LH. MEF2 is a key regulator of cognitive potential and confers resilience to neurodegeneration. Sci Transl Med 2021; 13:eabd7695. [PMID: 34731014 PMCID: PMC9258338 DOI: 10.1126/scitranslmed.abd7695] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Scarlett J Barker
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ravikiran M Raju
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Noah E P Milman
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jun Wang
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jose Davila-Velderrain
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fatima Gunter-Rahman
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cameron C Parro
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - P Lorenzo Bozzelli
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fatema Abdurrob
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karim Abdelaal
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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41
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A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 DOI: 10.1101/2020.10.19.343129v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 05/26/2023]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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Callaway EM, Dong HW, Ecker JR, Hawrylycz MJ, Huang ZJ, Lein ES, Ngai J, Osten P, Ren B, Tolias AS, White O, Zeng H, Zhuang X, Ascoli GA, Behrens MM, Chun J, Feng G, Gee JC, Ghosh SS, Halchenko YO, Hertzano R, Lim BK, Martone ME, Ng L, Pachter L, Ropelewski AJ, Tickle TL, Yang XW, Zhang K, Bakken TE, Berens P, Daigle TL, Harris JA, Jorstad NL, Kalmbach BE, Kobak D, Li YE, Liu H, Matho KS, Mukamel EA, Naeemi M, Scala F, Tan P, Ting JT, Xie F, Zhang M, Zhang Z, Zhou J, Zingg B, Armand E, Yao Z, Bertagnolli D, Casper T, Crichton K, Dee N, Diep D, Ding SL, Dong W, Dougherty EL, Fong O, Goldman M, Goldy J, Hodge RD, Hu L, Keene CD, Krienen FM, Kroll M, Lake BB, Lathia K, Linnarsson S, Liu CS, Macosko EZ, McCarroll SA, McMillen D, Nadaf NM, Nguyen TN, Palmer CR, Pham T, Plongthongkum N, Reed NM, Regev A, Rimorin C, Romanow WJ, Savoia S, Siletti K, Smith K, Sulc J, Tasic B, Tieu M, Torkelson A, Tung H, van Velthoven CTJ, Vanderburg CR, Yanny AM, Fang R, Hou X, Lucero JD, Osteen JK, Pinto-Duarte A, Poirion O, Preissl S, Wang X, Aldridge AI, Bartlett A, Boggeman L, O’Connor C, Castanon RG, Chen H, Fitzpatrick C, Luo C, Nery JR, Nunn M, Rivkin AC, Tian W, Dominguez B, Ito-Cole T, Jacobs M, Jin X, Lee CT, Lee KF, Miyazaki PA, Pang Y, Rashid M, Smith JB, Vu M, Williams E, Biancalani T, Booeshaghi AS, Crow M, Dudoit S, Fischer S, Gillis J, Hu Q, Kharchenko PV, Niu SY, Ntranos V, Purdom E, Risso D, de Bézieux HR, Somasundaram S, Street K, Svensson V, Vaishnav ED, Van den Berge K, Welch JD, An X, Bateup HS, Bowman I, Chance RK, Foster NN, Galbavy W, Gong H, Gou L, Hatfield JT, Hintiryan H, Hirokawa KE, Kim G, Kramer DJ, Li A, Li X, Luo Q, Muñoz-Castañeda R, Stafford DA, Feng Z, Jia X, Jiang S, Jiang T, Kuang X, Larsen R, Lesnar P, Li Y, Li Y, Liu L, Peng H, Qu L, Ren M, Ruan Z, Shen E, Song Y, Wakeman W, Wang P, Wang Y, Wang Y, Yin L, Yuan J, Zhao S, Zhao X, Narasimhan A, Palaniswamy R, Banerjee S, Ding L, Huilgol D, Huo B, Kuo HC, Laturnus S, Li X, Mitra PP, Mizrachi J, Wang Q, Xie P, Xiong F, Yu Y, Eichhorn SW, Berg J, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Dalley R, Hartmanis L, Horwitz GD, Jiang X, Ko AL, Miranda E, Mulherkar S, Nicovich PR, Owen SF, Sandberg R, Sorensen SA, Tan ZH, Allen S, Hockemeyer D, Lee AY, Veldman MB, Adkins RS, Ament SA, Bravo HC, Carter R, Chatterjee A, Colantuoni C, Crabtree J, Creasy H, Felix V, Giglio M, Herb BR, Kancherla J, Mahurkar A, McCracken C, Nickel L, Olley D, Orvis J, Schor M, Hood G, Dichter B, Grauer M, Helba B, Bandrowski A, Barkas N, Carlin B, D’Orazi FD, Degatano K, Gillespie TH, Khajouei F, Konwar K, Thompson C, Kelly K, Mok S, Sunkin S. A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 PMCID: PMC8494634 DOI: 10.1038/s41586-021-03950-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 12/14/2022]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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Allaway KC, Gabitto MI, Wapinski O, Saldi G, Wang CY, Bandler RC, Wu SJ, Bonneau R, Fishell G. Genetic and epigenetic coordination of cortical interneuron development. Nature 2021; 597:693-697. [PMID: 34552240 DOI: 10.1038/s41586-021-03933-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/18/2021] [Indexed: 11/09/2022]
Abstract
One of the hallmarks of the cerebral cortex is the extreme diversity of interneurons1-3. The two largest subtypes of cortical interneurons, parvalbumin- and somatostatin-positive cells, are morphologically and functionally distinct in adulthood but arise from common lineages within the medial ganglionic eminence4-11. This makes them an attractive model for studying the generation of cell diversity. Here we examine how developmental changes in transcription and chromatin structure enable these cells to acquire distinct identities in the mouse cortex. Generic interneuron features are first detected upon cell cycle exit through the opening of chromatin at distal elements. By constructing cell-type-specific gene regulatory networks, we observed that parvalbumin- and somatostatin-positive cells initiate distinct programs upon settling within the cortex. We used these networks to model the differential transcriptional requirement of a shared regulator, Mef2c, and confirmed the accuracy of our predictions through experimental loss-of-function experiments. We therefore reveal how a common molecular program diverges to enable these neuronal subtypes to acquire highly specialized properties by adulthood. Our methods provide a framework for examining the emergence of cellular diversity, as well as for quantifying and predicting the effect of candidate genes on cell-type-specific development.
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Affiliation(s)
- Kathryn C Allaway
- Neuroscience Institute, New York University, New York, NY, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Mariano I Gabitto
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Orly Wapinski
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Giuseppe Saldi
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA.,Department of Biology, New York University, New York, NY, USA
| | - Chen-Yu Wang
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Rachel C Bandler
- Neuroscience Institute, New York University, New York, NY, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Sherry Jingjing Wu
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. .,Department of Biology, New York University, New York, NY, USA. .,Center for Data Science, New York University, New York, NY, USA.
| | - Gord Fishell
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA.
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Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gordân R, Ashley-Koch AE, Crawford GE, Chiba-Falek O. Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. Mol Neurodegener 2021; 16:58. [PMID: 34429139 PMCID: PMC8383438 DOI: 10.1186/s13024-021-00481-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the post-GWAS era, there is an unmet need to decode the underpinning genetic etiologies of late-onset Alzheimer's disease (LOAD) and translate the associations to causation. METHODS We conducted ATAC-seq profiling using NeuN sorted-nuclei from 40 frozen brain tissues to determine LOAD-specific changes in chromatin accessibility landscape in a cell-type specific manner. RESULTS We identified 211 LOAD-specific differential chromatin accessibility sites in neuronal-nuclei, four of which overlapped with LOAD-GWAS regions (±100 kb of SNP). While the non-neuronal nuclei did not show LOAD-specific differences, stratification by sex identified 842 LOAD-specific chromatin accessibility sites in females. Seven of these sex-dependent sites in the non-neuronal samples overlapped LOAD-GWAS regions including APOE. LOAD loci were functionally validated using single-nuclei RNA-seq datasets. CONCLUSIONS Using brain sorted-nuclei enabled the identification of sex-dependent cell type-specific LOAD alterations in chromatin structure. These findings enhance the interpretation of LOAD-GWAS discoveries, provide potential pathomechanisms, and suggest novel LOAD-loci.
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Affiliation(s)
- Julio Barrera
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Julia E. Gamache
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Young Yun
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Ivana Premasinghe
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Daniel Sprague
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Danielle Chipman
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Jeffrey Li
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Hélène Fradin
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Karen Soldano
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27705 USA
- Department of Computer Science, Duke University, Durham, NC 27705 USA
| | - Allison E. Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
- Department of Medicine, Duke University Medical Center, DUMC, Box 104775, Durham, NC 27708 USA
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC, Box 3382, Durham, NC 27708 USA
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC 27708 USA
| | - Ornit Chiba-Falek
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
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Sunderaraman P, Cosentino S, Schupf N, Manly J, Gu Y, Barral S. MEF2C Common Genetic Variation Is Associated With Different Aspects of Cognition in Non-Hispanic White and Caribbean Hispanic Non-demented Older Adults. Front Genet 2021; 12:642327. [PMID: 34386032 PMCID: PMC8353395 DOI: 10.3389/fgene.2021.642327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES Myocyte Enhancer Factor 2C (MEF2C) is identified as a candidate gene contributing to the risk of developing Alzheimer's disease. However, little is known about whether MEF2C plays a role in specific aspects of cognition among older adults. The current study investigated the association of common variants in the MEF2C gene with four cognitive domains including memory, visuospatial functioning, processing speed and language among non-demented individuals. METHOD Participants from two ethnic groups, Non-Hispanic White (NHW; n = 537) and Caribbean Hispanic (CH; n = 1,197) from the Washington Heights-Inwood Community Aging Project (WHICAP) study, were included. Genetic association analyses using WHICAP imputed genome-wide data (GWAS) were conducted for the various cognition domains. RESULTS Single nucleotide polymorphisms (SNP) variants in the MEF2C gene showed nominally significant associations in all cognitive domains but for different SNPs across both the ethnic groups. In NHW participants, the strongest associations were present for memory (rs302484), language (rs619584), processing speed (rs13159808), and visuospatial functioning (several SNPs). In CH, strongest associations were observed for memory (rs34822815), processing speed (rs304141), visuospatial functioning (rs10066711 and rs10038371), and language (rs304153). DISCUSSION MEF2C variant-cognitive associations shed light on an apparent role for MEF2C in both memory and non-memory aspects of cognition in individuals from NHW and CH ancestries. However, the little overlap in the specific SNP-cognition associations in CH versus NHW highlights the differences in genetic architectural variations among those from different ancestries that should be considered while studying the MEF2C gene.
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Affiliation(s)
- Preeti Sunderaraman
- Cognitive Neuroscience Division of the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, G.H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States
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Jin T, Rehani P, Ying M, Huang J, Liu S, Roussos P, Wang D. scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks. Genome Med 2021; 13:95. [PMID: 34044854 PMCID: PMC8161957 DOI: 10.1186/s13073-021-00908-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding cell-type-specific gene regulatory mechanisms from genetic variants to diseases remains challenging. To address this, we developed a computational pipeline, scGRNom (single-cell Gene Regulatory Network prediction from multi-omics), to predict cell-type disease genes and regulatory networks including transcription factors and regulatory elements. With applications to schizophrenia and Alzheimer's disease, we predicted disease genes and regulatory networks for excitatory and inhibitory neurons, microglia, and oligodendrocytes. Further enrichment analyses revealed cross-disease and disease-specific functions and pathways at the cell-type level. Our machine learning analysis also found that cell-type disease genes improved clinical phenotype predictions. scGRNom is a general-purpose tool available at https://github.com/daifengwanglab/scGRNom .
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Affiliation(s)
- Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Peter Rehani
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA
- Department of Integrative Biology, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Present address: Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Mufang Ying
- Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Present address: Department of Statistics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jiawei Huang
- Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Panagiotis Roussos
- 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
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA.
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA.
- Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI, 53706, USA.
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Fazel Darbandi S, Robinson Schwartz SE, Pai ELL, Everitt A, Turner ML, Cheyette BNR, Willsey AJ, State MW, Sohal VS, Rubenstein JLR. Enhancing WNT Signaling Restores Cortical Neuronal Spine Maturation and Synaptogenesis in Tbr1 Mutants. Cell Rep 2021; 31:107495. [PMID: 32294447 PMCID: PMC7473600 DOI: 10.1016/j.celrep.2020.03.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/17/2020] [Accepted: 03/17/2020] [Indexed: 12/21/2022] Open
Abstract
Tbr1 is a high-confidence autism spectrum disorder (ASD)
gene encoding a transcription factor with distinct pre- and postnatal functions.
Postnatally, Tbr1 conditional knockout (CKO) mutants and
constitutive heterozygotes have immature dendritic spines and reduced synaptic
density. Tbr1 regulates expression of several genes that
underlie synaptic defects, including a kinesin (Kif1a) and a
WNT-signaling ligand (Wnt7b). Furthermore,
Tbr1 mutant corticothalamic neurons have reduced thalamic
axonal arborization. LiCl and a GSK3β inhibitor, two WNT-signaling
agonists, robustly rescue the dendritic spines and the synaptic and axonal
defects, suggesting that this could have relevance for therapeutic approaches in
some forms of ASD. Fazel Darbandi et al. demonstrate that TBR1 directly regulates
transcriptional circuits in cortical layers 5 and 6, which promote dendritic
spine and synaptic density. Enhancing WNT signaling rescues dendritic spine
maturation and synaptogenesis defects in Tbr1 mutants. These
results provide insights into mechanisms that underlie ASD pathophysiology.
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Affiliation(s)
- Siavash Fazel Darbandi
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah E Robinson Schwartz
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily Ling-Lin Pai
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marc L Turner
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin N R Cheyette
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vikaas S Sohal
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience and Sloan-Swartz Center for Theoretical Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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Zhang F, Rao S, Cao H, Zhang X, Wang Q, Xu Y, Sun J, Wang C, Chen J, Xu X, Zhang N, Tian L, Yuan J, Wang G, Cai L, Xu M, Baranova A. Genetic evidence suggests posttraumatic stress disorder as a subtype of major depressive disorder. J Clin Invest 2021; 132:145942. [PMID: 33905376 PMCID: PMC8803333 DOI: 10.1172/jci145942] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/22/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Major depressive disorder (MDD) and posttraumatic stress disorder (PTSD) are highly comorbid and exhibit strong correlations with one another. We aimed to investigate mechanisms of underlying relationships between PTSD and three kinds of depressive phenotypes, namely, MDD, depressed affect (DAF), and depression (DEP, including both MDD and the broad definition of depression). METHODS Genetic correlations between PTSD and the depressive phenotypes were tested using linkage disequilibrium score regression. Polygenic overlap analysis was used to estimate shared and trait-specific causal variants across a pair of traits. Causal relationships between PTSD and the depressive phenotypes were investigated using Mendelian randomization. Shared genomic loci between PTSD and MDD were identified using cross-trait meta-analysis. RESULTS Genetic correlations of PTSD with the depressive phenotypes were in the range of 0.71~0.80. The estimated numbers of causal variants were 14,565, 12,965, 10,565, and 4,986 for MDD, DEP, DAF, and PTSD, respectively. In each case, causal variants contributing to PTSD were completely or largely covered by causal variants defining each of the depressive phenotypes. Mendelian randomization analysis indicates that the genetically determined depressive phenotypes confer a causal effect on PTSD (b = 0.21~0.31). Notably, genetically determined PTSD confers a causal effect on DEP (b = 0.14) and DAF (b = 0.15), but not MDD. Cross-trait meta-analysis of MDD and PTSD identifies 47 genomic loci, including 29 loci shared between PTSD and MDD. CONCLUSION Evidence from shared genetics suggests that PTSD is a subtype of MDD. This study provides support to the efforts in reducing diagnostic heterogeneity in psychiatric nosology. FUNDING The National Key Research and Development Program of China (2018YFC1314300) and the National Natural Science Foundation of China (81471364 and 81971255).
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Affiliation(s)
- Fuquan Zhang
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Fairfax, United States of America
| | - Xiangrong Zhang
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Qiang Wang
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, China
| | - Yong Xu
- Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Jing Sun
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Chun Wang
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Jiu Chen
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Xijia Xu
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Ning Zhang
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Lin Tian
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Jianmin Yuan
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Guoqiang Wang
- Department of Psychiatry, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Lei Cai
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disor, Shanghai Jiao Tong University, Shanghai, China
| | - Mingqing Xu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disor, Shanghai Jiao Tong University, Shanghai, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, United States of America
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Chaudhary R, Agarwal V, Kaushik AS, Rehman M. Involvement of myocyte enhancer factor 2c in the pathogenesis of autism spectrum disorder. Heliyon 2021; 7:e06854. [PMID: 33981903 PMCID: PMC8082549 DOI: 10.1016/j.heliyon.2021.e06854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/09/2020] [Accepted: 04/15/2021] [Indexed: 12/29/2022] Open
Abstract
Myocyte enhancer factor 2 (MEF2), a family of transcription factor of MADS (minichromosome maintenance 1, agamous, deficiens and serum response factor)-box family needed in the growth and differentiation of a variety of human cells, such as neural, immune, endothelial, and muscles. As per existing literature, MEF2 transcription factors have also been associated with synaptic plasticity, the developmental mechanisms governing memory and learning, and several neurologic conditions, like autism spectrum disorders (ASDs). Recent genomic findings have ascertained a link between MEF2 defects, particularly in the MEF2C isoform and the ASD. In this review, we summarized a concise overview of the general regulation, structure and functional roles of the MEF2C transcription factor. We further outlined the potential role of MEF2C as a risk factor for various neurodevelopmental disorders, such as ASD, MEF2C Haploinsufficiency Syndrome and Fragile X syndrome.
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Affiliation(s)
- Rishabh Chaudhary
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Vipul Agarwal
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Arjun Singh Kaushik
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Mujeeba Rehman
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Eze UC, Bhaduri A, Haeussler M, Nowakowski TJ, Kriegstein AR. Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. Nat Neurosci 2021; 24:584-594. [PMID: 33723434 PMCID: PMC8012207 DOI: 10.1038/s41593-020-00794-1] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/23/2020] [Indexed: 01/31/2023]
Abstract
The human cortex comprises diverse cell types that emerge from an initially uniform neuroepithelium that gives rise to radial glia, the neural stem cells of the cortex. To characterize the earliest stages of human brain development, we performed single-cell RNA-sequencing across regions of the developing human brain, including the telencephalon, diencephalon, midbrain, hindbrain and cerebellum. We identify nine progenitor populations physically proximal to the telencephalon, suggesting more heterogeneity than previously described, including a highly prevalent mesenchymal-like population that disappears once neurogenesis begins. Comparison of human and mouse progenitor populations at corresponding stages identifies two progenitor clusters that are enriched in the early stages of human cortical development. We also find that organoid systems display low fidelity to neuroepithelial and early radial glia cell types, but improve as neurogenesis progresses. Overall, we provide a comprehensive molecular and spatial atlas of early stages of human brain and cortical development.
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Affiliation(s)
- Ugomma C Eze
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco (UCSF), San Francisco, CA, USA.
| | | | - Tomasz J Nowakowski
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco (UCSF), San Francisco, CA, USA.
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