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D'Incal CP, Van Rossem KE, De Man K, Konings A, Van Dijck A, Rizzuti L, Vitriolo A, Testa G, Gozes I, Vanden Berghe W, Kooy RF. Chromatin remodeler Activity-Dependent Neuroprotective Protein (ADNP) contributes to syndromic autism. Clin Epigenetics 2023; 15:45. [PMID: 36945042 PMCID: PMC10031977 DOI: 10.1186/s13148-023-01450-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individuals affected with autism often suffer additional co-morbidities such as intellectual disability. The genes contributing to autism cluster on a relatively limited number of cellular pathways, including chromatin remodeling. However, limited information is available on how mutations in single genes can result in such pleiotropic clinical features in affected individuals. In this review, we summarize available information on one of the most frequently mutated genes in syndromic autism the Activity-Dependent Neuroprotective Protein (ADNP). RESULTS Heterozygous and predicted loss-of-function ADNP mutations in individuals inevitably result in the clinical presentation with the Helsmoortel-Van der Aa syndrome, a frequent form of syndromic autism. ADNP, a zinc finger DNA-binding protein has a role in chromatin remodeling: The protein is associated with the pericentromeric protein HP1, the SWI/SNF core complex protein BRG1, and other members of this chromatin remodeling complex and, in murine stem cells, with the chromodomain helicase CHD4 in a ChAHP complex. ADNP has recently been shown to possess R-loop processing activity. In addition, many additional functions, for instance, in association with cytoskeletal proteins have been linked to ADNP. CONCLUSIONS We here present an integrated evaluation of all current aspects of gene function and evaluate how abnormalities in chromatin remodeling might relate to the pleiotropic clinical presentation in individual"s" with Helsmoortel-Van der Aa syndrome.
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Affiliation(s)
- Claudio Peter D'Incal
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Kirsten Esther Van Rossem
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Kevin De Man
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anthony Konings
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Ludovico Rizzuti
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Alessandro Vitriolo
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Giuseppe Testa
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Sackler School of Medicine, 727, 69978, Tel Aviv, Israel
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium.
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Karmon G, Sragovich S, Hacohen-Kleiman G, Ben-Horin-Hazak I, Kasparek P, Schuster B, Sedlacek R, Pasmanik-Chor M, Theotokis P, Touloumi O, Zoidou S, Huang L, Wu PY, Shi R, Kapitansky O, Lobyntseva A, Giladi E, Shapira G, Shomron N, Bereswill S, Heimesaat MM, Grigoriadis N, McKinney RA, Rubinstein M, Gozes I. Novel ADNP Syndrome Mice Reveal Dramatic Sex-Specific Peripheral Gene Expression With Brain Synaptic and Tau Pathologies. Biol Psychiatry 2022; 92:81-95. [PMID: 34865853 DOI: 10.1016/j.biopsych.2021.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/19/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND ADNP is essential for embryonic development. As such, de novo ADNP mutations lead to an intractable autism/intellectual disability syndrome requiring investigation. METHODS Mimicking humans, CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 editing produced mice carrying heterozygous Adnp p.Tyr718∗ (Tyr), a paralog of the most common ADNP syndrome mutation. Phenotypic rescue was validated by treatment with the microtubule/autophagy-protective ADNP fragment NAPVSIPQ (NAP). RESULTS RNA sequencing of spleens, representing a peripheral biomarker source, revealed Tyr-specific sex differences (e.g., cell cycle), accentuated in females (with significant effects on antigen processing and cellular senescence) and corrected by NAP. Differentially expressed, NAP-correctable transcripts, including the autophagy and microbiome resilience-linked FOXO3, were also deregulated in human patient-derived ADNP-mutated lymphoblastoid cells. There were also Tyr sex-specific microbiota signatures. Phenotypically, Tyr mice, similar to patients with ADNP syndrome, exhibited delayed development coupled with sex-dependent gait defects. Speech acquisition delays paralleled sex-specific mouse syntax abnormalities. Anatomically, dendritic spine densities/morphologies were decreased with NAP amelioration. These findings were replicated in the Adnp+/- mouse, including Foxo3 deregulation, required for dendritic spine formation. Grooming duration and nociception threshold (autistic traits) were significantly affected only in males. Early-onset tauopathy was accentuated in males (hippocampus and visual cortex), mimicking humans, and was paralleled by impaired visual evoked potentials and correction by acute NAP treatment. CONCLUSIONS Tyr mice model ADNP syndrome pathology. The newly discovered ADNP/NAP target FOXO3 controls the autophagy initiator LC3 (microtubule-associated protein 1 light chain 3), with known ADNP binding to LC3 augmented by NAP, protecting against tauopathy. NAP amelioration attests to specificity, with potential for drug development targeting accessible biomarkers.
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Affiliation(s)
- Gidon Karmon
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Shlomo Sragovich
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Gal Hacohen-Kleiman
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Inbar Ben-Horin-Hazak
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Petr Kasparek
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Björn Schuster
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Radislav Sedlacek
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Paschalis Theotokis
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Olga Touloumi
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Zoidou
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Linxuan Huang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Pei You Wu
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Roy Shi
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Oxana Kapitansky
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Alexandra Lobyntseva
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Eliezer Giladi
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shapira
- Department of Cell and Developmental Biology and Edmond J. Safra Center for Bioinformatics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology and Edmond J. Safra Center for Bioinformatics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Stefan Bereswill
- Gastrointestinal Microbiology Research Group, Institute for Microbiology, Infectious Diseases and Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - Markus M Heimesaat
- Gastrointestinal Microbiology Research Group, Institute for Microbiology, Infectious Diseases and Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - Nikolaos Grigoriadis
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Moran Rubinstein
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel; Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.
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Agrawal M, Welshhans K. Local Translation Across Neural Development: A Focus on Radial Glial Cells, Axons, and Synaptogenesis. Front Mol Neurosci 2021; 14:717170. [PMID: 34434089 PMCID: PMC8380849 DOI: 10.3389/fnmol.2021.717170] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
In the past two decades, significant progress has been made in our understanding of mRNA localization and translation at distal sites in axons and dendrites. The existing literature shows that local translation is regulated in a temporally and spatially restricted manner and is critical throughout embryonic and post-embryonic life. Here, recent key findings about mRNA localization and local translation across the various stages of neural development, including neurogenesis, axon development, and synaptogenesis, are reviewed. In the early stages of development, mRNAs are localized and locally translated in the endfeet of radial glial cells, but much is still unexplored about their functional significance. Recent in vitro and in vivo studies have provided new information about the specific mechanisms regulating local translation during axon development, including growth cone guidance and axon branching. Later in development, localization and translation of mRNAs help mediate the major structural and functional changes that occur in the axon during synaptogenesis. Clinically, changes in local translation across all stages of neural development have important implications for understanding the etiology of several neurological disorders. Herein, local translation and mechanisms regulating this process across developmental stages are compared and discussed in the context of function and dysfunction.
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Affiliation(s)
- Manasi Agrawal
- School of Biomedical Sciences, Kent State University, Kent, OH, United States
| | - Kristy Welshhans
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
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Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC. Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. J Alzheimers Dis 2021; 75:1417-1435. [PMID: 32417785 PMCID: PMC7369085 DOI: 10.3233/jad-200207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Gene Ontology (GO) is a major bioinformatic resource used for analysis of large biomedical datasets, for example from genome-wide association studies, applied universally across biological fields, including Alzheimer's disease (AD) research. OBJECTIVE We aim to demonstrate the applicability of GO for interpretation of AD datasets to improve the understanding of the underlying molecular disease mechanisms, including the involvement of inflammatory pathways and dysregulated microRNAs (miRs). METHODS We have undertaken a systematic full article GO annotation approach focused on microglial proteins implicated in AD and the miRs regulating their expression. PANTHER was used for enrichment analysis of previously published AD data. Cytoscape was used for visualizing and analyzing miR-target interactions captured from published experimental evidence. RESULTS We contributed 3,084 new annotations for 494 entities, i.e., on average six new annotations per entity. This included a total of 1,352 annotations for 40 prioritized microglial proteins implicated in AD and 66 miRs regulating their expression, yielding an average of twelve annotations per prioritized entity. The updated GO resource was then used to re-analyze previously published data. The re-analysis showed novel processes associated with AD-related genes, not identified in the original study, such as 'gliogenesis', 'regulation of neuron projection development', or 'response to cytokine', demonstrating enhanced applicability of GO for neuroscience research. CONCLUSIONS This study highlights ongoing development of the neurobiological aspects of GO and demonstrates the value of biocuration activities in the area, thus helping to delineate the molecular bases of AD to aid the development of diagnostic tools and treatments.
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Affiliation(s)
- Barbara Kramarz
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
| | - Rachael P Huntley
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
| | - Milagros Rodríguez-López
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shirin C C Saverimuttu
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rina Bandopadhyay
- UCL Institute of Neurology and Reta Lila Weston Institute of Neurological Studies, University College London, London, UK
| | - Maria-Jesus Martin
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nigel M Hooper
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Ruth C Lovering
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
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Reichova A, Bacova Z, Bukatova S, Kokavcova M, Meliskova V, Frimmel K, Ostatnikova D, Bakos J. Abnormal neuronal morphology and altered synaptic proteins are restored by oxytocin in autism-related SHANK3 deficient model. Mol Cell Endocrinol 2020; 518:110924. [PMID: 32619581 DOI: 10.1016/j.mce.2020.110924] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/22/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Oxytocin has been suggested as a potential therapeutic agent in autism and other neuropsychiatric conditions. Although, the link between the deficit in "SH3 domain and ankyrin repeat containing protein 3" (SHANK3) and autism spectrum disorders is highly studied topic, developmental mechanisms are still poorly understood. In this study, we clearly confirm that SHANK3 deficiency is accompanied with abnormalities in neurite number and length, which are reversed by oxytocin treatment (1 μM, 48h) in primary hippocampal neurons. Transient silencing for the SHANK3 gene (siSHANK3) in neuron-like cell line (SH-SY5Y) revealed a significant decrease in the expression levels of Neurexins 1α, 1β, 2α and 2β. Oxytocin treatment compensated reduced levels of Synapsin I, PSD95 and Neuroligin 3 in siSHANK3 cells suggesting a marked potential of oxytocin to ameliorate defects present in conditions of SHANK3 deficiency. Further analysis of hippocampal tissue revealed that oxytocin application (0.1 μg/μl, s.c. at P2 and P3 day) affects levels of synaptic proteins and GTPases in both WT and SHANK3 deficient mice on day P5. Oxytocin stimulated the mRNA expression of RhoB and Rac1 in both WT and SHANK3 deficient mice. Our data suggest that autism relevant synaptic pathologies could be reversed by oxytocin treatment.
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Affiliation(s)
- Alexandra Reichova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Bacova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Stanislava Bukatova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Kokavcova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Veronika Meliskova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Karel Frimmel
- Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Daniela Ostatnikova
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Jan Bakos
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
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Wanner NM, Colwell M, Drown C, Faulk C. Subacute cannabidiol alters genome-wide DNA methylation in adult mouse hippocampus. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:890-900. [PMID: 32579259 PMCID: PMC7765463 DOI: 10.1002/em.22396] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/29/2020] [Accepted: 06/09/2020] [Indexed: 05/15/2023]
Abstract
Use of cannabidiol (CBD), the most abundant non-psychoactive compound found in cannabis (Cannabis sativa), has recently increased as a result of widespread availability of CBD-containing products. CBD is FDA-approved for the treatment of epilepsy and exhibits anxiolytic, antipsychotic, prosocial, and other behavioral effects in animal studies and clinical trials, however, the underlying mechanisms governing these phenotypes are still being elucidated. The epigenome, particularly DNA methylation, is responsive to environmental input and can govern persistent patterns of gene regulation affecting phenotype across the life course. In order to understand the epigenomic activity of cannabidiol exposure in the adult brain, 12-week-old male wild-type a/a Agouti viable yellow (Avy ) mice were exposed to either 20 mg/kg CBD or vehicle daily by oral administration for 14 days. Hippocampal tissue was collected and reduced-representation bisulfite sequencing (RRBS) was performed. Analyses revealed 3,323 differentially methylated loci (DMLs) in CBD-exposed animals with a small skew toward global hypomethylation. Genes for cell adhesion and migration, dendritic spine development, and excitatory postsynaptic potential were found to be enriched in a gene ontology term analysis of DML-containing genes, and disease ontology enrichment revealed an overrepresentation of DMLs in gene sets associated with autism spectrum disorder, schizophrenia, and other phenotypes. These results suggest that the epigenome may be a key substrate for CBD's behavioral effects and provides a wealth of gene regulatory information for further study.
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Affiliation(s)
- Nicole M Wanner
- Department of Veterinary and Biomedical Sciences, University of Minnesota College of Veterinary Medicine
| | | | - Chelsea Drown
- Department of Animal Science, University of Minnesota
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Abstract
Myosin XVI (Myo16), a vertebrate-specific motor protein, is a recently discovered member of the myosin superfamily. The detailed functionality regarding myosin XVI requires elucidating or clarification; however, it appears to portray an important role in neural development and in the proper functioning of the nervous system. It is expressed in the largest amount in neural tissues in the late embryonic-early postnatal period, specifically the time in which neuronal cell migration and dendritic elaboration coincide. The impaired expression of myosin XVI has been found lurking in the background of several neuropsychiatric disorders including autism, schizophrenia and/or bipolar disorders.Two principal isoforms of class XVI myosins have been thus far described: Myo16a, the tailless cytoplasmic isoform and Myo16b, the full-length molecule featuring both cytoplasmic and nuclear localization. Both isoforms contain a class-specific N-terminal ankyrin repeat domain that binds to the protein phosphatase catalytic subunit. Myo16b, the predominant isoform, exhibits a diverse function. In the cytoplasm, it participates in the reorganization of the actin cytoskeleton through activation of the PI3K pathway and the WAVE-complex, while in the nucleus it may possess a role in cell cycle regulation. Based on the sequence, myosin XVI may have a compromised ATPase activity, implying a potential stationary role.
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Affiliation(s)
- Beáta Bugyi
- Department of Biophysics, University of Pécs, Medical School, Pécs, Hungary
| | - András Kengyel
- Department of Biophysics, University of Pécs, Medical School, Pécs, Hungary.
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Su S, Zhang L, Liu J. An Effective Method to Measure Disease Similarity Using Gene and Phenotype Associations. Front Genet 2019; 10:466. [PMID: 31164903 PMCID: PMC6536643 DOI: 10.3389/fgene.2019.00466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Motivation: In order to create controlled vocabularies for shared use in different biomedical domains, a large number of biomedical ontologies such as Disease Ontology (DO) and Human Phenotype Ontology (HPO), etc., are created in the bioinformatics community. Quantitative measures of the associations among diseases could help researchers gain a deep insight of human diseases, since similar diseases are usually caused by similar molecular origins or have similar phenotypes, which is beneficial to reveal the common attributes of diseases and improve the corresponding diagnoses and treatment plans. Some previous are proposed to measure the disease similarity using a particular biomedical ontology during the past few years, but for a newly discovered disease or a disease with few related genetic information in Disease Ontology (i.e., a disease with less disease-gene associations), these previous approaches usually ignores the joint computation of disease similarity by integrating gene and phenotype associations. Results: In this paper we propose a novel method called GPSim to effectively deduce the semantic similarity of diseases. In particular, GPSim calculates the similarity by jointly utilizing gene, disease and phenotype associations extracted from multiple biomedical ontologies and databases. We also explore the phenotypic factors such as the depth of HPO terms and the number of phenotypic associations that affect the evaluation performance. A final experimental evaluation is carried out to evaluate the performance of GPSim and shows its advantages over previous approaches.
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Affiliation(s)
- Shuhui Su
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lei Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Jian Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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9
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Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC. Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. Genes (Basel) 2018; 9:E593. [PMID: 30501127 PMCID: PMC6315915 DOI: 10.3390/genes9120593] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/28/2022] Open
Abstract
The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well as processing pipelines and analysis tools. Gene Ontology (GO, geneontology.org) is a major resource for gene enrichment analysis. The aim of this project, funded by the Alzheimer's Research United Kingdom (ARUK) foundation and led by the University College London (UCL) biocuration team, was to enhance the GO resource by developing new neurological GO terms, and use GO terms to annotate gene products associated with dementia. Specifically, proteins and protein complexes relevant to processes involving amyloid-beta and tau have been annotated and the resulting annotations are denoted in GO databases as 'ARUK-UCL'. Biological knowledge presented in the scientific literature was captured through the association of GO terms with dementia-relevant protein records; GO itself was revised, and new GO terms were added. This literature biocuration increased the number of Alzheimer's-relevant gene products that were being associated with neurological GO terms, such as 'amyloid-beta clearance' or 'learning or memory', as well as neuronal structures and their compartments. Of the total 2055 annotations that we contributed for the prioritised gene products, 526 have associated proteins and complexes with neurological GO terms. To ensure that these descriptive annotations could be provided for Alzheimer's-relevant gene products, over 70 new GO terms were created. Here, we describe how the improvements in ontology development and biocuration resulting from this initiative can benefit the scientific community and enhance the interpretation of dementia data.
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Affiliation(s)
- Barbara Kramarz
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Birgit H M Meldal
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Rachael P Huntley
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
| | - Maria J Martin
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK.
| | - Rina Bandopadhyay
- UCL Queen Square Institute of Neurology and Reta Lila Weston Institute of Neurological Studies, 1 Wakefield Street, London WC1N 1PJ, UK.
| | - Nigel M Hooper
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK.
| | - Ruth C Lovering
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
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10
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Gupta P, Uner OE, Nayak S, Grant GR, Kalb RG. SAP97 regulates behavior and expression of schizophrenia risk enriched gene sets in mouse hippocampus. PLoS One 2018; 13:e0200477. [PMID: 29995933 PMCID: PMC6040763 DOI: 10.1371/journal.pone.0200477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/27/2018] [Indexed: 01/10/2023] Open
Abstract
Synapse associated protein of 97KDa (SAP97) belongs to a family of scaffolding proteins, the membrane-associated guanylate kinases (MAGUKs), that are highly enriched in the postsynaptic density of synapses and play an important role in organizing protein complexes necessary for synaptic development and plasticity. The Dlg-MAGUK family of proteins are structurally very similar, and an effort has been made to parse apart the unique function of each Dlg-MAGUK protein by characterization of knockout mice. Knockout mice have been generated and characterized for PSD-95, PSD-93, and SAP102, however SAP97 knockout mice have been impossible to study because the SAP97 null mice die soon after birth due to a craniofacial defect. We studied the transcriptomic and behavioral consequences of a brain-specific conditional knockout of SAP97 (SAP97-cKO). RNA sequencing from hippocampi from control and SAP97-cKO male animals identified 67 SAP97 regulated transcripts. As large-scale genetic studies have implicated MAGUKs in neuropsychiatric disorders such as intellectual disability, autism spectrum disorders, and schizophrenia (SCZ), we analyzed our differentially expressed gene (DEG) set for enrichment of disease risk-associated genes, and found our DEG set to be specifically enriched for SCZ-related genes. Subjecting SAP97-cKO mice to a battery of behavioral tests revealed a subtle male-specific cognitive deficit and female-specific motor deficit, while other behaviors were largely unaffected. These data suggest that loss of SAP97 may have a modest contribution to organismal behavior. The SAP97-cKO mouse serves as a stepping stone for understanding the unique role of SAP97 in biology.
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Affiliation(s)
- Preetika Gupta
- Neuroscience Graduate Group, Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ogul E. Uner
- School of Arts and Sciences, Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert G. Kalb
- Feinberg School of Medicine, Department of Neurology, Northwestern University, Chicago, Illinois, United States of America
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11
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Horder J, Petrinovic MM, Mendez MA, Bruns A, Takumi T, Spooren W, Barker GJ, Künnecke B, Murphy DG. Glutamate and GABA in autism spectrum disorder-a translational magnetic resonance spectroscopy study in man and rodent models. Transl Psychiatry 2018; 8:106. [PMID: 29802263 PMCID: PMC5970172 DOI: 10.1038/s41398-018-0155-1] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 03/04/2018] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a pervasive neurodevelopmental syndrome with a high human and economic burden. The pathophysiology of ASD is largely unclear, thus hampering development of pharmacological treatments for the core symptoms of the disorder. Abnormalities in glutamate and GABA signaling have been hypothesized to underlie ASD symptoms, and may form a therapeutic target, but it is not known whether these abnormalities are recapitulated in humans with ASD, as well as in rodent models of the disorder. We used translational proton magnetic resonance spectroscopy ([1H]MRS) to compare glutamate and GABA levels in adult humans with ASD and in a panel of six diverse rodent ASD models, encompassing genetic and environmental etiologies. [1H]MRS was performed in the striatum and the medial prefrontal cortex, of the humans, mice, and rats in order to allow for direct cross-species comparisons in specific cortical and subcortical brain regions implicated in ASD. In humans with ASD, glutamate concentration was reduced in the striatum and this was correlated with the severity of social symptoms. GABA levels were not altered in either brain region. The reduction in striatal glutamate was recapitulated in mice prenatally exposed to valproate, and in mice and rats carrying Nlgn3 mutations, but not in rodent ASD models with other etiologies. Our findings suggest that glutamate/GABA abnormalities in the corticostriatal circuitry may be a key pathological mechanism in ASD; and may be linked to alterations in the neuroligin-neurexin signaling complex.
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Affiliation(s)
- Jamie Horder
- 0000 0001 2322 6764grid.13097.3cDepartment of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London, SE5 8AF UK
| | - Marija M. Petrinovic
- 0000 0004 0374 1269grid.417570.0Roche Pharma Research & Early Development, Neuroscience, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland ,0000 0001 2322 6764grid.13097.3cPresent Address: Department of Forensic and Neurodevelopmental Sciences, and The Sackler Institute for Translational Development, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London, SE5 8AF UK
| | - Maria A. Mendez
- 0000 0001 2322 6764grid.13097.3cDepartment of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London, SE5 8AF UK
| | - Andreas Bruns
- 0000 0004 0374 1269grid.417570.0Roche Pharma Research & Early Development, Neuroscience, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Toru Takumi
- grid.474690.8RIKEN Brain Science Institute, Wako, Japan
| | - Will Spooren
- 0000 0004 0374 1269grid.417570.0Roche Pharma Research & Early Development, Neuroscience, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Gareth J. Barker
- 0000 0001 2322 6764grid.13097.3cCentre for Neuroimaging Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London, SE5 8AF UK
| | - Basil Künnecke
- 0000 0004 0374 1269grid.417570.0Roche Pharma Research & Early Development, Neuroscience, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Declan G. Murphy
- 0000 0001 2322 6764grid.13097.3cDepartment of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London, SE5 8AF UK ,grid.415717.1Autism Assessment and Behavioural Genetics Clinic, South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Beckenham, UK ,0000 0001 2322 6764grid.13097.3cSackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 8AF United Kingdom
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12
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Hertz-Picciotto I, Schmidt RJ, Krakowiak P. Understanding environmental contributions to autism: Causal concepts and the state of science. Autism Res 2018; 11:554-586. [PMID: 29573218 DOI: 10.1002/aur.1938] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/12/2017] [Accepted: 10/19/2017] [Indexed: 11/06/2022]
Abstract
The complexity of neurodevelopment, the rapidity of early neurogenesis, and over 100 years of research identifying environmental influences on neurodevelopment serve as backdrop to understanding factors that influence risk and severity of autism spectrum disorder (ASD). This Keynote Lecture, delivered at the May 2016 annual meeting of the International Society for Autism Research, describes concepts of causation, outlines the trajectory of research on nongenetic factors beginning in the 1960s, and briefly reviews the current state of this science. Causal concepts are introduced, including root causes; pitfalls in interpreting time trends as clues to etiologic factors; susceptible time windows for exposure; and implications of a multi-factorial model of ASD. An historical background presents early research into the origins of ASD. The epidemiologic literature from the last fifteen years is briefly but critically reviewed for potential roles of, for example, air pollution, pesticides, plastics, prenatal vitamins, lifestyle and family factors, and maternal obstetric and metabolic conditions during her pregnancy. Three examples from the case-control CHildhood Autism Risks from Genes and the Environment Study are probed to illustrate methodological approaches to central challenges in observational studies: capturing environmental exposure; causal inference when a randomized controlled clinical trial is either unethical or infeasible; and the integration of genetic, epigenetic, and environmental influences on development. We conclude with reflections on future directions, including exposomics, new technologies, the microbiome, gene-by-environment interaction in the era of -omics, and epigenetics as the interface of those two. As the environment is malleable, this research advances the goal of a productive and fulfilling life for all children, teen-agers and adults. Autism Res 2018, 11: 554-586. © 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY This Keynote Lecture, delivered at the 2016 meeting of the International Society for Autism Research, discusses evidence from human epidemiologic studies of prenatal factors contributing to autism, such as pesticides, maternal nutrition and her health. There is no single cause for autism. Examples highlight the features of a high-quality epidemiology study, and what comprises a compelling case for causation. Emergent research directions hold promise for identifying potential interventions to reduce disabilities, enhance giftedness, and improve lives of those with ASD.
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Affiliation(s)
- Irva Hertz-Picciotto
- Department of Public Health Sciences, MIND Institute (Medical Investigations of Neurodevelopmental Disorders), University of California, Davis, Davis, California
| | - Rebecca J Schmidt
- Department of Public Health Sciences, MIND Institute (Medical Investigations of Neurodevelopmental Disorders), University of California, Davis, Davis, California
| | - Paula Krakowiak
- Department of Public Health Sciences, MIND Institute (Medical Investigations of Neurodevelopmental Disorders), University of California, Davis, Davis, California
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13
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Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. Exploring autophagy with Gene Ontology. Autophagy 2018; 14:419-436. [PMID: 29455577 PMCID: PMC5915032 DOI: 10.1080/15548627.2017.1415189] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of ‘annotations’ that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study.
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Affiliation(s)
- Paul Denny
- a Functional Gene Annotation , Institute of Cardiovascular Science, University College London , London , UK
| | - Marc Feuermann
- b SIB Swiss Institute of Bioinformatics , Geneva , Switzerland
| | - David P Hill
- c The Jackson Laboratory , Bar Harbor , ME , USA.,f The Gene Ontology Consortium
| | - Ruth C Lovering
- a Functional Gene Annotation , Institute of Cardiovascular Science, University College London , London , UK
| | - Helene Plun-Favreau
- d Department of Molecular Neuroscience , UCL Institute of Neurology , London , UK
| | - Paola Roncaglia
- e European Bioinformatics Institute (EMBL-EBI) , European Molecular Biology Laboratory, Wellcome Genome Campus , Hinxton , Cambridge , UK.,f The Gene Ontology Consortium
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14
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Chen K, Kardys A, Chen Y, Flink S, Tabakoff B, Shih JC. Altered gene expression in early postnatal monoamine oxidase A knockout mice. Brain Res 2017; 1669:18-26. [PMID: 28535982 PMCID: PMC5531263 DOI: 10.1016/j.brainres.2017.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/10/2017] [Accepted: 05/16/2017] [Indexed: 11/19/2022]
Abstract
We reported previously that monoamine oxidase (MAO) A knockout (KO) mice show increased serotonin (5-hydroxytryptamine, 5-HT) levels and autistic-like behaviors characterized by repetitive behaviors, and anti-social behaviors. We showed that administration of the serotonin synthesis inhibitor para-chlorophenylalanine (pCPA) from post-natal day 1 (P1) through 7 (P7) in MAO A KO mice reduced the serotonin level to normal and reverses the repetitive behavior. These results suggested that the altered gene expression at P1 and P7 may be important for the autistic-like behaviors seen in MAO A KO mice and was studied here. In this study, Affymetrix mRNA array data for P1 and P7 MAO A KO mice were analyzed using Partek Genomics Suite and Ingenuity Pathways Analysis to identify genes differentially expressed versus wild-type and assess their functions and relationships. The number of significant differentially expressed genes (DEGs) varied with age: P1 (664) and P7 (3307) [false discovery rate (FDR) <0.05, fold-change (FC) >1.5 for autism-linked genes and >2.0 for functionally categorized genes]. Eight autism-linked genes were differentially expressed in P1 (upregulated: NLGN3, SLC6A2; down-regulated: HTR2C, MET, ADSL, MECP2, ALDH5A1, GRIN3B) while four autism-linked genes were differentially expressed at P7 (upregulated: HTR2B; downregulated: GRIN2D, GRIN2B, CHRNA4). Many other genes involved in neurodevelopment, apoptosis, neurotransmission, and cognitive function were differentially expressed at P7 in MAO A KO mice. This result suggests that modulation of these genes by the increased serotonin may lead to neurodevelopmental alteration in MAO A KO mice and results in autistic-like behaviors.
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Affiliation(s)
- Kevin Chen
- Dept. of Pharmacology & Pharmaceutical Science, School of Pharmacy, Los Angeles, CA 90089, United States
| | - Abbey Kardys
- Dept. of Pharmacology & Pharmaceutical Science, School of Pharmacy, Los Angeles, CA 90089, United States
| | - Yibu Chen
- Norris Medical Library, University of Southern California, Los Angeles, CA 90089, United States
| | - Stephen Flink
- University of Colorado Health Science Center, Denver, CO 80262, United States
| | - Boris Tabakoff
- University of Colorado Health Science Center, Denver, CO 80262, United States
| | - Jean C Shih
- Dept. of Pharmacology & Pharmaceutical Science, School of Pharmacy, Los Angeles, CA 90089, United States; USC-Taiwan Center for Translational Research, University of Southern California, Los Angeles, CA 90089, United States; Dept. of Cell & Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, United States.
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15
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Abstract
Collaborations between the scientific community and members of the Gene Ontology (GO) Consortium have led to an increase in the number and specificity of GO terms, as well as increasing the number of GO annotations. A variety of approaches have been taken to encourage research scientists to contribute to the GO, but the success of these approaches has been variable. This chapter reviews both the successes and failures of engaging the scientific community in GO development and annotation, as well as, providing motivation and advice to encourage individual researchers to contribute to GO.
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Affiliation(s)
- Ruth C Lovering
- Functional Gene Annotation Initiative, Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, 5 University Street, London, WC1E 6JF, UK.
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16
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Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res 2016; 45:D331-D338. [PMID: 27899567 PMCID: PMC5210579 DOI: 10.1093/nar/gkw1108] [Citation(s) in RCA: 1317] [Impact Index Per Article: 164.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022] Open
Abstract
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.
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