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Mitchell B, Thor S, Piper M. Cellular and molecular functions of SETD2 in the central nervous system. J Cell Sci 2023; 136:jcs261406. [PMID: 37921122 DOI: 10.1242/jcs.261406] [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] [Indexed: 11/04/2023] Open
Abstract
The covalent modification of histones is critical for many biological functions in mammals, including gene regulation and chromatin structure. Posttranslational histone modifications are added and removed by specialised 'writer' and 'eraser' enzymes, respectively. One such writer protein implicated in a wide range of cellular processes is SET domain-containing 2 (SETD2), a histone methyltransferase that catalyses the trimethylation of lysine 36 on histone H3 (H3K36me3). Recently, SETD2 has also been found to modify proteins other than histones, including actin and tubulin. The emerging roles of SETD2 in the development and function of the mammalian central nervous system (CNS) are of particular interest as several SETD2 variants have been implicated in neurodevelopmental disorders, such as autism spectrum disorder and the overgrowth disorder Luscan-Lumish syndrome. Here, we summarise the numerous roles of SETD2 in mammalian cellular functions and development, with a focus on the CNS. We also provide an overview of the consequences of SETD2 variants in human disease and discuss future directions for understanding essential cellular functions of SETD2.
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Affiliation(s)
- Benjamin Mitchell
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefan Thor
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Michael Piper
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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2
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McCanlies EC, Gu JK, Kashon M, Yucesoy B, Ma CC, Sanderson WT, Kim K, Ludeña-Rodriguez YJ, Hertz-Picciotto I. Parental occupational exposure to solvents and autism spectrum disorder: An exploratory look at gene-environment interactions. ENVIRONMENTAL RESEARCH 2023; 228:115769. [PMID: 37004853 PMCID: PMC10273405 DOI: 10.1016/j.envres.2023.115769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Erin C McCanlies
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA.
| | - Ja Kook Gu
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | - Michael Kashon
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | - Berran Yucesoy
- Former Affiliate of Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | - Claudia C Ma
- Former Affiliate of Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | | | - Kyoungmi Kim
- Department of Public Health Sciences, University of California, Davis, CA, 95616, USA
| | | | - Irva Hertz-Picciotto
- Department of Public Health Sciences, University of California, Davis, CA, 95616, USA
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3
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Sampath D, Branyan TE, Markowsky KG, Gunda R, Samiya N, Obenaus A, Sohrabji F. Sex differences in cognitive impairment after focal ischemia in middle-aged rats and the effect of iv miR-20a-3p treatment. Neurobiol Aging 2023; 129:168-177. [PMID: 37336171 DOI: 10.1016/j.neurobiolaging.2023.05.001] [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: 01/22/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 06/21/2023]
Abstract
Stroke is a major cause of death and disability worldwide and is also a leading cause of vascular dementia and Alzheimer's disease, with older women experiencing accelerated decline. Our previous studies show that intravenous (iv) injections of miR-20a-3p, a small noncoding RNA (miRNA) delivered after stroke improves acute stroke outcomes in middle-aged male and female rats. The present study tested whether mir-20a-3p treatment would also ameliorate stroke-induced cognitive decline in the chronic phase. Acyclic middle-aged females and age-matched male Sprague Dawley rats were subjected to middle cerebral artery occlusion using endothelin-1 or sham surgery, and treated iv with miR-20a-3p mimics or scrambled oligos at 4 hours, 24 hours, and 70 days post-stroke. Stroke resulted in a significant sensory motor deficit, while miR-20a-3p treatment reduced these deficits in both sexes. Cognitive impairment was assessed periodically for 3 months after stroke using contextual fear conditioning and the novel object recognition task. Overall, the tests of associative and episodic memory were affected by focal ischemia only in female rats, and miR-20a-3p ameliorated the rate of decline.
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Affiliation(s)
- Dayalan Sampath
- Women's Health in Neuroscience Program, Department of Neuroscience and Experimental Therapeutics, College of Medicine and Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, USA
| | - Taylor E Branyan
- Women's Health in Neuroscience Program, Department of Neuroscience and Experimental Therapeutics, College of Medicine and Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, USA
| | - Kylee G Markowsky
- Women's Health in Neuroscience Program, Department of Neuroscience and Experimental Therapeutics, College of Medicine and Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, USA
| | - Rithvik Gunda
- Women's Health in Neuroscience Program, Department of Neuroscience and Experimental Therapeutics, College of Medicine and Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, USA
| | - Nadia Samiya
- Women's Health in Neuroscience Program, Department of Neuroscience and Experimental Therapeutics, College of Medicine and Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, USA
| | - Andre Obenaus
- Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Farida Sohrabji
- Women's Health in Neuroscience Program, Department of Neuroscience and Experimental Therapeutics, College of Medicine and Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, USA.
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4
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Zhang P, Omanska A, Ander B, Gandal M, Stamova B, Schumann C. Neuron-specific transcriptomic signatures indicate neuroinflammation and altered neuronal activity in ASD temporal cortex. Proc Natl Acad Sci U S A 2023; 120:e2206758120. [PMID: 36862688 PMCID: PMC10013873 DOI: 10.1073/pnas.2206758120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/28/2022] [Indexed: 03/03/2023] Open
Abstract
Autism spectrum disorder (ASD) is a highly heterogeneous disorder, yet transcriptomic profiling of bulk brain tissue has identified substantial convergence among dysregulated genes and pathways in ASD. However, this approach lacks cell-specific resolution. We performed comprehensive transcriptomic analyses on bulk tissue and laser-capture microdissected (LCM) neurons from 59 postmortem human brains (27 ASD and 32 controls) in the superior temporal gyrus (STG) of individuals ranging from 2 to 73 years of age. In bulk tissue, synaptic signaling, heat shock protein-related pathways, and RNA splicing were significantly altered in ASD. There was age-dependent dysregulation of genes involved in gamma aminobutyric acid (GABA) (GAD1 and GAD2) and glutamate (SLC38A1) signaling pathways. In LCM neurons, AP-1-mediated neuroinflammation and insulin/IGF-1 signaling pathways were upregulated in ASD, while mitochondrial function, ribosome, and spliceosome components were downregulated. GABA synthesizing enzymes GAD1 and GAD2 were both downregulated in ASD neurons. Mechanistic modeling suggested a direct link between inflammation and ASD in neurons, and prioritized inflammation-associated genes for future study. Alterations in small nucleolar RNAs (snoRNAs) associated with splicing events suggested interplay between snoRNA dysregulation and splicing disruption in neurons of individuals with ASD. Our findings supported the fundamental hypothesis of altered neuronal communication in ASD, demonstrated that inflammation was elevated at least in part in ASD neurons, and may reveal windows of opportunity for biotherapeutics to target the trajectory of gene expression and clinical manifestation of ASD throughout the human lifespan.
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Affiliation(s)
- Pan Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA90095
| | - Alicja Omanska
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, Davis, Sacramento, CA95817
- University of California, Davis, MIND Institute, Sacramento, CA95817
| | - Bradley P. Ander
- University of California, Davis, MIND Institute, Sacramento, CA95817
- Department of Neurology, University of California, Davis, School of Medicine, Sacramento, CA95817
| | - Michael J. Gandal
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA90095
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Lifespan Brain Institute, Penn Med and the Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Boryana Stamova
- University of California, Davis, MIND Institute, Sacramento, CA95817
- Department of Neurology, University of California, Davis, School of Medicine, Sacramento, CA95817
| | - Cynthia M. Schumann
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, Davis, Sacramento, CA95817
- University of California, Davis, MIND Institute, Sacramento, CA95817
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5
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Scala M, Drouot N, MacLennan SC, Wessels MW, Krygier M, Pavinato L, Telegrafi A, de Man SA, van Slegtenhorst M, Iacomino M, Madia F, Scudieri P, Uva P, Giacomini T, Nobile G, Mancardi MM, Balagura G, Galloni GB, Verrotti A, Umair M, Khan A, Liebelt J, Schmidts M, Langer T, Brusco A, Lipska-Ziętkiewicz BS, Saris JJ, Charlet-Berguerand N, Zara F, Striano P, Piton A. De novo truncating NOVA2 variants affect alternative splicing and lead to heterogeneous neurodevelopmental phenotypes. Hum Mutat 2022; 43:1299-1313. [PMID: 35607920 PMCID: PMC9543825 DOI: 10.1002/humu.24414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/02/2022] [Accepted: 05/22/2022] [Indexed: 11/10/2022]
Abstract
Alternative splicing (AS) is crucial for cell-type specific gene transcription and plays a critical role in neuronal differentiation and synaptic plasticity. De novo frameshift variants in NOVA2, encoding a neuron-specific key splicing factor, have been recently associated with a new neurodevelopmental disorder (NDD) with hypotonia, neurological features, and brain abnormalities. We investigated eight unrelated individuals by exome sequencing (ES) and identified seven novel pathogenic NOVA2 variants, including two with a novel localization at the KH1 and KH3 domains. In addition to a severe NDD phenotype, novel clinical features included psychomotor regression, attention deficit-hyperactivity disorder (ADHD), dyspraxia, and urogenital and endocrinological manifestations. To test the effect of the variants on splicing regulation, we transfected HeLa cells with wildtype and mutant NOVA2 cDNA. The novel variants NM_002516.4: c.754_756delCTGinsTT p.(Leu252Phefs*144) and c.1329dup p.(Lys444Glnfs*82) all negatively affected AS events. The distal p.(Lys444Glnfs*82) variant, causing a partial removal of the KH3 domain, had a milder functional effect leading to an intermediate phenotype. Our findings expand the molecular and phenotypic spectrum of NOVA2-related NDD, supporting the pathogenic role of AS disruption by truncating variants and suggesting that this is a heterogeneous condition with variable clinical course. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France
| | - Suzanna C MacLennan
- Department of Paediatric Neurology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Marja W Wessels
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Magdalena Krygier
- Department of Developmental Neurology, Medical University of Gdańsk, ul. Dębinki 7 80-952, Gdańsk, Poland
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.,Center for Molecular Medicine Cologne, Institute of Human Genetics, University of Cologne, 50931, Cologne, Germany
| | - Aida Telegrafi
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | | | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Francesca Madia
- Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Paolo Scudieri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Paolo Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Thea Giacomini
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Giulia Nobile
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Maria Margherita Mancardi
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giovanni Battista Galloni
- Struttura Complessa Neuropsichiatria Infantile Sud, Azienda Sanitaria Locale Città di Torino, Torino, Italy
| | | | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Amjad Khan
- Faculty of Biological Science, Department of Zoology, University of Lakki Marwat, Lakki Marwat, Pakistan
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Miriam Schmidts
- Department of General Pediatrics and Adolescent Medicine, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thorsten Langer
- Department of Neuropediatrics and Muscle Disorders, Center for Pediatrics, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.,Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, 10126, Turin, Italy
| | - Beata S Lipska-Ziętkiewicz
- Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdańsk, Gdańsk, Poland.,27Centre for Rare Diseases, Medical University of Gdańsk, Gdańsk, Poland
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France.,Laboratory of Genetic Diagnostic, Hôpitaux Universitaires de Strasbourg, Strasbourg, 67000, France.,Institut Universitaire de France, Paris, Île-de-France, France
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6
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Villa CE, Cheroni C, Dotter CP, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli MR, Lyudchik J, Sommer C, Gabitto M, Danzl JG, Testa G, Novarino G. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Rep 2022; 39:110615. [PMID: 35385734 DOI: 10.1016/j.celrep.2022.110615] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/18/2021] [Accepted: 03/13/2022] [Indexed: 12/13/2022] Open
Abstract
Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients' macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.
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Affiliation(s)
- Carlo Emanuele Villa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Christoph P Dotter
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Alejandro López-Tóbon
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Bárbara Oliveira
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Roberto Sacco
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Aysan Çerağ Yahya
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Jasmin Morandell
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Michele Gabriele
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy
| | - Mojtaba R Tavakoli
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Julia Lyudchik
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Christoph Sommer
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | | | - Johann G Danzl
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.
| | - Gaia Novarino
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria.
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7
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Ejlersen M, Ilieva M, Michel TM. Superoxide dismutase isozymes in cerebral organoids from autism spectrum disorder patients. J Neural Transm (Vienna) 2022; 129:617-626. [PMID: 35266053 DOI: 10.1007/s00702-022-02472-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder is a pervasive neurodevelopmental disorder with a substantial contribution to the global disease burden. Despite intensive research efforts, the aetiopathogenesis remains unclear. The Janus-faced antioxidant enzymes superoxide dismutase 1-3 have been implicated in initiating oxidative stress and as such may constitute a potential therapeutic target. However, no measurement has been taken in human autistic brain samples. The aim of this study is to measure superoxide dismutase 1-3 in autistic cerebral organoids as an in vitro model of human foetal neurodevelopment. Whole brain organoids were created from induced pluripotent stem cells from healthy individuals (n = 5) and individuals suffering from autism (n = 4). Using Pierce bicinchoninic acid and enzyme-linked immunosorbent assays, the protein and superoxide dismutase 1, 2, and 3 concentrations were quantified in the cerebral organoids at days 22, 32, and 42. Measurements were normalized to the protein concentration. Results represented using medians and interquartile ranges. Using Wilcoxon matched-pairs signed-rank test, an abrupt rise in the superoxide dismutase concentration was observed at day 32 and onwards. Using Wilcoxon rank-sum test, no differences were observed between healthy (SOD1: 35.56 ng/mL ± 3.46; SOD2: 2435.80 ng/mL ± 1327.00; SOD3: 1854.88 ng/mL ± 867.94) and autistic (SOD1: 32.85 ng/mL ± 5.26; SOD2: 2717.80 ng/mL ± 1889.10; SOD3: 1690.18 ng/mL ± 615.49) organoids. Cerebral organoids recapitulate many aspects of human neurodevelopment, but the diffusion restriction may render efforts in modelling differences in oxidative stress futile due to the intrinsic hypoxia and central necrosis.
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Affiliation(s)
- Morten Ejlersen
- Faculty of Health Sciences, University of Southern Denmark, J.B. Winsløws Vej 19.3, 5000, Odense, Denmark
| | - Mirolyuba Ilieva
- Research Unit of the Department of Psychiatry, University Hospital of Southern Denmark, J.B. Winsløws Vej 20, 5000, Odense, Denmark
| | - Tanja Maria Michel
- Faculty of Health Sciences, University of Southern Denmark, J.B. Winsløws Vej 19.3, 5000, Odense, Denmark.
- Research Unit of the Department of Psychiatry, University Hospital of Southern Denmark, J.B. Winsløws Vej 20, 5000, Odense, Denmark.
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8
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Lipina T, Blundell M. From atypical senses to autism: towards new therapeutic targets and improved diagnostics. Pharmacol Biochem Behav 2021; 212:173312. [PMID: 34883136 DOI: 10.1016/j.pbb.2021.173312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/18/2021] [Accepted: 11/30/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Tatiana Lipina
- University of Toronto, Department of Pharmacology & Toxicology, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Matisse Blundell
- University of Toronto, Department of Pharmacology & Toxicology, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
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9
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Soremekun O, Soremekun C, Machipisa T, Soliman M, Nashiru O, Chikowore T, Fatumo S. Genome-Wide Association and Mendelian Randomization Analysis Reveal the Causal Relationship Between White Blood Cell Subtypes and Asthma in Africans. Front Genet 2021; 12:749415. [PMID: 34925446 PMCID: PMC8674726 DOI: 10.3389/fgene.2021.749415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/01/2021] [Indexed: 12/03/2022] Open
Abstract
Background: White blood cell (WBC) traits and their subtypes such as basophil count (Bas), eosinophil count (Eos), lymphocyte count (Lym), monocyte count (Mon), and neutrophil counts (Neu) are known to be associated with diseases such as stroke, peripheral arterial disease, and coronary heart disease. Methods: We meta-analyze summary statistics from genome-wide association studies in 17,802 participants from the African Partnership for Chronic Disease Research (APCDR) and African ancestry individuals from the Blood Cell Consortium (BCX2) using GWAMA. We further carried out a Bayesian fine mapping to identify causal variants driving the association with WBC subtypes. To access the causal relationship between WBC subtypes and asthma, we conducted a two-sample Mendelian randomization (MR) analysis using summary statistics of the Consortium on Asthma among African Ancestry Populations (CAAPA: n cases = 7,009, n control = 7,645) as our outcome phenotype. Results: Our metanalysis identified 269 loci at a genome-wide significant value of (p = 5 × 10-9) in a composite of the WBC subtypes while the Bayesian fine-mapping analysis identified genetic variants that are more causal than the sentinel single-nucleotide polymorphism (SNP). We found for the first time five novel genes (LOC126987/MTCO3P14, LINC01525, GAPDHP32/HSD3BP3, FLG-AS1/HMGN3P1, and TRK-CTT13-1/MGST3) not previously reported to be associated with any WBC subtype. Our MR analysis showed that Mon (IVW estimate = 0.38, CI: 0.221, 0.539, p < 0.001), Neu (IVW estimate = 0.189, CI: 0.133, 0.245, p < 0.001), and WBCc (IVW estimate = 0.185, CI: 0.108, 0.262, p < 0.001) are associated with increased risk of asthma. However, there was no evidence of causal relationship between Lym and asthma risk. Conclusion: This study provides insight into the relationship between some WBC subtypes and asthma and potential route in the treatment of asthma and may further inform a new therapeutic approach.
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Affiliation(s)
- Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
| | - Chisom Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Tafadzwa Machipisa
- Department of Medicine, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
- The Department of Pathology and Molecular Medicine, Population Health Research Institute (PHRI), Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Mahmoud Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Tinashe Chikowore
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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10
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Shah S, Richter JD. Do Fragile X Syndrome and Other Intellectual Disorders Converge at Aberrant Pre-mRNA Splicing? Front Psychiatry 2021; 12:715346. [PMID: 34566717 PMCID: PMC8460907 DOI: 10.3389/fpsyt.2021.715346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fragile X Syndrome is a neuro-developmental disorder caused by the silencing of the FMR1 gene, resulting in the loss of its protein product, FMRP. FMRP binds mRNA and represses general translation in the brain. Transcriptome analysis of the Fmr1-deficient mouse hippocampus reveals widespread dysregulation of alternative splicing of pre-mRNAs. Many of these aberrant splicing changes coincide with those found in post-mortem brain tissue from individuals with autism spectrum disorders (ASDs) as well as in mouse models of intellectual disability such as PTEN hamartoma syndrome (PHTS) and Rett Syndrome (RTT). These splicing changes could result from chromatin modifications (e.g., in FXS, RTT) and/or splicing factor alterations (e.g., PTEN, autism). Based on the identities of the RNAs that are mis-spliced in these disorders, it may be that they are at least partly responsible for some shared pathophysiological conditions. The convergence of splicing aberrations among these autism spectrum disorders might be crucial to understanding their underlying cognitive impairments.
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Affiliation(s)
| | - Joel D. Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
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11
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Okay K, Varış PÜ, Miral S, Ekinci B, Yaraş T, Karakülah G, Oktay Y. Alternative splicing and gene co-expression network-based analysis of dizygotic twins with autism-spectrum disorder and their parents. Genomics 2021; 113:2561-2571. [PMID: 34087420 DOI: 10.1016/j.ygeno.2021.05.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/25/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high heritability, however, understanding the complexity of the underlying genetic basis has proven to be a challenging task. We hypothesized that dissecting the aberrations in alternative splicing (AS) and their effects on expression networks might provide insight. Therefore, we performed AS and co-expression analyses of total RNA isolated from Peripheral Blood Mononuclear Cells (PBMCs) of two pairs of dizygotic (DZ) twins with non-syndromic autism and their parents. We identified 183 differential AS events in 146 genes, seven of them being Simons Foundation Autism Research Initiative (SFARI) Category 1-3 genes, three of which had previously been reported to be alternatively spliced in ASD post-mortem brains. Gene co-expression analysis identified 7 modules with 513 genes, 5 of which were SFARI Category 1 or Category 2 genes. Among differentially AS genes within the modules, ZNF322 and NR4A1 could be potentially interesting targets for further investigations.
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Affiliation(s)
- Kaan Okay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Pelin Ünal Varış
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey; Barış Psychiatric Hospital, Nicosia, Cyprus
| | - Süha Miral
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey
| | - Burcu Ekinci
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Tutku Yaraş
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey.
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey; Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey.
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12
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Fukushi D, Inaba M, Katoh K, Suzuki Y, Enokido Y, Nomura N, Tokita Y, Hayashi S, Mizuno S, Yamada K, Wakamatsu N. R3HDM1 haploinsufficiency is associated with mild intellectual disability. Am J Med Genet A 2021; 185:1776-1786. [PMID: 33750005 DOI: 10.1002/ajmg.a.62173] [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: 11/04/2020] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 11/07/2022]
Abstract
R3HDM1 (R3H domain containing 1) is an uncharacterized RNA-binding protein that is highly expressed in the human cerebral cortex. We report the first case of a 12-year-old Japanese male with haploinsufficiency of R3HDM1. He presented with mild intellectual disability (ID) and developmental delay. He had a pericentric inversion of 46,XY,inv(2)(p16.1q21.3)dn with breakpoints in intron 19 of R3HDM1 (2q21.3) and the intergenic region (2p16.1). The R3HDM1 levels in his lymphoblastoid cells were reduced to approximately half that of the healthy controls. However, the expression of MIR128-1, in intron 18 of R3HDM1, was not affected via the pericentric inversion. Knockdown of R3HDM1 in mouse embryonic hippocampal neurons suppressed dendritic growth and branching. Notably, the Database of Genomic Variants reported the case of a healthy control with a 488-kb deletion that included both R3HDM1 and MIR128-1. miR-128 has been reported to inhibit dendritic growth and branching in mouse brain neurons, which directly opposes the novel functions of R3HDM1. These findings suggest that deleting both R3HDM1 and MIR128-1 alleviates the symptoms of the disease caused by loss-of-function mutations in R3HDM1 only. Thus, haploinsufficiency of R3HDM1 in the patient may be the cause of the mild ID due to the genetic imbalance between R3HDM1 and MIR128-1.
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Affiliation(s)
- Daisuke Fukushi
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Mie Inaba
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Kimiko Katoh
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Yasuyo Suzuki
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Yasushi Enokido
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Noriko Nomura
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Yoshihito Tokita
- Department of Disease Model, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Shin Hayashi
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Kenichiro Yamada
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Nobuaki Wakamatsu
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan.,Department of Pathology and Host Defense, Faculty of Medicine, Kagawa University, Miki, Japan
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13
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Pintacuda G, Martín JM, Eggan KC. Mind the translational gap: using iPS cell models to bridge from genetic discoveries to perturbed pathways and therapeutic targets. Mol Autism 2021; 12:10. [PMID: 33557935 PMCID: PMC7869517 DOI: 10.1186/s13229-021-00417-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a group of neurodevelopmental disorders characterized by impaired social interactions as well as the presentation of restrictive and repetitive behaviors. ASD is highly heritable but genetically heterogenous with both common and rare genetic variants collaborating to predispose individuals to the disorder. In this review, we synthesize recent efforts to develop human induced pluripotent stem cell (iPSC)-derived models of ASD-related phenotypes. We firstly address concerns regarding the relevance and validity of available neuronal iPSC-derived models. We then critically evaluate the robustness of various differentiation and cell culture protocols used for producing cell types of relevance to ASD. By exploring iPSC models of ASD reported thus far, we examine to what extent cellular and neuronal phenotypes with potential relevance to ASD can be linked to genetic variants found to underlie it. Lastly, we outline promising strategies by which iPSC technology can both enhance the power of genetic studies to identify ASD risk factors and nominate pathways that are disrupted across groups of ASD patients that might serve as common points for therapeutic intervention.
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Affiliation(s)
- Greta Pintacuda
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Jacqueline M Martín
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin C Eggan
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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14
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Yao F, Zhang K, Feng C, Gao Y, Shen L, Liu X, Ni J. Protein Biomarkers of Autism Spectrum Disorder Identified by Computational and Experimental Methods. Front Psychiatry 2021; 12:554621. [PMID: 33716802 PMCID: PMC7947305 DOI: 10.3389/fpsyt.2021.554621] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that affects millions of people worldwide. However, there are currently no reliable biomarkers for ASD diagnosis. Materials and Methods: The strategy of computational prediction combined with experimental verification was used to identify blood protein biomarkers for ASD. First, brain tissue-based transcriptome data of ASD were collected from Gene Expression Omnibus database and analyzed to find ASD-related genes by bioinformatics method of significance analysis of microarrays. Then, a prediction program of blood-secretory proteins was applied on these genes to predict ASD-related proteins in blood. Furthermore, ELISA was used to verify these proteins in plasma samples of ASD patients. Results: A total of 364 genes were identified differentially expressed in brain tissue of ASD, among which 59 genes were predicted to encode ASD-related blood-secretory proteins. After functional analysis and literature survey, six proteins were chosen for experimental verification and five were successfully validated. Receiver operating characteristic curve analyses showed that the area under the curve of SLC25A12, LIMK1, and RARS was larger than 0.85, indicating that they are more powerful in discriminating ASD cases from controls. Conclusion: SLC25A12, LIMK1, and RARS might serve as new potential blood protein biomarkers for ASD. Our findings provide new insights into the pathogenesis and diagnosis of ASD.
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Affiliation(s)
- Fang Yao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Kaoyuan Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China.,Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Chengyun Feng
- Department of Child Healthcare, Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Yan Gao
- Department of Child Healthcare, Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Xukun Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiazuan Ni
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
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15
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Qu W, Jin H, Chen BP, Liu J, Li R, Guo W, Tian H. CPEB3 regulates neuron-specific alternative splicing and involves neurogenesis gene expression. Aging (Albany NY) 2020; 13:2330-2347. [PMID: 33318303 PMCID: PMC7880327 DOI: 10.18632/aging.202259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022]
Abstract
In the mammalian brain, alternative pre-mRNA splicing is a fundamental mechanism that modifies neuronal function dynamically where secretion of different splice variants regulates neurogenesis, development, pathfinding, maintenance, migration, and synaptogenesis. Sequence-specific RNA-Binding Protein CPEB3 has distinctive isoform-distinct biochemical interactions and neuronal development assembly roles. Nonetheless, the mechanisms moderating splice isoform options remain unclear. To establish the modulatory trend of CPEB3, we cloned and excessively expressed CPEB3 in HT22 cells. We used RNA-seq to analyze CPEB3-regulated alternative splicing on control and CPEB3-overexpressing cells. Consequently, we used iRIP-seq to identify CPEB-binding targets. We additionally validated CPEB3-modulated genes using RT-qPCR. CPEB3 overexpression had insignificant effects on gene expression in HT22 cells. Notably, CPEB3 partially modulated differential gene splicing enhanced in the modulation of neural development, neuron cycle, neurotrophin, synapse, and specific development pathway, implying an alternative splicing regulatory mechanism associated with neurogenesis. Moreover, qRT-PCR verified the CPEB3-modulated transcription of neurogenesis genes LCN2 and NAV2, synaptogenesis gene CYLD, as well as neural development gene JADE1. Herein, we established that CPEB3 is a critical modulator of alternative splicing in neurogenesis, which remarkably enhances the current understanding of the CPEB3 mediated alternative pre-mRNA splicing.
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Affiliation(s)
- Wenrui Qu
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Hongjuan Jin
- Department of Plastic and Reconstructive Surgery, The First Hospital of Jilin University, Changchun, China
| | - Bing-Peng Chen
- Orthopedic Medical Center, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Jun Liu
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Rui Li
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Wenlai Guo
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Heng Tian
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
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16
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Ebrahimi Meimand S, Rostam-Abadi Y, Rezaei N. Autism spectrum disorders and natural killer cells: a review on pathogenesis and treatment. Expert Rev Clin Immunol 2020; 17:27-35. [PMID: 33191807 DOI: 10.1080/1744666x.2020.1850273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Autism spectrum disorder (ASD), as a wide spectrum of neurodevelopmental disorders, is characterized by early-onset impairments in social-communication, repetitive behaviors, and restrictive interests.Areas covered: Although still unknown, there are some pieces of evidence suggesting altered immune function in the etiology of ASD. This review aims to summarize studies linking Natural Killer (NK) cells to ASD by searching through databases like MEDLINE and Scopus up to October 2020. NK cells play important roles in the innate immune system and immune regulation. As parts of the immune system, they interact with the neural system as well. Immune dysregulations such as autoimmunity and improper immune responses to both internal and external stimulations, especially in early developmental stages of the brain, may induce neurodevelopmental disorders. NK cells' dysfunction in children with ASD as well as their parents have been highlighted in many studies.Expert opinion: Changes in the frequency, gene expressions, cytotoxicity features, and receptors of NK cells are reported in children with ASD. Immune therapy for children with ASD with immune abnormality has shown promising results. However, further studies are needed to elucidate the exact role of NK cells in the pathogenesis of ASD providing future treatment options for these children.
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Affiliation(s)
- Sepideh Ebrahimi Meimand
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Yasna Rostam-Abadi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Iranian National Center for Addiction Studies (INCAS), Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
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17
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Dykstra-Aiello C, Sharp FR, Jickling GC, Hull H, Hamade F, Shroff N, Durocher M, Cheng X, Zhan X, Liu D, Ander BP, Stamova BS. Alternative Splicing of Putative Stroke/Vascular Risk Factor Genes Expressed in Blood Following Ischemic Stroke Is Sexually Dimorphic and Cause-Specific. Front Neurol 2020; 11:584695. [PMID: 33193047 PMCID: PMC7642687 DOI: 10.3389/fneur.2020.584695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies have identified putative ischemic stroke risk genes, yet, their expression after stroke is unexplored in spite of growing interest in elucidating their specific role and identifying candidate genes for stroke treatment. Thus, we took an exploratory approach to investigate sexual dimorphism, alternative splicing, and etiology in putative risk gene expression in blood following cardioembolic, atherosclerotic large vessel disease and small vessel disease/lacunar causes of ischemic stroke in each sex compared to controls. Whole transcriptome arrays assessed 71 putative stroke/vascular risk factor genes for blood RNA expression at gene-, exon-, and alternative splicing-levels. Male (n = 122) and female (n = 123) stroke and control volunteers from three university medical centers were matched for race, age, vascular risk factors, and blood draw time since stroke onset. Exclusion criteria included: previous stroke, drug abuse, subarachnoid or intracerebral hemorrhage, hemorrhagic transformation, infection, dialysis, cancer, hematological abnormalities, thrombolytics, anticoagulants or immunosuppressants. Significant differential gene expression (fold change > |1.2|, p < 0.05, partial correlation > |0.4|) and alternative splicing (false discovery rate p < 0.3) were assessed. At gene level, few were differentially expressed: ALDH2, ALOX5AP, F13A1, and IMPA2 (males, all stroke); ITGB3 (females, cardioembolic); ADD1 (males, atherosclerotic); F13A1, IMPA2 (males, lacunar); and WNK1 (females, lacunar). GP1BA and ITGA2B were alternatively spliced in both sexes (all patients vs. controls). Six genes in males, five in females, were alternatively spliced in all stroke compared to controls. Alternative splicing and exon-level analyses associated many genes with specific etiology in either sex. Of 71 genes, 70 had differential exon-level expression in stroke patients compared to control subjects. Among stroke patients, 24 genes represented by differentially expressed exons were male-specific, six were common between sexes, and two were female-specific. In lacunar stroke, expression of 19 differentially expressed exons representing six genes (ADD1, NINJ2, PCSK9, PEMT, SMARCA4, WNK1) decreased in males and increased in females. Results demonstrate alternative splicing and sexually dimorphic expression of most putative risk genes in stroke patients' blood. Since expression was also often cause-specific, sex, and etiology are factors to consider in stroke treatment trials and genetic association studies as society trends toward more personalized medicine.
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Affiliation(s)
- Cheryl Dykstra-Aiello
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Frank R Sharp
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Glen C Jickling
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Heather Hull
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Farah Hamade
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Natasha Shroff
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Marc Durocher
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Xiyuan Cheng
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Xinhua Zhan
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - DaZhi Liu
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Bradley P Ander
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Boryana S Stamova
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
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18
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Pecorelli A, Ferrara F, Messano N, Cordone V, Schiavone ML, Cervellati F, Woodby B, Cervellati C, Hayek J, Valacchi G. Alterations of mitochondrial bioenergetics, dynamics, and morphology support the theory of oxidative damage involvement in autism spectrum disorder. FASEB J 2020; 34:6521-6538. [PMID: 32246805 DOI: 10.1096/fj.201902677r] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/21/2020] [Accepted: 03/06/2020] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorder (ASD) has been hypothesized to be a result of the interplay between genetic predisposition and increased vulnerability to early environmental insults. Mitochondrial dysfunctions appear also involved in ASD pathophysiology, but the mechanisms by which such alterations develop are not completely understood. Here, we analyzed ASD primary fibroblasts by measuring mitochondrial bioenergetics, ultrastructural and dynamic parameters to investigate the hypothesis that defects in these pathways could be interconnected phenomena responsible or consequence for the redox imbalance observed in ASD. High levels of 4-hydroxynonenal protein adducts together with increased NADPH (nicotinamide adenine dinucleotide phosphateoxidase) activity and mitochondrial superoxide production coupled with a compromised antioxidant response guided by a defective Nuclear Factor Erythroid 2-Related Factor 2 pathway confirmed an unbalanced redox homeostasis in ASD. Moreover, ASD fibroblasts showed overactive mitochondrial bioenergetics associated with atypical morphology and altered expression of mitochondrial electron transport chain complexes and dynamics-regulating factors. We suggest that many of the changes observed in mitochondria could represent compensatory mechanisms by which ASD cells try to adapt to altered energy demand, possibly resulting from a chronic oxinflammatory status.
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Affiliation(s)
- Alessandra Pecorelli
- Department of Animal Science, Plants for Human Health Institute, NC Research Campus, NC State University, Kannapolis, NC, USA
| | - Francesca Ferrara
- Department of Animal Science, Plants for Human Health Institute, NC Research Campus, NC State University, Kannapolis, NC, USA.,Department of Biomedical and Specialist Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Nicolò Messano
- Department of Animal Science, Plants for Human Health Institute, NC Research Campus, NC State University, Kannapolis, NC, USA
| | - Valeria Cordone
- Department of Biomedical and Specialist Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria Lucia Schiavone
- Department of Animal Science, Plants for Human Health Institute, NC Research Campus, NC State University, Kannapolis, NC, USA.,Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Franco Cervellati
- Department of Biomedical and Specialist Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Brittany Woodby
- Department of Animal Science, Plants for Human Health Institute, NC Research Campus, NC State University, Kannapolis, NC, USA
| | - Carlo Cervellati
- Department of Biomedical and Specialist Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Joussef Hayek
- Child Neuropsychiatry Unit, University General Hospital, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Giuseppe Valacchi
- Department of Animal Science, Plants for Human Health Institute, NC Research Campus, NC State University, Kannapolis, NC, USA.,Department of Biomedical and Specialist Surgical Sciences, University of Ferrara, Ferrara, Italy.,Department of Food and Nutrition, Kyung Hee University, Seoul, South Korea
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19
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Pirooznia M, Niranjan T, Chen YC, Tunc I, Goes FS, Avramopoulos D, Potash JB, Huganir RL, Zandi PP, Wang T. Affected Sib-Pair Analyses Identify Signaling Networks Associated With Social Behavioral Deficits in Autism. Front Genet 2019; 10:1186. [PMID: 31827489 PMCID: PMC6892440 DOI: 10.3389/fgene.2019.01186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/25/2019] [Indexed: 11/29/2022] Open
Abstract
Autism spectrum disorders (ASDs) are characterized by deficits in three core behavioral domains: reciprocal social interactions, communication, and restricted interests and/or repetitive behaviors. Several hundreds of risk genes for autism have been identified, however, it remains a challenge to associate these genes with specific core behavioral deficits. In multiplex autism families, affected sibs often show significant differences in severity of individual core phenotypes. We hypothesize that a higher mutation burden contributes to a larger difference in the severity of specific core phenotypes between affected sibs. We tested this hypothesis on social behavioral deficits in autism. We sequenced synaptome genes (n = 1,886) in affected male sib-pairs (n = 274) in families from the Autism Genetics Research Exchange (AGRE) and identified rare (MAF ≤ 1%) and predicted functional variants. We selected affected sib-pairs with a large (≥10; n = 92 pairs) or a small (≤4; n = 108 pairs) difference in total cumulative Autism Diagnostic Interview-Revised (ADI-R) social scores (SOCT_CS). We compared burdens of unshared variants present only in sibs with severe social deficits and found a higher burden in SOCT_CS≥10 compared to SOCT_CS ≤ 4 (SOCT_CS≥10: 705.1 ± 16.2; SOCT_CS ≤ 4, 668.3 ± 9.0; p = 0.025). Unshared SOCT_CS≥10 genes only in sibs with severe social deficits are significantly enriched in the SFARI gene set. Network analyses of these genes using InWeb_IM, molecular signatures database (MSigDB), and GeNetMeta identified enrichment for phosphoinositide 3-kinase (PI3K)-AKT-mammalian target of rapamycin (mTOR) (Enrichment Score [eScore] p value = 3.36E−07; n = 8 genes) and Nerve growth factor (NGF) (eScore p value = 8.94E−07; n = 9 genes) networks. These studies support a key role for these signaling networks in social behavioral deficits and present a novel approach to associate risk genes and signaling networks with core behavioral domains in autism.
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Affiliation(s)
- Mehdi Pirooznia
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tejasvi Niranjan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yun-Ching Chen
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States
| | - Ilker Tunc
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Dimitrios Avramopoulos
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - James B Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Mental Health and Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, United States
| | - Tao Wang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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20
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Maternal diabetes induces autism-like behavior by hyperglycemia-mediated persistent oxidative stress and suppression of superoxide dismutase 2. Proc Natl Acad Sci U S A 2019; 116:23743-23752. [PMID: 31685635 PMCID: PMC6876200 DOI: 10.1073/pnas.1912625116] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hyperglycemia induces persistent oxidative stress and superoxide dismutase 2 (SOD2) suppression in neurons. SOD2 suppression is caused by oxidative stress-mediated histone methylation and subsequent dissociation of Egr1 on the SOD2 promoter. Maternal diabetes induces autism-like behavior in offspring with SOD2 suppression in the amygdala in rats, while SOD2 overexpression in the amygdala ameliorates autism-like behavior. Postnatal treatment of the blood–brain barrier-permeable antioxidant resveratrol partly restores this effect. This study describes a potential mechanism for maternal diabetes-induced autism-like behavior in offspring. Epidemiological studies show that maternal diabetes is associated with an increased risk of autism spectrum disorders (ASDs), although the detailed mechanisms remain unclear. The present study aims to investigate the potential effect of maternal diabetes on autism-like behavior in offspring. The results of in vitro study showed that transient hyperglycemia induces persistent reactive oxygen species (ROS) generation with suppressed superoxide dismutase 2 (SOD2) expression. Additionally, we found that SOD2 suppression is due to oxidative stress-mediated histone methylation and the subsequent dissociation of early growth response 1 (Egr1) on the SOD2 promoter. Furthermore, in vivo rat experiments showed that maternal diabetes induces SOD2 suppression in the amygdala, resulting in autism-like behavior in offspring. SOD2 overexpression restores, while SOD2 knockdown mimics, this effect, indicating that oxidative stress and SOD2 expression play important roles in maternal diabetes-induced autism-like behavior in offspring, while prenatal and postnatal treatment using antioxidants permeable to the blood–brain barrier partly ameliorated this effect. We conclude that maternal diabetes induces autism-like behavior through hyperglycemia-mediated persistent oxidative stress and SOD2 suppression. Here we report a potential mechanism for maternal diabetes-induced ASD.
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21
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Sunwoo JS, Jeon D, Lee ST, Moon J, Yu JS, Park DK, Bae JY, Lee DY, Kim S, Jung KH, Park KI, Jung KY, Kim M, Lee SK, Chu K. Maternal immune activation alters brain microRNA expression in mouse offspring. Ann Clin Transl Neurol 2018; 5:1264-1276. [PMID: 30349861 PMCID: PMC6186947 DOI: 10.1002/acn3.652] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/27/2018] [Indexed: 01/15/2023] Open
Abstract
Objective Maternal immune activation (MIA) is associated with an increased risk of autism spectrum disorder (ASD) in offspring. Herein, we investigate the altered expression of microRNAs (miRNA), and that of their target genes, in the brains of MIA mouse offspring. Methods To generate MIA model mice, pregnant mice were injected with polyriboinosinic:polyribocytidylic acid on embryonic day 12.5. We performed miRNA microarray and mRNA sequencing in order to determine the differential expression of miRNA and mRNA between MIA mice and controls, at 3 weeks of age. We further identified predicted target genes of dysregulated miRNAs, and miRNA‐target interactions, based on the inverse correlation of their expression levels. Results Mice prenatally subjected to MIA exhibited behavioral abnormalities typical of ASD, such as a lack of preference for social novelty and reduced prepulse inhibition. We found 29 differentially expressed miRNAs (8 upregulated and 21 downregulated) and 758 differentially expressed mRNAs (542 upregulated and 216 downregulated) in MIA offspring compared to controls. Based on expression levels of the predicted target genes, 18 downregulated miRNAs (340 target genes) and three upregulated miRNAs (60 target genes) were found to be significantly enriched among the differentially expressed genes. miRNA and target gene interactions were most significant between mmu‐miR‐466i‐3p and Hfm1 (ATP‐dependent DNA helicase homolog), and between mmu‐miR‐877‐3p and Aqp6 (aquaporin 6). Interpretation Our results provide novel information regarding miRNA expression changes and their putative targets in the early postnatal period of brain development. Further studies will be needed to evaluate potential pathogenic roles of the dysregulated miRNAs.
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Affiliation(s)
- Jun-Sang Sunwoo
- Department of Neurology Soonchunhyang University College of Medicine Seoul South Korea
| | | | - Soon-Tae Lee
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea.,Program in Neuroscience Seoul National University College of Medicine Seoul South Korea
| | - Jangsup Moon
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea.,Program in Neuroscience Seoul National University College of Medicine Seoul South Korea.,Department of Neurosurgery Seoul National University Hospital Seoul South Korea
| | - Jung-Suk Yu
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea
| | - Dong-Kyu Park
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea
| | - Ji-Yeon Bae
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea
| | - Doo Young Lee
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea
| | - Sangwoo Kim
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea
| | - Keun-Hwa Jung
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea.,Program in Neuroscience Seoul National University College of Medicine Seoul South Korea
| | - Kyung-Il Park
- Department of Neurology Seoul National University Hospital Healthcare System Gangnam Center Seoul South Korea
| | - Ki-Young Jung
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea.,Program in Neuroscience Seoul National University College of Medicine Seoul South Korea
| | - Manho Kim
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea.,Program in Neuroscience Seoul National University College of Medicine Seoul South Korea.,Protein Metabolism Medical Research Center Seoul National University College of Medicine Seoul South Korea
| | - Sang Kun Lee
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea.,Program in Neuroscience Seoul National University College of Medicine Seoul South Korea
| | - Kon Chu
- Laboratory for Neurotherapeutics Department of Neurology Comprehensive Epilepsy Center Biomedical Research Institute Seoul National University Hospital Seoul South Korea.,Program in Neuroscience Seoul National University College of Medicine Seoul South Korea
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22
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Crawford B, Craig Z, Mansell G, White I, Smith A, Spaull S, Imm J, Hannon E, Wood A, Yaghootkar H, Ji Y, Mullins N, Lewis CM, Mill J, Murphy TM. DNA methylation and inflammation marker profiles associated with a history of depression. Hum Mol Genet 2018; 27:2840-2850. [PMID: 29790996 PMCID: PMC6680088 DOI: 10.1093/hmg/ddy199] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/13/2022] Open
Abstract
Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n = 100) and individuals without a history of depression (n = 100) using the Illumina 450K microarray. Our analysis identified six significant (Šidák corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Šidák corrected P = 1.27 × 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples, respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype.
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Affiliation(s)
- Bethany Crawford
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Zoe Craig
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Isobel White
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Adam Smith
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Steve Spaull
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Jennifer Imm
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Andrew Wood
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Hanieh Yaghootkar
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Yingjie Ji
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | | | - Niamh Mullins
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- Division of Genetics and Molecular Medicine, King’s College London, London SE1 9RT, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Therese M Murphy
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
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23
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Pascarella A, Ferrandino G, Credendino SC, Moccia C, D'Angelo F, Miranda B, D'Ambrosio C, Bielli P, Spadaro O, Ceccarelli M, Scaloni A, Sette C, De Felice M, De Vita G, Amendola E. DNAJC17 is localized in nuclear speckles and interacts with splicing machinery components. Sci Rep 2018; 8:7794. [PMID: 29773831 PMCID: PMC5958099 DOI: 10.1038/s41598-018-26093-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 05/04/2018] [Indexed: 01/23/2023] Open
Abstract
DNAJC17 is a heat shock protein (HSP40) family member, identified in mouse as susceptibility gene for congenital hypothyroidism. DNAJC17 knockout mouse embryos die prior to implantation. In humans, germline homozygous mutations in DNAJC17 have been found in syndromic retinal dystrophy patients, while heterozygous mutations represent candidate pathogenic events for myeloproliferative disorders. Despite widespread expression and involvement in human diseases, DNAJC17 function is still poorly understood. Herein, we have investigated its function through high-throughput transcriptomic and proteomic approaches. DNAJC17-depleted cells transcriptome highlighted genes involved in general functional categories, mainly related to gene expression. Conversely, DNAJC17 interactome can be classified in very specific functional networks, with the most enriched one including proteins involved in splicing. Furthermore, several splicing-related interactors, were independently validated by co-immunoprecipitation and in vivo co-localization. Accordingly, co-localization of DNAJC17 with SC35, a marker of nuclear speckles, further supported its interaction with spliceosomal components. Lastly, DNAJC17 up-regulation enhanced splicing efficiency of minigene reporter in live cells, while its knockdown induced perturbations of splicing efficiency at whole genome level, as demonstrated by specific analysis of RNAseq data. In conclusion, our study strongly suggests a role of DNAJC17 in splicing-related processes and provides support to its recognized essential function in early development.
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Affiliation(s)
- A Pascarella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - G Ferrandino
- Istituto di Ricerche Genetiche G. Salvatore, Biogem s.c.ar.l, Ariano Irpino (AV), Italy
| | - S C Credendino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - C Moccia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - F D'Angelo
- Istituto di Ricerche Genetiche G. Salvatore, Biogem s.c.ar.l, Ariano Irpino (AV), Italy
| | - B Miranda
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - C D'Ambrosio
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Napoli, Italy
| | - P Bielli
- Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143, Rome, Italy.,Department of Biomedicine and Prevention, Università di Roma Tor Vergata, 00133, Rome, Italy
| | - O Spadaro
- Istituto di Ricerche Genetiche G. Salvatore, Biogem s.c.ar.l, Ariano Irpino (AV), Italy
| | - M Ceccarelli
- Istituto di Ricerche Genetiche G. Salvatore, Biogem s.c.ar.l, Ariano Irpino (AV), Italy
| | - A Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Napoli, Italy
| | - C Sette
- Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143, Rome, Italy.,Institute of Human Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - M De Felice
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy.,Istituto di Ricerche Genetiche G. Salvatore, Biogem s.c.ar.l, Ariano Irpino (AV), Italy
| | - G De Vita
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy.
| | - E Amendola
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy.
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24
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Zhang R, Zhou J, Ren J, Sun S, Di Y, Wang H, An X, Zhang K, Zhang J, Qian Z, Shi M, Qiao Y, Ren W, Tian Y. Transcriptional and splicing dysregulation in the prefrontal cortex in valproic acid rat model of autism. Reprod Toxicol 2018; 77:53-61. [PMID: 29427782 DOI: 10.1016/j.reprotox.2018.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 01/02/2023]
Abstract
Gene-environmental interaction could be the major cause of autism. The aim of the current study is to detect the effects of valproic acid on gene expression profiles and alternatively spliced genes in the prefrontal cortex in rat models of autism. Female rats received a single intraperitoneal injection of 600 mg/kg valproic acid at day 12.5 post-conception, and controls were injected with saline. Only male offspring were employed in the current study. RNA sequencing was used to investigate transcriptome in the prefrontal cortex of VPA-exposed rats. There were 3228 differently expressed genes and 637 alternative spliced genes, in VPA rats compared to controls. Pathways enrichment among the differently expressed genes and alternatively spliced genes were associated with neurological diseases and neural system development. The results implied VPA affected transcriptional and splicing events genome-wide and the transcriptional and splicing events may be associated with the autistic behaviors of VPA rats.
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Affiliation(s)
- Ruoxin Zhang
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Xi'an, Shaanxi, 710062, China; College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Jinlong Zhou
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Junrong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Siqi Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Yuanyuan Di
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Hanyu Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Xiaoqin An
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Kexin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Junfeng Zhang
- Department of Anatomy, Xi'an Medical University, Xi'an, Shaanxi, 710021, China
| | - Zhaoqiang Qian
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Xi'an, Shaanxi, 710062, China
| | - Meimei Shi
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Xi'an, Shaanxi, 710062, China
| | - Yanning Qiao
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Xi'an, Shaanxi, 710062, China
| | - Wei Ren
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Xi'an, Shaanxi, 710062, China
| | - Yingfang Tian
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Xi'an, Shaanxi, 710062, China; College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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25
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Reble E, Dineen A, Barr CL. The contribution of alternative splicing to genetic risk for psychiatric disorders. GENES BRAIN AND BEHAVIOR 2017; 17:e12430. [PMID: 29052934 DOI: 10.1111/gbb.12430] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/25/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022]
Abstract
A genetic contribution to psychiatric disorders has clearly been established and genome-wide association studies now provide the location of risk genes and genetic variants associated with risk. However, the mechanism by which these genes and variants contribute to psychiatric disorders is mostly undetermined. This is in part because non-synonymous protein coding changes cannot explain the majority of variants associated with complex genetic traits. Based on this, it is predicted that these variants are causing gene expression changes, including changes to alternative splicing. Genetic changes influencing alternative splicing have been identified as risk factors in Mendelian disorders; however, currently there is a paucity of research on the role of alternative splicing in complex traits. This stems partly from the difficulty of predicting the role of genetic variation in splicing. Alterations to canonical splice site sequences, nucleotides adjacent to splice junctions, and exonic and intronic splicing regulatory sequences can influence splice site choice. Recent studies have identified global changes in alternatively spliced transcripts in brain tissues, some of which correlate with altered levels of splicing trans factors. Disease-associated variants have also been found to affect cis-acting splicing regulatory sequences and alter the ratio of alternatively spliced transcripts. These findings are reviewed here, as well as the current datasets and resources available to study alternative splicing in psychiatric disorders. Identifying and understanding risk variants that cause alternative splicing is critical to understanding the mechanisms of risk as well as to pave the way for new therapeutic options.
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Affiliation(s)
- E Reble
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - A Dineen
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C L Barr
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
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26
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Tseng E, Tang HT, AlOlaby RR, Hickey L, Tassone F. Altered expression of the FMR1 splicing variants landscape in premutation carriers. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1117-1126. [PMID: 28888471 DOI: 10.1016/j.bbagrm.2017.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 01/17/2023]
Abstract
FMR1 premutation carriers (55-200 CGG repeats) are at risk for developing Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), an adult onset neurodegenerative disorder. Approximately 20% of female carriers will develop Fragile X-associated Primary Ovarian Insufficiency (FXPOI), in addition to a number of clinical problems affecting premutation carriers throughout their life span. Marked elevation in FMR1 mRNA levels have been observed with premutation alleles resulting in RNA toxicity, the leading molecular mechanism proposed for the FMR1 associated disorders observed in premutation carriers. The FMR1 gene undergoes alternative splicing and we have recently reported that the relative abundance of all FMR1 mRNA isoforms is significantly increased in premutation carriers. In this study, we characterized the transcriptional FMR1 isoforms distribution pattern in different tissues and identified a total of 49 isoforms, some of which observed only in premutation carriers and which might play a role in the pathogenesis of FXTAS. Further, we investigated the distribution pattern and expression levels of the FMR1 isoforms in asymptomatic premutation carriers and in those with FXTAS and found no significant differences between the two groups. Our findings suggest that the characterization of the expression levels of the different FMR1 isoforms is fundamental for understanding the regulation of the FMR1 gene as imbalance in their expression could lead to an altered functional diversity with neurotoxic consequences. Their characterization will also help to elucidating the mechanism(s) by which "toxic gain of function" of the FMR1 mRNA may play a role in FXTAS and/or in the other FMR1-associated conditions.
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Affiliation(s)
| | - Hiu-Tung Tang
- Biochemistry and Molecular Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Reem Rafik AlOlaby
- Biochemistry and Molecular Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Luke Hickey
- Pacific Biosciences, Inc., Menlo Park, CA 94025, USA
| | - Flora Tassone
- Biochemistry and Molecular Medicine, UC Davis, Sacramento, CA 95817, USA; MIND Institute, UC Davis, Sacramento, CA 95817, USA.
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27
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Khoshnam SE, Winlow W, Farbood Y, Moghaddam HF, Farzaneh M. Emerging Roles of microRNAs in Ischemic Stroke: As Possible Therapeutic Agents. J Stroke 2017; 19:166-187. [PMID: 28480877 PMCID: PMC5466283 DOI: 10.5853/jos.2016.01368] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/08/2017] [Accepted: 02/27/2017] [Indexed: 01/06/2023] Open
Abstract
Stroke is one of the leading causes of death and physical disability worldwide. The consequences of stroke injuries are profound and persistent, causing in considerable burden to both the individual patient and society. Current treatments for ischemic stroke injuries have proved inadequate, partly owing to an incomplete understanding of the cellular and molecular changes that occur following ischemic stroke. MicroRNAs (miRNA) are endogenously expressed RNA molecules that function to inhibit mRNA translation and have key roles in the pathophysiological processes contributing to ischemic stroke injuries. Potential therapeutic areas to compensate these pathogenic processes include promoting angiogenesis, neurogenesis and neuroprotection. Several miRNAs, and their target genes, are recognized to be involved in these recoveries and repair mechanisms. The capacity of miRNAs to simultaneously regulate several target genes underlies their unique importance in ischemic stroke therapeutics. In this Review, we focus on the role of miRNAs as potential diagnostic and prognostic biomarkers, as well as promising therapeutic agents in cerebral ischemic stroke.
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Affiliation(s)
- Seyed Esmaeil Khoshnam
- Department of Physiology, Faculty of Medicine, Physiology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - William Winlow
- Dipartimento di Biologia, Università degli Studi di Napoli, Napoli, Italia.,Institute of Ageing and Chronic Diseases, University of Liverpool, Liverpool, UK
| | - Yaghoob Farbood
- Department of Physiology, Faculty of Medicine, Physiology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hadi Fathi Moghaddam
- Department of Physiology, Faculty of Medicine, Physiology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Farzaneh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Delineating the Common Biological Pathways Perturbed by ASD's Genetic Etiology: Lessons from Network-Based Studies. Int J Mol Sci 2017; 18:ijms18040828. [PMID: 28420080 PMCID: PMC5412412 DOI: 10.3390/ijms18040828] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 12/26/2022] Open
Abstract
In recent decades it has become clear that Autism Spectrum Disorder (ASD) possesses a diverse and heterogeneous genetic etiology. Aberrations in hundreds of genes have been associated with ASD so far, which include both rare and common variations. While one may expect that these genes converge on specific common molecular pathways, which drive the development of the core ASD characteristics, the task of elucidating these common molecular pathways has been proven to be challenging. Several studies have combined genetic analysis with bioinformatical techniques to uncover molecular mechanisms that are specifically targeted by autism-associated genetic aberrations. Recently, several analysis have suggested that particular signaling mechanisms, including the Wnt and Ca2+/Calmodulin-signaling pathways are often targeted by autism-associated mutations. In this review, we discuss several studies that determine specific molecular pathways affected by autism-associated mutations, and then discuss more in-depth into the biological roles of a few of these pathways, and how they may be involved in the development of ASD. Considering that these pathways may be targeted by specific pharmacological intervention, they may prove to be important therapeutic targets for the treatment of ASD.
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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:322-336.e5. [PMID: 28392072 PMCID: PMC5405110 DOI: 10.1016/j.neuron.2017.03.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/02/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Recent progress revealed the complexity of RNA processing and its association to human disorders. Here, we unveil a new facet of this complexity. Complete loss of function of the ubiquitous splicing factor SFPQ affects zebrafish motoneuron differentiation cell autonomously. In addition to its nuclear localization, the protein unexpectedly localizes to motor axons. The cytosolic version of SFPQ abolishes motor axonal defects, rescuing key transcripts, and restores motility in the paralyzed sfpq null mutants, indicating a non-nuclear processing role in motor axons. Novel variants affecting the conserved coiled-coil domain, so far exclusively found in fALS exomes, specifically affect the ability of SFPQ to localize in axons. They broadly rescue morphology and motility in the zebrafish mutant, but alter motor axon morphology, demonstrating functional requirement for axonal SFPQ. Altogether, we uncover the axonal function of the splicing factor SFPQ in motor development and highlight the importance of the coiled-coil domain in this process. Video Abstract
SFPQ splicing factor is present in motor axons Non-nuclear SFPQ is able to drive axon maturation and connectivity Loss of axonal SFPQ affects axonal morphology Coiled-coil domain of the protein is important for non-nuclear localization
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Affiliation(s)
- Swapna Thomas-Jinu
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Victoria Snowden
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eric Blanc
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Chun-Hao Wong
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Holger Bielen
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, University of Sydney, Concord Hospital, Sydney, NSW 2139, Australia
| | - Alejandro Pan-Vazquez
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Archa H Fox
- School of Anatomy, Physiology, and Human Biology, University of Western Australia, Crawley, WA 6009, Australia; Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
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SFPQ associates to LSD1 and regulates the migration of newborn pyramidal neurons in the developing cerebral cortex. Int J Dev Neurosci 2016; 57:1-11. [PMID: 28034769 DOI: 10.1016/j.ijdevneu.2016.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
The development of the cerebral cortex requires the coordination of multiple processes ranging from the proliferation of progenitors to the migration and establishment of connectivity of the newborn neurons. Epigenetic regulation carried out by the COREST/LSD1 complex has been identified as a mechanism that regulates the development of pyramidal neurons of the cerebral cortex. We now identify the association of the multifunctional RNA-binding protein SFPQ to LSD1 during the development of the cerebral cortex. In vivo reduction of SFPQ dosage by in utero electroporation of a shRNA results in impaired radial migration of newborn pyramidal neurons, in a similar way to that observed when COREST or LSD1 expressions are decreased. Diminished SFPQ expression also associates to decreased proliferation of progenitor cells, while it does not affect the acquisition of neuronal fate. These results are compatible with the idea that SFPQ, plays an important role regulating proliferation and migration during the development of the cerebral cortex.
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Shen L, Lin Y, Sun Z, Yuan X, Chen L, Shen B. Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers. Sci Rep 2016; 6:39663. [PMID: 28000768 PMCID: PMC5175196 DOI: 10.1038/srep39663] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/24/2016] [Indexed: 01/02/2023] Open
Abstract
Autism spectrum disorder (ASD) is a severe neurodevelopmental disease with a high incidence and effective biomarkers are urgently needed for its diagnosis. A few previous studies have reported the detection of miRNA biomarkers for autism diagnosis, especially those based on bioinformatics approaches. In this study, we developed a knowledge-guided bioinformatics model for identifying autism miRNA biomarkers. We downloaded gene expression microarray data from the GEO Database and extracted genes with expression levels that differed in ASD and the controls. We then constructed an autism-specific miRNA-mRNA network and inferred candidate autism biomarker miRNAs based on their regulatory modes and functions. We defined a novel parameter called the autism gene percentage as autism-specific knowledge to further facilitate the identification of autism-specific biomarker miRNAs. Finally, 11 miRNAs were screened as putative autism biomarkers, where eight miRNAs (72.7%) were significantly dysregulated in ASD samples according to previous reports. Functional enrichment results indicated that the targets of the identified miRNAs were enriched in autism-associated pathways, such as Wnt signaling (in KEGG and IPA), cell cycle (in KEGG), and glioblastoma multiforme signaling (in IPA), thereby supporting the predictive power of our model.
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Affiliation(s)
- Li Shen
- Center for Systems Biology, Soochow University, Suzhou, 215006, China.,Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Zhandong Sun
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Xuye Yuan
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Luonan Chen
- Key laboratory of Systems Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
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32
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De-novo 'pure' partial trisomy (6)(p22.3→pter): a case report and review of the literature. Clin Dysmorphol 2016; 26:26-32. [PMID: 27759572 DOI: 10.1097/mcd.0000000000000160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Partial trisomy of the short arm of chromosome 6 is a rare and clinically distinct syndrome. The breakpoints have been found to be variable ranging from bands 6p11 to 6p25. This study reports partial trisomy for 6p22.3→pter in a 2-year-old boy referred with a complaint of developmental delay and facial dysmorphism. Conventional cytogenetic analysis showed the presence of an abnormal chromosome 5 resulting from an unbalanced translocation in the proband. Array comparative genomic hybridization revealed trisomy of distal 6p which was confirmed by fluorescence in situ hybridization using subtelomeric probes for chromosomes 5 and 6. A comparison of the phenotypic features in similar cases of trisomy for different segments of 6p will facilitate an accurate karyotype-phenotype correlation and, subsequently, in the identification of the candidate genes through molecular characterization of the potential genes mapped to these loci.
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33
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Stamova B, Ander BP, Barger N, Sharp FR, Schumann CM. Specific Regional and Age-Related Small Noncoding RNA Expression Patterns Within Superior Temporal Gyrus of Typical Human Brains Are Less Distinct in Autism Brains. J Child Neurol 2015; 30:1930-46. [PMID: 26350727 PMCID: PMC4647182 DOI: 10.1177/0883073815602067] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 07/28/2015] [Indexed: 12/16/2022]
Abstract
Small noncoding RNAs play a critical role in regulating messenger RNA throughout brain development and when altered could have profound effects leading to disorders such as autism spectrum disorders (ASD). We assessed small noncoding RNAs, including microRNA and small nucleolar RNA, in superior temporal sulcus association cortex and primary auditory cortex in typical and ASD brains from early childhood to adulthood. Typical small noncoding RNA expression profiles were less distinct in ASD, both between regions and changes with age. Typical micro-RNA coexpression associations were absent in ASD brains. miR-132, miR-103, and miR-320 micro-RNAs were dysregulated in ASD and have previously been associated with autism spectrum disorders. These diminished region- and age-related micro-RNA expression profiles are in line with previously reported findings of attenuated messenger RNA and long noncoding RNA in ASD brain. This study demonstrates alterations in superior temporal sulcus in ASD, a region implicated in social impairment, and is the first to demonstrate molecular alterations in the primary auditory cortex.
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Affiliation(s)
- Boryana Stamova
- Department of Neurology, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Bradley P. Ander
- Department of Neurology, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Nicole Barger
- Department of Psychiatry & Behavioral Sciences, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Frank R. Sharp
- Department of Neurology, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Cynthia M. Schumann
- Department of Psychiatry & Behavioral Sciences, University of California at Davis, MIND Institute, Sacramento, CA, USA,Cynthia M. Schumann, PhD, Departments of Psychiatry & Behavioral Sciences, University of California at Davis, MIND Institute, 2805 50th Street, Sacramento, CA 95817, USA.
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34
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Chapman NH, Nato AQ, Bernier R, Ankenman K, Sohi H, Munson J, Patowary A, Archer M, Blue EM, Webb SJ, Coon H, Raskind WH, Brkanac Z, Wijsman EM. Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes. Hum Genet 2015; 134:1055-68. [PMID: 26204995 PMCID: PMC4578871 DOI: 10.1007/s00439-015-1585-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/11/2015] [Indexed: 12/26/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders, characterized by impairment in communication and social interactions, and by repetitive behaviors. ASDs are highly heritable, and estimates of the number of risk loci range from hundreds to >1000. We considered 7 extended families (size 12-47 individuals), each with ≥3 individuals affected by ASD. All individuals were genotyped with dense SNP panels. A small subset of each family was typed with whole exome sequence (WES). We used a 3-step approach for variant identification. First, we used family-specific parametric linkage analysis of the SNP data to identify regions of interest. Second, we filtered variants in these regions based on frequency and function, obtaining exactly 200 candidates. Third, we compared two approaches to narrowing this list further. We used information from the SNP data to impute exome variant dosages into those without WES. We regressed affected status on variant allele dosage, using pedigree-based kinship matrices to account for relationships. The p value for the test of the null hypothesis that variant allele dosage is unrelated to phenotype was used to indicate strength of evidence supporting the variant. A cutoff of p = 0.05 gave 28 variants. As an alternative third filter, we required Mendelian inheritance in those with WES, resulting in 70 variants. The imputation- and association-based approach was effective. We identified four strong candidate genes for ASD (SEZ6L, HISPPD1, FEZF1, SAMD11), all of which have been previously implicated in other studies, or have a strong biological argument for their relevance.
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Affiliation(s)
- Nicola H Chapman
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Alejandro Q Nato
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Katy Ankenman
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Harkirat Sohi
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Center on Child Development and Disability, University of Washington, Seattle, WA, USA
| | - Ashok Patowary
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Marilyn Archer
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Elizabeth M Blue
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Sara Jane Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Center on Child Development and Disability, University of Washington, Seattle, WA, USA
| | - Hilary Coon
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Department of Psychiatry, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Wendy H Raskind
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Ellen M Wijsman
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- University of Washington, University of Washington Tower, T15, 4333 Brooklyn Ave, NE, BOX 359460, Seattle, WA, 98195-9460, USA.
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35
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Yarosh CA, Tapescu I, Thompson MG, Qiu J, Mallory MJ, Fu XD, Lynch KW. TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells. Nucleic Acids Res 2015; 43:9006-16. [PMID: 26261210 PMCID: PMC4605305 DOI: 10.1093/nar/gkv816] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/31/2015] [Indexed: 01/08/2023] Open
Abstract
PSF (a.k.a. SFPQ) is a ubiquitously expressed, essential nuclear protein with important roles in DNA damage repair and RNA biogenesis. In stimulated T cells, PSF binds to and suppresses the inclusion of CD45 exon 4 in the final mRNA; however, in resting cells, TRAP150 binds PSF and prevents access to the CD45 RNA, though the mechanism for this inhibition has remained unclear. Here, we show that TRAP150 binds a region encompassing the RNA recognition motifs (RRMs) of PSF using a previously uncharacterized, 70 residue region we have termed the PSF-interacting domain (PID). TRAP150's PID directly inhibits the interaction of PSF RRMs with RNA, which is mediated through RRM2. However, interaction of PSF with TRAP150 does not appear to inhibit the dimerization of PSF with other Drosophila Behavior, Human Splicing (DBHS) proteins, which is also dependent on RRM2. Finally, we use RASL-Seq to identify ∼40 T cell splicing events sensitive to PSF knockdown, and show that for the majority of these, PSF's effect is antagonized by TRAP150. Together these data suggest a model in which TRAP150 interacts with dimeric PSF to block access of RNA to RRM2, thereby regulating the activity of PSF toward a broad set of splicing events in T cells.
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Affiliation(s)
- Christopher A Yarosh
- Department of Biochemistry and Biophysics Perelman, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Iulia Tapescu
- Department of Biochemistry and Biophysics Perelman, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew G Thompson
- Department of Biochemistry and Biophysics Perelman, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jinsong Qiu
- Department of Cell and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Michael J Mallory
- Department of Biochemistry and Biophysics Perelman, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiang-Dong Fu
- Department of Cell and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics Perelman, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Chen X, Long F, Cai B, Chen X, Chen G. A novel relationship for schizophrenia, bipolar and major depressive disorder Part 7: A hint from chromosome 7 high density association screen. Behav Brain Res 2015; 293:241-51. [PMID: 26192912 DOI: 10.1016/j.bbr.2015.06.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/25/2015] [Accepted: 06/25/2015] [Indexed: 11/18/2022]
Abstract
Convergent evidence from genetics, symptology and psychopharmacology imply that there are intrinsic connection between schizophrenia (SCZ), bipolar disorder (BPD) and major depressive disorder (MDD). Also, any two or even three of these disorders could co-existe in some families. A total of 47,144 single nucleotide polymorphism (SNPs) on chromosome 7 were genotyped by Affymetrix Genome-Wide Human SNP array 6.0 on 119 SCZ, 253 BPD (type-I), 177 MDD, and 1000 controls. Associated SNP loci were comprehensively revealed and outstanding susceptibility genes were identified including CNTNAP2. a neurexin family gene. Unexpectedly, flanking genes for up to 94.74 % of of the associated SNPs were replicated (P≤9.9 E-8) in an enlarged cohort of 986 SCZ patients. Considering other convergent evidence, our results further implicate that BPD and MDD are subtypes of SCZ.
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Affiliation(s)
- Xing Chen
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, People's Republic of China
| | - Feng Long
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, People's Republic of China
| | - Bin Cai
- CapitalBio corporation, 18 Life Science Parkway, Changping District, Beijing 102206, People's Republic of China
| | - Xiaohong Chen
- CapitalBio corporation, 18 Life Science Parkway, Changping District, Beijing 102206, People's Republic of China
| | - Gang Chen
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, People's Republic of China.
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Ander BP, Barger N, Stamova B, Sharp FR, Schumann CM. Atypical miRNA expression in temporal cortex associated with dysregulation of immune, cell cycle, and other pathways in autism spectrum disorders. Mol Autism 2015; 6:37. [PMID: 26146533 PMCID: PMC4491207 DOI: 10.1186/s13229-015-0029-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/27/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASDs) likely involve dysregulation of multiple genes related to brain function and development. Abnormalities in individual regulatory small non-coding RNA (sncRNA), including microRNA (miRNA), could have profound effects upon multiple functional pathways. We assessed whether a brain region associated with core social impairments in ASD, the superior temporal sulcus (STS), would evidence greater transcriptional dysregulation of sncRNA than adjacent, yet functionally distinct, primary auditory cortex (PAC). METHODS We measured sncRNA expression levels in 34 samples of postmortem brain from STS and PAC to find differentially expressed sncRNA in ASD compared with control cases. For differentially expressed miRNA, we further analyzed their predicted mRNA targets and carried out functional over-representation analysis of KEGG pathways to examine their functional significance and to compare our findings to reported alterations in ASD gene expression. RESULTS Two mature miRNAs (miR-4753-5p and miR-1) were differentially expressed in ASD relative to control in STS and four (miR-664-3p, miR-4709-3p, miR-4742-3p, and miR-297) in PAC. In both regions, miRNA were functionally related to various nervous system, cell cycle, and canonical signaling pathways, including PI3K-Akt signaling, previously implicated in ASD. Immune pathways were only disrupted in STS. snoRNA and pre-miRNA were also differentially expressed in ASD brain. CONCLUSIONS Alterations in sncRNA may underlie dysregulation of molecular pathways implicated in autism. sncRNA transcriptional abnormalities in ASD were apparent in STS and in PAC, a brain region not directly associated with core behavioral impairments. Disruption of miRNA in immune pathways, frequently implicated in ASD, was unique to STS.
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Affiliation(s)
- Bradley P Ander
- Department of Neurology, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Nicole Barger
- Department of Psychiatry & Behavioral Sciences, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Boryana Stamova
- Department of Neurology, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Frank R Sharp
- Department of Neurology, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Cynthia M Schumann
- Department of Psychiatry & Behavioral Sciences, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
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38
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Codina-Solà M, Rodríguez-Santiago B, Homs A, Santoyo J, Rigau M, Aznar-Laín G, Del Campo M, Gener B, Gabau E, Botella MP, Gutiérrez-Arumí A, Antiñolo G, Pérez-Jurado LA, Cuscó I. Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders. Mol Autism 2015; 6:21. [PMID: 25969726 PMCID: PMC4427998 DOI: 10.1186/s13229-015-0017-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/19/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders with high heritability. Recent findings support a highly heterogeneous and complex genetic etiology including rare de novo and inherited mutations or chromosomal rearrangements as well as double or multiple hits. METHODS We performed whole-exome sequencing (WES) and blood cell transcriptome by RNAseq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. RESULTS We detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L, KCNV1, CUL3, and PTEN) and two inherited X-linked variants (MAOA and CDKL5). Transcriptomic analyses allowed the identification of intronic causative mutations missed by the usual filtering of WES and revealed functional consequences of some rare mutations. These included aberrant transcripts (PTEN, POLR3C), deregulated expression in 1.7% of mutated genes (that is, SEMA6B, MECP2, ANK3, CREBBP), allele-specific expression (FUS, MTOR, TAF1C), and non-sense-mediated decay (RIT1, ALG9). The analysis of rare inherited variants showed enrichment in relevant pathways such as the PI3K-Akt signaling and the axon guidance. CONCLUSIONS Integrative analysis of WES and blood RNAseq data has proven to be an efficient strategy to identify likely monogenic forms of ASD (19% in our cohort), as well as additional rare inherited mutations that can contribute to ASD risk in a multifactorial manner. Blood transcriptomic data, besides validating 88% of expressed variants, allowed the identification of missed intronic mutations and revealed functional correlations of genetic variants, including changes in splicing, expression levels, and allelic expression.
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Affiliation(s)
- Marta Codina-Solà
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | | | - Aïda Homs
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | - Javier Santoyo
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), C/Albert Einstein, Cartuja Scientific and Technology Park, INSUR Builiding, Sevilla, 41092 Spain
| | - Maria Rigau
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain
| | - Gemma Aznar-Laín
- Pediatric Neurology, Hospital del Mar, Passeig Marítim 25-29, Barcelona, 08003 Spain
| | - Miguel Del Campo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain ; Servicio de Genética, Hospital Vall d'Hebron, Passeig Vall d'Hebron, 119-129, Barcelona, 08015 Spain
| | - Blanca Gener
- Genetics Service, BioCruces Health Research Institute, Hospital Universitario Cruces, Plaza de Cruces 12, Barakaldo, Bizkaia 48093 Spain
| | - Elisabeth Gabau
- Pediatrics Service, Corporació Sanitària Parc Taulí, Parc Taulí 1, Sabadell, 08208 Spain
| | - María Pilar Botella
- Pediatric Neurology, Hospital de Txagorritxu, C/José de Atxotegui s/n, Victoria-Gasteiz, 01009 Spain
| | - Armand Gutiérrez-Arumí
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | - Guillermo Antiñolo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain ; Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), C/Albert Einstein, Cartuja Scientific and Technology Park, INSUR Builiding, Sevilla, 41092 Spain ; Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Avda Manuel Siurot s/n, Sevilla, 41013 Spain
| | - Luis Alberto Pérez-Jurado
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | - Ivon Cuscó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
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Yarosh CA, Iacona JR, Lutz CS, Lynch KW. PSF: nuclear busy-body or nuclear facilitator? WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:351-67. [PMID: 25832716 PMCID: PMC4478221 DOI: 10.1002/wrna.1280] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 01/25/2023]
Abstract
PTB-associated splicing factor (PSF) is an abundant and essential nucleic acid-binding protein that participates in a wide range of gene regulatory processes and cellular response pathways. At the protein level, PSF consists of multiple domains, many of which remain poorly characterized. Although grouped in a family with the proteins p54nrb/NONO and PSPC1 based on sequence homology, PSF contains additional protein sequence not included in other family members. Consistently, PSF has also been implicated in functions not ascribed to p54nrb/NONO or PSPC1. Here, we provide a review of the cellular activities in which PSF has been implicated and what is known regarding the mechanisms by which PSF functions in each case. We propose that the complex domain arrangement of PSF allows for its diversity of function and integration of activities. Finally, we discuss recent evidence that individual activities of PSF can be regulated independently from one another through the activity of domain-specific co-factors.
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Affiliation(s)
- Christopher A Yarosh
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph R Iacona
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences-New Jersey Medical School, Newark, NJ, USA
| | - Carol S Lutz
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences-New Jersey Medical School, Newark, NJ, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
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Liu P, Zhao H, Wang R, Wang P, Tao Z, Gao L, Yan F, Liu X, Yu S, Ji X, Luo Y. MicroRNA-424 protects against focal cerebral ischemia and reperfusion injury in mice by suppressing oxidative stress. Stroke 2014; 46:513-9. [PMID: 25523055 DOI: 10.1161/strokeaha.114.007482] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE We previously showed that the microRNA miR-424 protects against permanent cerebral ischemic injury in mice by suppressing microglia activation. This study investigated the role of miR-424 in transient cerebral ischemia in mice with a focus on oxidative stress-induced neuronal injury. METHODS Transient cerebral ischemia was induced in C57/BL6 mice by middle cerebral artery occlusion for 1 hour followed by reperfusion (ischemia/reperfusion). The miR-424 level in the peri-infarct cortex was quantified. Mice were also administered miR-424 angomir by intracerebroventricular injection. Cerebral infarct volume, neuronal apoptosis, and levels of oxidative stress markers and antioxidants were evaluated. In an in vitro experiment, primary cortical neurons were exposed to H2O2 and treated with miR-424 angomir, nuclear factor erythroid 2-related factor 2 siRNA, and superoxide dismutase (SOD) inhibitor; cell activity, lactate dehydrogenase release, malondialdehyde level, and manganese (Mn)SOD activity were then evaluated. RESULTS MiR-424 levels in the peri-infarct cortex increased at 1 and 4 hours then decreased 24 hours after reperfusion. Treatment with miR-424 decreased infarct volume and inhibited neuronal apoptosis after ischemia/reperfusion, reduced reactive oxygen species and malondialdehyde levels in the cortex, and increased the expression and activation of MnSOD as well as the expression of extracellular SOD and the redox-sensitive transcription factor nuclear factor erythroid 2-related factor. In neuronal cultures, miR-424 treatment abrogated H2O2-induced injury, as evidenced by decreased lactate dehydrogenase leakage and malondialdehyde level and increased cell viability and MnSOD activity; the protective effects of miR-424 against oxidative stress were reversed by nuclear factor erythroid 2-related factor knockdown and SOD inhibitor treatment. CONCLUSIONS MiR-424 protects against transient cerebral ischemia/reperfusion injury by inhibiting oxidative stress.
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Affiliation(s)
- Ping Liu
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Haiping Zhao
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Rongliang Wang
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Peng Wang
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Zhen Tao
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Li Gao
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Feng Yan
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Xiangrong Liu
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Shun Yu
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Xunming Ji
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.)
| | - Yumin Luo
- From the Cerebrovascular Diseases Research Institute and Department of Neurology, Xuan Wu Hospital of Capital Medical University (P.L., H.Z., R.W., Z.T., L.G., F.Y., X.L., X.J., Y.L.); Beijing Institute for Brain Disorders, Beijing, China (X.J., Y.L.); Beijing Geriatric Medical Research Center (P.L., H.Z., R.W., Z.T., F.Y., X.L., X.J., Y.L.) and Key Laboratory of Neurodegenerative Diseases of Ministry of Education, and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases (P.L., H.Z., R.W., Z.T., F.Y., X.L., S.Y., X.J., Y.L.), Beijing, China; and Key Laboratory of Neurodegenerative Diseases of Liaoning Province, Department of Neurobiology, Liaoning Medical University, Jinzhou, China (P.W.).
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Frye RE, James SJ. Metabolic pathology of autism in relation to redox metabolism. Biomark Med 2014; 8:321-30. [PMID: 24712422 DOI: 10.2217/bmm.13.158] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
An imbalance in glutathione-dependent redox metabolism has been shown to be associated with autism spectrum disorder (ASD). Glutathione synthesis and intracellular redox balance are linked to folate and methylation metabolism, metabolic pathways that have also been shown to be abnormal in ASD. Together, these metabolic abnormalities define a distinct ASD endophenotype that is closely associated with genetic, epigenetic and mitochondrial abnormalities, as well as environmental factors related to ASD. Biomarkers that reflect these metabolic abnormalities will be discussed in the context of an ASD metabolic endophenotype that may lead to a better understanding of the pathophysiological mechanisms underlying core and associated ASD symptoms. Last, we discuss how these biomarkers have been used to guide the development of novel ASD treatments.
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Affiliation(s)
- Richard E Frye
- Arkansas Children's Hospital Research Institute, Department of Pediatrics, University of Arkansas for Medical Sciences, Slot 512-41B, 13 Children's Way, Little Rock, AR 72202, USA
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Jasien JM, Daimon CM, Wang R, Shapiro BK, Martin B, Maudsley S. The effects of aging on the BTBR mouse model of autism spectrum disorder. Front Aging Neurosci 2014; 6:225. [PMID: 25225482 PMCID: PMC4150363 DOI: 10.3389/fnagi.2014.00225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/08/2014] [Indexed: 01/11/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex heterogeneous neurodevelopmental disorder characterized by alterations in social functioning, communicative abilities, and engagement in repetitive or restrictive behaviors. The process of aging in individuals with autism and related neurodevelopmental disorders is not well understood, despite the fact that the number of individuals with ASD aged 65 and older is projected to increase by over half a million individuals in the next 20 years. To elucidate the effects of aging in the context of a modified central nervous system, we investigated the effects of age on the BTBR T + tf/j mouse, a well characterized and widely used mouse model that displays an ASD-like phenotype. We found that a reduction in social behavior persists into old age in male BTBR T + tf/j mice. We employed quantitative proteomics to discover potential alterations in signaling systems that could regulate aging in the BTBR mice. Unbiased proteomic analysis of hippocampal and cortical tissue of BTBR mice compared to age-matched wild-type controls revealed a significant decrease in brain derived neurotrophic factor and significant increases in multiple synaptic markers (spinophilin, Synapsin I, PSD 95, NeuN), as well as distinct changes in functional pathways related to these proteins, including “Neural synaptic plasticity regulation” and “Neurotransmitter secretion regulation.” Taken together, these results contribute to our understanding of the effects of aging on an ASD-like mouse model in regards to both behavior and protein alterations, though additional studies are needed to fully understand the complex interplay underlying aging in mouse models displaying an ASD-like phenotype.
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Affiliation(s)
- Joan M Jasien
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA ; Department of Neurology, Johns Hopkins University School of Medicine, Kennedy Krieger Institute Baltimore, MD, USA
| | - Caitlin M Daimon
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA
| | - Rui Wang
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA
| | - Bruce K Shapiro
- Department of Neurology, Johns Hopkins University School of Medicine, Kennedy Krieger Institute Baltimore, MD, USA
| | - Bronwen Martin
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA
| | - Stuart Maudsley
- Receptor Pharmacology Unit, Laboratory of Neurosciences, National Institute on Aging Baltimore, MD, USA ; VIB-Department of Molecular Genetics, University of Antwerp Antwerp, Belgium
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