1
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Pandini C, Rey F, Cereda C, Carelli S, Gandellini P. Study of lncRNAs in Pediatric Neurological Diseases: Methods, Analysis of the State-of-Art and Possible Therapeutic Implications. Pharmaceuticals (Basel) 2023; 16:1616. [PMID: 38004481 PMCID: PMC10675345 DOI: 10.3390/ph16111616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as crucial regulators in various cellular processes, and their roles in pediatric neurological diseases are increasingly being explored. This review provides an overview of lncRNA implications in the central nervous system, both in its physiological state and when a pathological condition is present. We describe the role of lncRNAs in neural development, highlighting their significance in processes such as neural stem cell proliferation, differentiation, and synaptogenesis. Dysregulation of specific lncRNAs is associated with multiple pediatric neurological diseases, such as neurodevelopmental or neurodegenerative disorders and brain tumors. The collected evidence indicates that there is a need for further research to uncover the full spectrum of lncRNA involvement in pediatric neurological diseases and brain tumors. While challenges exist, ongoing advancements in technology and our understanding of lncRNA biology offer hope for future breakthroughs in the field of pediatric neurology, leveraging lncRNAs as potential therapeutic targets and biomarkers.
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Affiliation(s)
- Cecilia Pandini
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Federica Rey
- Pediatric Clinical Research Center “Fondazione Romeo ed Enrica Invernizzi”, Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (F.R.); (S.C.)
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, 20157 Milan, Italy;
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, 20157 Milan, Italy;
| | - Stephana Carelli
- Pediatric Clinical Research Center “Fondazione Romeo ed Enrica Invernizzi”, Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (F.R.); (S.C.)
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children’s Hospital, 20157 Milan, Italy;
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
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2
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Suliman M, Al-Hawary SIS, Al-Dolaimy F, Hjazi A, Almalki SG, Alkhafaji AT, Alawadi AH, Alsaalamy A, Bijlwan S, Mustafa YF. Inflammatory diseases: Function of LncRNAs in their emergence and the role of mesenchymal stem cell secretome in their treatment. Pathol Res Pract 2023; 249:154758. [PMID: 37660657 DOI: 10.1016/j.prp.2023.154758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023]
Abstract
One of the best treatments for inflammatory diseases such as COVID-19, respiratory diseases and brain diseases is treatment with stem cells. Here we investigate the effect of stem cell therapy in the treatment of brain diseases.Preclinical studies have shown promising results, including improved functional recovery and tissue repair in animal models of neurodegenerative diseases, strokes,and traumatic brain injuries. However,ethical implications, safety concerns, and regulatory frameworks necessitate thorough evaluation before transitioning to clinical applications. Additionally, the complex nature of the brain and its intricate cellular environment present unique obstacles that must be overcome to ensure the successful integration and functionality of genetically engineered MSCs. The careful navigation of this path will determine whether the application of genetically engineered MSCs in brain tissue regeneration ultimately lives up to the hype surrounding it.
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Affiliation(s)
- Muath Suliman
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | | | | | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia.
| | - Sami G Almalki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, Saudi Arabia
| | | | - Ahmed Hussien Alawadi
- College of technical engineering, the Islamic University, Najaf, Iraq; College of technical engineering, the Islamic University of Al Diwaniyah, Iraq; College of technical engineering, the Islamic University of Babylon, Iraq
| | - Ali Alsaalamy
- College of technical engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
| | - Sheela Bijlwan
- Uttaranchal School of Computing Sciences, Uttaranchal University, Dehradun, India
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, Iraq
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3
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Tokunaga M, Imamura T. Emerging concepts involving inhibitory and activating RNA functionalization towards the understanding of microcephaly phenotypes and brain diseases in humans. Front Cell Dev Biol 2023; 11:1168072. [PMID: 37408531 PMCID: PMC10318543 DOI: 10.3389/fcell.2023.1168072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
Microcephaly is characterized as a small head circumference, and is often accompanied by developmental disorders. Several candidate risk genes for this disease have been described, and mutations in non-coding regions are occasionally found in patients with microcephaly. Various non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), SINEUPs, telomerase RNA component (TERC), and promoter-associated lncRNAs (pancRNAs) are now being characterized. These ncRNAs regulate gene expression, enzyme activity, telomere length, and chromatin structure through RNA binding proteins (RBPs)-RNA interaction. Elucidating the potential roles of ncRNA-protein coordination in microcephaly pathogenesis might contribute to its prevention or recovery. Here, we introduce several syndromes whose clinical features include microcephaly. In particular, we focus on syndromes for which ncRNAs or genes that interact with ncRNAs may play roles. We discuss the possibility that the huge ncRNA field will provide possible new therapeutic approaches for microcephaly and also reveal clues about the factors enabling the evolutionary acquisition of the human-specific "large brain."
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4
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Kainer D, Templeton AR, Prates ET, Jacboson D, Allan ER, Climer S, Garvin MR. Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder. HGG ADVANCES 2022; 4:100150. [PMCID: PMC9634371 DOI: 10.1016/j.xhgg.2022.100150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The heritability of autism spectrum disorder (ASD), based on 680,000 families and five countries, is estimated to be nearly 80%, yet heritability reported from SNP-based studies are consistently lower, and few significant loci have been identified with genome-wide association studies. This gap in genomic information may reside in rare variants, interaction among variants (epistasis), or cryptic structural variation (SV) and may provide mechanisms that underlie ASD. Here we use a method to identify potential SVs based on non-Mendelian inheritance patterns in pedigrees using parent-child genotypes from ASD families and demonstrate that they are enriched in ASD-risk genes. Most are in non-coding genic space and are over-represented in expression quantitative trait loci, suggesting that they affect gene regulation, which we confirm with their overlap of differentially expressed genes in postmortem brain tissue of ASD individuals. We then identify an SV in the GRIK2 gene that alters RNA splicing and a regulatory region of the ACMSD gene in the kynurenine pathway as significantly associated with a non-verbal ASD phenotype, supporting our hypothesis that these currently excluded loci can provide a clearer mechanistic understanding of ASD. Finally, we use an explainable artificial intelligence approach to define subgroups demonstrating their use in the context of precision medicine.
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Affiliation(s)
- David Kainer
- Computational Systems Biology, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R. Templeton
- Department of Biology, Washington University – St Louis, St. Louis, MO, USA
| | - Erica T. Prates
- Computational Systems Biology, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel Jacboson
- Computational Systems Biology, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Sharlee Climer
- Department of Computer Science, University of Missouri, St. Louis, MO, USA
| | - Michael R. Garvin
- Computational Systems Biology, Oak Ridge National Laboratory, Oak Ridge, TN, USA,Williwaw Biosciences, LLC, Clarkston, MI, USA,Corresponding author
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5
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Pastorek M, Drobná D, Celec P. Could neutrophil extracellular traps drive the development of autism? Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [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: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
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7
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Prokop JW, Jdanov V, Savage L, Morris M, Lamb N, VanSickle E, Stenger CL, Rajasekaran S, Bupp CP. Computational and Experimental Analysis of Genetic Variants. Compr Physiol 2022; 12:3303-3336. [PMID: 35578967 DOI: 10.1002/cphy.c210012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics has grown exponentially over the last decade. Common variants are associated with physiological changes through statistical strategies such as Genome-Wide Association Studies (GWAS) and quantitative trail loci (QTL). Rare variants are associated with diseases through extensive filtering tools, including population genomics and trio-based sequencing (parents and probands). However, the genomic associations require follow-up analyses to narrow causal variants, identify genes that are influenced, and to determine the physiological changes. Large quantities of data exist that can be used to connect variants to gene changes, cell types, protein pathways, clinical phenotypes, and animal models that establish physiological genomics. This data combined with bioinformatics including evolutionary analysis, structural insights, and gene regulation can yield testable hypotheses for mechanisms of genomic variants. Molecular biology, biochemistry, cell culture, CRISPR editing, and animal models can test the hypotheses to give molecular variant mechanisms. Variant characterizations can be a significant component of educating future professionals at the undergraduate, graduate, or medical training programs through teaching the basic concepts and terminology of genetics while learning independent research hypothesis design. This article goes through the computational and experimental analysis strategies of variant characterization and provides examples of these tools applied in publications. © 2022 American Physiological Society. Compr Physiol 12:3303-3336, 2022.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Vladislav Jdanov
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Lane Savage
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA.,Office of Research, Spectrum Health, Grand Rapids, Michigan, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Medical Genetics, Spectrum Health, Grand Rapids, Michigan, USA
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8
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Erbescu A, Papuc SM, Budisteanu M, Arghir A, Neagu M. Re-emerging concepts of immune dysregulation in autism spectrum disorders. Front Psychiatry 2022; 13:1006612. [PMID: 36339838 PMCID: PMC9626859 DOI: 10.3389/fpsyt.2022.1006612] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by communication and social interaction deficits, and by restricted interests and stereotyped, repetitive behavior patterns. ASD has a strong genetic component and a complex architecture characterized by the interplay of rare and common genetic variants. Recently, increasing evidence suggest a significant contribution of immune system dysregulation in ASD. The present paper reviews the latest updates regarding the altered immune landscape of this complex disorder highlighting areas with potential for biomarkers discovery as well as personalization of therapeutic approaches. Cross-talk between the central nervous system and immune system has long been envisaged and recent evidence brings insights into the pathways connecting the brain to the immune system. Disturbance of cytokine levels plays an important role in the establishment of a neuroinflammatory milieu in ASD. Several other immune molecules involved in antigen presentation and inflammatory cellular phenotypes are also at play in ASD. Maternal immune activation, the presence of brain-reactive antibodies and autoimmunity are other potential prenatal and postnatal contributors to ASD pathophysiology. The molecular players involved in oxidative-stress response and mitochondrial system function, are discussed as contributors to the pro-inflammatory pattern. The gastrointestinal inflammation pathways proposed to play a role in ASD are also discussed. Moreover, the body of evidence regarding some of the genetic factors linked to the immune system dysregulation is reviewed and discussed. Last, but not least, the epigenetic traits and their interactions with the immune system are reviewed as an expanding field in ASD research. Understanding the immune-mediated pathways that influence brain development and function, metabolism, and intestinal homeostasis, may lead to the identification of robust diagnostic or predictive biomarkers for ASD individuals. Thus, novel therapeutic approaches could be developed, ultimately aiming to improve their quality of life.
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Affiliation(s)
- Alina Erbescu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania
| | | | - Magdalena Budisteanu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Prof. Dr. Alex. Obregia Clinical Hospital of Psychiatry, Bucharest, Romania.,Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Monica Neagu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania.,Colentina Clinical Hospital, Bucharest, Romania
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9
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Ghafouri-Fard S, Noroozi R, Brand S, Hussen BM, Eghtedarian R, Taheri M, Ebrahimzadeh K. Emerging Role of Non-coding RNAs in Autism Spectrum Disorder. J Mol Neurosci 2021; 72:201-216. [PMID: 34767189 DOI: 10.1007/s12031-021-01934-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023]
Abstract
Autism spectrum disorders (ASD) embrace a diverse set of neurodevelopmental diseases with a multifaceted genetic basis. Non-coding RNAs (ncRNAs) are among putative loci with critical participation in the development of ASD. Expression of some lncRNAs, namely RP11-466P24.2, SYP-AS1, STXBP5-AS1, and IFNG-AS1 has been decreased in ASD, while AK128569, CTD-2516F10.2, MSNP1AS, RPS10P2-AS1, LINC00693, LINC00689, NEAT1, TUG1, and Shank2-AS lncRNAs have been over-expressed in ASD. Expression of several miRNAs which are implicated in the immunological developmental, immune responses, and protein synthesis as well as those participating in the regulation of PI3K/Akt/mTOR and EGFR signaling pathways is dysregulated in the context of ASD. In the present article, we describe investigations which appraised the role of lncRNAs, miRNAs, and circRNAs in the pathobiology of ASD.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Serge Brand
- Psychiatric Clinics, Center for Affective, Stress and Sleep Disorders, University of Basel, Basel, Switzerland
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Reyhane Eghtedarian
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Institute of Human Genetics, Jena University Hospital, 07740, Jena, Germany.
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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10
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Wu N, Wang Y, Jia JY, Pan YH, Yuan XB. Association of CDH11 with Autism Spectrum Disorder Revealed by Matched-gene Co-expression Analysis and Mouse Behavioral Studies. Neurosci Bull 2021; 38:29-46. [PMID: 34523068 PMCID: PMC8783018 DOI: 10.1007/s12264-021-00770-0] [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: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022] Open
Abstract
A large number of putative risk genes for autism spectrum disorder (ASD) have been reported. The functions of most of these susceptibility genes in developing brains remain unknown, and causal relationships between their variation and autism traits have not been established. The aim of this study was to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high-confidence ASD risk genes (hcASDs). The results showed that three gene features - gene size, mRNA abundance, and guanine-cytosine content - affect the genome-wide co-expression profiles of hcASDs. To circumvent the interference of these features in gene co-expression analysis, we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes. This method is referred to as "matched-gene co-expression analysis" (MGCA). With MGCA, we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction. The results of analysis of two recently-reported ASD candidate genes, CDH11 and CDH9, suggested the involvement of CDH11, but not CDH9, in ASD. Consistent with this prediction, behavioral studies showed that Cdh11-null mice, but not Cdh9-null mice, have multiple autism-like behavioral alterations. This study highlights the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.
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Affiliation(s)
- Nan Wu
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yue Wang
- Hussman Institute for Autism, Baltimore, 21201, USA
| | - Jing-Yan Jia
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China.
| | - Xiao-Bing Yuan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China. .,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, 21201, USA.
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11
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Gill PS, Clothier JL, Veerapandiyan A, Dweep H, Porter-Gill PA, Schaefer GB. Molecular Dysregulation in Autism Spectrum Disorder. J Pers Med 2021; 11:848. [PMID: 34575625 PMCID: PMC8466026 DOI: 10.3390/jpm11090848] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Autism Spectrum Disorder (ASD) comprises a heterogeneous group of neurodevelopmental disorders with a strong heritable genetic component. At present, ASD is diagnosed solely by behavioral criteria. Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD, where rare mutations and s common variants contribute to its susceptibility. Moreover, studies show rare de novo variants, copy number variation and single nucleotide polymorphisms (SNPs) also impact neurodevelopment signaling. Exploration of rare and common variants involved in common dysregulated pathways can provide new diagnostic and therapeutic strategies for ASD. Contributions of current innovative molecular strategies to understand etiology of ASD will be explored which are focused on whole exome sequencing (WES), whole genome sequencing (WGS), microRNA, long non-coding RNAs and CRISPR/Cas9 models. Some promising areas of pharmacogenomic and endophenotype directed therapies as novel personalized treatment and prevention will be discussed.
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Affiliation(s)
- Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA;
| | - Jeffery L. Clothier
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Aravindhan Veerapandiyan
- Pediatric Neurology, Arkansas Children’s Hospital, 1 Children’s Way, Little Rock, AR 72202, USA;
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA;
| | | | - G. Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Genetics and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Hospital NW, Springdale, AR 72762, USA
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12
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Fetit R, Hillary RF, Price DJ, Lawrie SM. The neuropathology of autism: A systematic review of post-mortem studies of autism and related disorders. Neurosci Biobehav Rev 2021; 129:35-62. [PMID: 34273379 DOI: 10.1016/j.neubiorev.2021.07.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/13/2021] [Accepted: 07/10/2021] [Indexed: 02/07/2023]
Abstract
Post-mortem studies allow for the direct investigation of brain tissue in those with autism and related disorders. Several review articles have focused on aspects of post-mortem abnormalities but none has brought together the entire post-mortem literature. Here, we systematically review the evidence from post-mortem studies of autism, and of related disorders that present with autistic features. The literature consists of a small body of studies with small sample sizes, but several remarkably consistent findings are evident. Cortical layering is largely undisturbed, but there are consistent reductions in minicolumn numbers and aberrant myelination. Transcriptomics repeatedly implicate abberant synaptic, metabolic, proliferation, apoptosis and immune pathways. Sufficient replicated evidence is available to implicate non-coding RNA, aberrant epigenetic profiles, GABAergic, glutamatergic and glial dysfunction in autism pathogenesis. Overall, the cerebellum and frontal cortex are most consistently implicated, sometimes revealing distinct region-specific alterations. The literature on related disorders such as Rett syndrome, Fragile X and copy number variations (CNVs) predisposing to autism is particularly small and inconclusive. Larger studies, matched for gender, developmental stage, co-morbidities and drug treatment are required.
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Affiliation(s)
- Rana Fetit
- Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK.
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David J Price
- Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Stephen M Lawrie
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH10 5HF, UK; Patrick Wild Centre, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH10 5HF, UK
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13
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Aliperti V, Skonieczna J, Cerase A. Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders. Noncoding RNA 2021; 7:36. [PMID: 34204536 PMCID: PMC8293397 DOI: 10.3390/ncrna7020036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.
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Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Justyna Skonieczna
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| | - Andrea Cerase
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
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14
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Ciomborowska-Basheer J, Staszak K, Kubiak MR, Makałowska I. Not So Dead Genes-Retrocopies as Regulators of Their Disease-Related Progenitors and Hosts. Cells 2021; 10:cells10040912. [PMID: 33921034 PMCID: PMC8071448 DOI: 10.3390/cells10040912] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Retroposition is RNA-based gene duplication leading to the creation of single exon nonfunctional copies. Nevertheless, over time, many of these duplicates acquire transcriptional capabilities. In human in most cases, these so-called retrogenes do not code for proteins but function as regulatory long noncoding RNAs (lncRNAs). The mechanisms by which they can regulate other genes include microRNA sponging, modulation of alternative splicing, epigenetic regulation and competition for stabilizing factors, among others. Here, we summarize recent findings related to lncRNAs originating from retrocopies that are involved in human diseases such as cancer and neurodegenerative, mental or cardiovascular disorders. Special attention is given to retrocopies that regulate their progenitors or host genes. Presented evidence from the literature and our bioinformatics analyses demonstrates that these retrocopies, often described as unimportant pseudogenes, are significant players in the cell’s molecular machinery.
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15
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Yang S, Lim KH, Kim SH, Joo JY. Molecular landscape of long noncoding RNAs in brain disorders. Mol Psychiatry 2021; 26:1060-1074. [PMID: 33173194 DOI: 10.1038/s41380-020-00947-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/28/2020] [Accepted: 10/27/2020] [Indexed: 02/08/2023]
Abstract
According to current paradigms, various risk factors, such as genetic mutations, oxidative stress, neural network dysfunction, and abnormal protein degradation, contribute to the progression of brain disorders. Through the cooperation of gene transcripts in biological processes, the study of noncoding RNAs can lead to insights into the cause and treatment of brain disorders. Recently, long noncoding RNAs (lncRNAs) which are longer than 200 nucleotides in length have been suggested as key factors in various brain disorders. Accumulating evidence suggests the potential of lncRNAs as diagnostic or prognostic biomarkers and therapeutic targets. High-throughput screening-based sequencing has been instrumental in identification of lncRNAs that demand new approaches to understanding the progression of brain disorders. In this review, we discuss the recent progress in the study of lncRNAs, and addresses the pathogenesis of brain disorders that involve lncRNAs and describes the associations of lncRNAs with neurodegenerative disorders such as Alzheimer disease (AD), Parkinson disease (PD), and neurodevelopmental disorders. We also discuss potential targets of lncRNAs and their promise as novel therapeutics and biomarkers in brain disorders.
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Affiliation(s)
- Sumin Yang
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Key-Hwan Lim
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Sung-Hyun Kim
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Jae-Yeol Joo
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea.
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16
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Xie X, Li L, Wu H, Hou F, Chen Y, Xue Q, Zhou Y, Zhang J, Gong J, Song R. Comprehensive Integrative Analyses Identify TIGD5 rs75547282 as a Risk Variant for Autism Spectrum Disorder. Autism Res 2021; 14:631-644. [PMID: 33393181 DOI: 10.1002/aur.2466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
Although recent genome-wide association studies have identified risk loci that strongly associates with autism spectrum disorder (ASD), how to pinpoint the causal genes remains a challenge. We aimed to pinpoint the potential causal genes and explore the possible susceptibility and mechanism. A convergent functional genomics (CFG) method was used to prioritize the candidate genes by combining lines of evidence, including Sherlock analysis, spatio-temporal expression patterns, expression analysis, protein-protein interactions, co-expression and association with brain structure. A higher score in the CFG approach suggested that more evidence supported this gene as an ASD risk gene. We screened genes with higher CFG scores for candidate functional single nucleotide polymorphisms (SNPs). A genotyping experiment (602 ASD children and 604 healthy sex-matched children) and the dual-luciferase reporter gene assay were followed to validate the effects of SNPs. We identified three genes (MAPT, ZNF285, and TIGD5) as candidate causal genes using the CFG approach. The genotyping experiment showed that TIGD5 rs75547282 was associated with an increased risk of ASD under the dominant model (OR = 1.37, 95% CI = 1.09-1.72, P = 0.006) though the statistical power was limited (5.2%). The T allele of rs75547282 activated the expression of TIGD5 compared with the C allele in the dual-luciferase reporter assay. Our study indicates that such comprehensive integrative analyses may be an effective way to explore promising ASD susceptibility variants and needs to be further investigated in future research. Genotyping experiments should, however, be based on a larger population sample to increase statistical power. LAY SUMMARY: We set out to pinpoint the potential causal genes of ASD and explore the possible susceptibility and mechanism by combining lines of evidence from different analyses. Our results show that TIGD5 rs75547282 is associated with the risk of ASD in the Han Chinese population. In addition, a similar framework to seek promising ASD risk variants could be further investigated in future research Autism Res 2021, 14: 631-644. © 2021 International Society for Autism Research and Wiley Periodicals LLC.
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Affiliation(s)
- Xinyan Xie
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Li
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Hao Wu
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Hou
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Yanlin Chen
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Qi Xue
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhou
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiajia Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Jianhua Gong
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Ranran Song
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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17
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Luo T, Ou JN, Cao LF, Peng XQ, Li YM, Tian YQ. The Autism-Related lncRNA MSNP1AS Regulates Moesin Protein to Influence the RhoA, Rac1, and PI3K/Akt Pathways and Regulate the Structure and Survival of Neurons. Autism Res 2020; 13:2073-2082. [PMID: 33215882 DOI: 10.1002/aur.2413] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 01/13/2023]
Abstract
Autism spectrum disorder (ASD) is a complex disease involving multiple genes and multiple sites, and it is closely related to environmental factors. It has been gradually revealed that long noncoding RNAs (lncRNAs) may regulate the pathogenesis of ASD at the epigenetic level. In neuronal cells, the lncRNA moesin pseudogene 1 antisense (MSNP1AS) forms a double-stranded RNA with moesin (MSN) to suppress moesin protein expression. MSNP1AS overexpression can activate the RhoA pathway and inhibit the Rac1 and PI3K/Akt pathways; however, the regulation of Rac1 by MSNP1AS is not associated with MSN, and the effect on the RhoA pathway may also be associated with other factors. MSNP1AS can decrease the number and length of neurites, inhibit neuronal cell viability and migration, and promote apoptosis. Downregulation of MSN expression functions similarly to MSNP1AS, and its overexpression can block the above functions of MSNP1AS. In addition, in vivo experiments show that MSN improves social interactions and reduces repetitive behaviors in BTBR mice, decreases the activity of RhoA and restores the activity of PI3K/Akt pathway. Therefore, the abnormal expression of MSNP1AS in ASD patients might influence the structure and survival of neuronal cells through the regulation of moesin protein expression to facilitate the development and progression of ASD. These findings provide new evidence for studying the mechanisms of lncRNAs in ASD. LAY SUMMARY: Autism spectrum disorder (ASD) is a common neurodevelopmental disease and its neurodevelopmental mechanisms have not been elucidated. More and more studies have found that long noncoding RNAs (lncRNAs) can regulate the development of central nervous system in many ways and affect the pathogenic process of ASD. Moesin pseudogene 1 antisense (MSNP1AS) is an up-regulated lncRNA in ASD patients. In-depth functional experiments showed that MSNP1AS inhibited moesin protein expression and regulated the activation of multiple signaling pathways, thus decreasing the number and length of neurites, inhibiting neuronal cell viability and migration, and promoting apoptosis. Therefore, MSNP1AS is an important lncRNA related to ASD and can regulate the biological function of neurons.
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Affiliation(s)
- Ting Luo
- XiangYa School of Public Health, Central South University, Changsha, China.,Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jin-Nan Ou
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Li-Fang Cao
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiao-Qing Peng
- Medical Administration Department, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Ya-Min Li
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yong-Quan Tian
- XiangYa School of Public Health, Central South University, Changsha, China
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18
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Xiong C, Sun S, Jiang W, Ma L, Zhang J. ASDmiR: A Stepwise Method to Uncover miRNA Regulation Related to Autism Spectrum Disorder. Front Genet 2020; 11:562971. [PMID: 33173536 PMCID: PMC7591752 DOI: 10.3389/fgene.2020.562971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Autism spectrum disorder (ASD) is a class of neurodevelopmental disorders characterized by genetic and environmental risk factors. The pathogenesis of ASD has a strong genetic basis, consisting of rare de novo or inherited variants among a variety of multiple molecules. Previous studies have shown that microRNAs (miRNAs) are involved in neurogenesis and brain development and are closely associated with the pathogenesis of ASD. However, the regulatory mechanisms of miRNAs in ASD are largely unclear. In this work, we present a stepwise method, ASDmiR, for the identification of underlying pathogenic genes, networks, and modules associated with ASD. First, we conduct a comparison study on 12 miRNA target prediction methods by using the matched miRNA, lncRNA, and mRNA expression data in ASD. In terms of the number of experimentally confirmed miRNA-target interactions predicted by each method, we choose the best method for identifying miRNA-target regulatory network. Based on the miRNA-target interaction network identified by the best method, we further infer miRNA-target regulatory bicliques or modules. In addition, by integrating high-confidence miRNA-target interactions and gene expression data, we identify three types of networks, including lncRNA-lncRNA, lncRNA-mRNA, and mRNA-mRNA related miRNA sponge interaction networks. To reveal the community of miRNA sponges, we further infer miRNA sponge modules from the identified miRNA sponge interaction network. Functional analysis results show that the identified hub genes, as well as miRNA-associated networks and modules, are closely linked with ASD. ASDmiR is freely available at https://github.com/chenchenxiong/ASDmiR.
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Affiliation(s)
- Chenchen Xiong
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China
| | - Shaoping Sun
- Department of Medical Engineering, People's Hospital of Yuxi City, Yuxi, China
| | - Weili Jiang
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China
| | - Lei Ma
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China
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19
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Quach BC, Bray MJ, Gaddis NC, Liu M, Palviainen T, Minica CC, Zellers S, Sherva R, Aliev F, Nothnagel M, Young KA, Marks JA, Young H, Carnes MU, Guo Y, Waldrop A, Sey NYA, Landi MT, McNeil DW, Drichel D, Farrer LA, Markunas CA, Vink JM, Hottenga JJ, Iacono WG, Kranzler HR, Saccone NL, Neale MC, Madden P, Rietschel M, Marazita ML, McGue M, Won H, Winterer G, Grucza R, Dick DM, Gelernter J, Caporaso NE, Baker TB, Boomsma DI, Kaprio J, Hokanson JE, Vrieze S, Bierut LJ, Johnson EO, Hancock DB. Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits. Nat Commun 2020; 11:5562. [PMID: 33144568 PMCID: PMC7642344 DOI: 10.1038/s41467-020-19265-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Cigarette smoking is the leading cause of preventable morbidity and mortality. Genetic variation contributes to initiation, regular smoking, nicotine dependence, and cessation. We present a Fagerström Test for Nicotine Dependence (FTND)-based genome-wide association study in 58,000 European or African ancestry smokers. We observe five genome-wide significant loci, including previously unreported loci MAGI2/GNAI1 (rs2714700) and TENM2 (rs1862416), and extend loci reported for other smoking traits to nicotine dependence. Using the heaviness of smoking index from UK Biobank (N = 33,791), rs2714700 is consistently associated; rs1862416 is not associated, likely reflecting nicotine dependence features not captured by the heaviness of smoking index. Both variants influence nearby gene expression (rs2714700/MAGI2-AS3 in hippocampus; rs1862416/TENM2 in lung), and expression of genes spanning nicotine dependence-associated variants is enriched in cerebellum. Nicotine dependence (SNP-based heritability = 8.6%) is genetically correlated with 18 other smoking traits (rg = 0.40-1.09) and co-morbidities. Our results highlight nicotine dependence-specific loci, emphasizing the FTND as a composite phenotype that expands genetic knowledge of smoking.
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Affiliation(s)
- Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Michael J Bray
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Nathan C Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
| | - Camelia C Minica
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Stephanie Zellers
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
| | - Fazil Aliev
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Faculty of Business, Karabuk University, 78050, Kılavuzlar/Karabük Merkez/Karabük, Turkey
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Hannah Young
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Megan U Carnes
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Yuelong Guo
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- GeneCentric Therapeutics, Research Triangle Park, NC, 27709, USA
| | - Alex Waldrop
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Nancy Y A Sey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Maria T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Daniel W McNeil
- Department of Psychology, West Virginia University, Morgantown, WV, 26505, USA
- Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, 26505, USA
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Christina A Markunas
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Jacqueline M Vink
- Behavioural Science Institute, Radboud University, 6500 HE, Nijmegen, The Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - William G Iacono
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- VISN 4 MIRECC, Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Nancy L Saccone
- Department of Genetics, Washington University, St. Louis, MO, 63130, USA
- Division of Biostatistics, Washington University, St. Louis, MO, 63130, USA
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Pamela Madden
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, 68159, Mannheim, Germany
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Matthew McGue
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Georg Winterer
- Experimental & Clinical Research Center, Department of Anesthesiology and Operative Intensive Care Medicine, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Richard Grucza
- Departments of Family and Community Medicine and Health and Clinical Outcomes Research, Saint Louis University, St. Louis, MO, 63130, USA
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Psychiatry, VA CT Healthcare Center, West Haven, CT, 06511, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA.
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20
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Schmitz-Abe K, Sanchez-Schmitz G, Doan RN, Hill RS, Chahrour MH, Mehta BK, Servattalab S, Ataman B, Lam ATN, Morrow EM, Greenberg ME, Yu TW, Walsh CA, Markianos K. Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder. Sci Rep 2020; 10:14045. [PMID: 32820185 PMCID: PMC7441318 DOI: 10.1038/s41598-020-70656-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/29/2020] [Indexed: 11/09/2022] Open
Abstract
More than 98% of the human genome is made up of non-coding DNA, but techniques to ascertain its contribution to human disease have lagged far behind our understanding of protein coding variations. Autism spectrum disorder (ASD) has been mostly associated with coding variations via de novo single nucleotide variants (SNVs), recessive/homozygous SNVs, or de novo copy number variants (CNVs); however, most ASD cases continue to lack a genetic diagnosis. We analyzed 187 consanguineous ASD families for biallelic CNVs. Recessive deletions were significantly enriched in affected individuals relative to their unaffected siblings (17% versus 4%, p < 0.001). Only a small subset of biallelic deletions were predicted to result in coding exon disruption. In contrast, biallelic deletions in individuals with ASD were enriched for overlap with regulatory regions, with 23/28 CNVs disrupting histone peaks in ENCODE (p < 0.009). Overlap with regulatory regions was further demonstrated by comparisons to the 127-epigenome dataset released by the Roadmap Epigenomics project, with enrichment for enhancers found in primary brain tissue and neuronal progenitor cells. Our results suggest a novel noncoding mechanism of ASD, describe a powerful method to identify important noncoding regions in the human genome, and emphasize the potential significance of gene activation and regulation in cognitive and social function.
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Affiliation(s)
- Klaus Schmitz-Abe
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Divisions of Newborn Medicine and Manton Center for Orphan Disease Research, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA
| | - Guzman Sanchez-Schmitz
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Infectious Diseases, Department of Pediatrics and Precision Vaccines Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria H Chahrour
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bhaven K Mehta
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah Servattalab
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bulent Ataman
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anh-Thu N Lam
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry and Department of Psychiatry and Human Behavior, Brown University, Providence, RI, 02912, USA
| | | | - Timothy W Yu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA. .,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Kyriacos Markianos
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA. .,Center for Data and Computational Sciences, Cooperative Studies Program, VA Boston Healthcare system, Boston, MA, 02130, USA.
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21
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Ross PJ, Mok RSF, Smith BS, Rodrigues DC, Mufteev M, Scherer SW, Ellis J. Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells. Mol Autism 2020; 11:33. [PMID: 32398033 PMCID: PMC7218542 DOI: 10.1186/s13229-020-00333-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/03/2020] [Indexed: 12/27/2022] Open
Abstract
Genetic factors contribute to the development of autism spectrum disorder (ASD), and although non-protein-coding regions of the genome are being increasingly implicated in ASD, the functional consequences of these variants remain largely uncharacterized. Induced pluripotent stem cells (iPSCs) enable the production of personalized neurons that are genetically matched to people with ASD and can therefore be used to directly test the effects of genomic variation on neuronal gene expression, synapse function, and connectivity. The combined use of human pluripotent stem cells with genome editing to introduce or correct specific variants has proved to be a powerful approach for exploring the functional consequences of ASD-associated variants in protein-coding genes and, more recently, long non-coding RNAs (lncRNAs). Here, we review recent studies that implicate lncRNAs, other non-coding mutations, and regulatory variants in ASD susceptibility. We also discuss experimental design considerations for using iPSCs and genome editing to study the role of the non-protein-coding genome in ASD.
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Affiliation(s)
- P Joel Ross
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada.
| | - Rebecca S F Mok
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Brandon S Smith
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Deivid C Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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22
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New Horizons for Molecular Genetics Diagnostic and Research in Autism Spectrum Disorder. ADVANCES IN NEUROBIOLOGY 2020; 24:43-81. [PMID: 32006356 DOI: 10.1007/978-3-030-30402-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder (ASD) is a highly heritable, heterogeneous, and complex pervasive neurodevelopmental disorder (PND) characterized by distinctive abnormalities of human cognitive functions, social interaction, and speech development.Nowadays, several genetic changes including chromosome abnormalities, genetic variations, transcriptional epigenetics, and noncoding RNA have been identified in ASD. However, the association between these genetic modifications and ASDs has not been confirmed yet.The aim of this review is to summarize the key findings in ASD from genetic viewpoint that have been identified from the last few decades of genetic and molecular research.
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23
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Zhang SF, Gao J, Liu CM. The Role of Non-Coding RNAs in Neurodevelopmental Disorders. Front Genet 2019; 10:1033. [PMID: 31824553 PMCID: PMC6882276 DOI: 10.3389/fgene.2019.01033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 09/25/2019] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs, a group of ribonucleic acids that are ubiquitous in the body and do not encode proteins, emerge as important regulatory factors in almost all biological processes in the brain. Extensive studies have suggested the involvement of non-coding RNAs in brain development and neurodevelopmental disorders, and dysregulation of non-coding RNAs is associated with abnormal brain development and the etiology of neurodevelopmental disorders. Here we provide an overview of the roles and working mechanisms of non-coding RNAs, and discuss potential clinical applications of non-coding RNAs as diagnostic and prognostic markers and as therapeutic targets in neurodevelopmental disorders.
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Affiliation(s)
- Shuang-Feng Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jun Gao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medicine Sciences & Peking Union Medical College, Beijing, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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24
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Wu W, Ji X, Zhao Y. Emerging Roles of Long Non-coding RNAs in Chronic Neuropathic Pain. Front Neurosci 2019; 13:1097. [PMID: 31680832 PMCID: PMC6813851 DOI: 10.3389/fnins.2019.01097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Chronic neuropathic pain, a type of chronic and potentially disabling pain caused by a disease or injury of the somatosensory nervous system, spinal cord injury, or various chronic conditions, such as viral infections (e.g., post-herpetic neuralgia), autoimmune diseases, cancers, and metabolic disorders (e.g., diabetes mellitus), is one of the most intense types of chronic pain, which incurs a major socio-economic burden and is a serious public health issue, with an estimated prevalence of 7–10% in adults throughout the world. Presently, the available drug treatments (e.g., anticonvulsants acting at calcium channels, serotonin-noradrenaline reuptake inhibitors, tricyclic antidepressants, opioids, topical lidocaine, etc.) for chronic neuropathic pain patients are still rare and have disappointing efficacy, which makes it difficult to relieve the patients’ painful symptoms, and, at best, they only try to reduce the patients’ ability to tolerate pain. Long non-coding RNAs (lncRNAs), a type of transcript of more than 200 nucleotides with no protein-coding or limited capacity, were identified to be abnormally expressed in the spinal cord, dorsal root ganglion, hippocampus, and prefrontal cortex under chronic neuropathic pain conditions. Moreover, a rapidly growing body of data has clearly pointed out that nearly 40% of lncRNAs exist specifically in the nervous system. Hence, it was speculated that these dysregulated lncRNAs might participate in the occurrence, development, and progression of chronic neuropathic pain. In other words, if we deeply delve into the potential roles of lncRNAs in the pathogenesis of chronic neuropathic pain, this may open up new strategies and directions for the development of novel targeted drugs to cure this refractory disorder. In this article, we primarily review the status of chronic neuropathic pain and provide a general overview of lncRNAs, the detailed roles of lncRNAs in the nervous system and its related diseases, and the abnormal expression of lncRNAs and their potential clinical applications in chronic neuropathic pain. We hope that through the above description, readers can gain a better understanding of the emerging roles of lncRNAs in chronic neuropathic pain.
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Affiliation(s)
- Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Ji
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yang Zhao
- Department of Anesthesiology, Affiliated Hospital to Qingdao University, Qingdao, China
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25
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Bilinovich SM, Lewis K, Grepo N, Campbell DB. The Long Noncoding RNA RPS10P2-AS1 Is Implicated in Autism Spectrum Disorder Risk and Modulates Gene Expression in Human Neuronal Progenitor Cells. Front Genet 2019; 10:970. [PMID: 31681417 PMCID: PMC6804435 DOI: 10.3389/fgene.2019.00970] [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: 06/17/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Most of the genetic risk for autism spectrum disorder (ASD) is inherited as common genetic variants, although some rare mutations have been identified in individuals with ASD. Common genetic variants are most parsimoniously identified by genome wide association studies. Genome wide association studies have identified several genetic loci with genome wide association with ASD. However, genome wide association studies only identify regions of the genome associated with phenotypic traits. Identification of the functional elements requires additional experimental evidence. Here, we demonstrate that a genome wide association study locus for ASD on chromosome 20p12.1, rs4141463, implicates a noncoding RNA as a functional element. Although rs4141463 lies within an intron of the protein-coding MACROD2 (MACRO domain containing 2) gene, expression of MACROD2 is neither altered in postmortem temporal cortex of individuals with ASD nor correlated with rs4141463 genotype. Our bioinformatics approaches revealed a noncoding RNA transcript near the autism susceptibility signal, RPS10P2-AS1 (ribosomal protein S10 pseudogene 2 anti-sense 1). In a panel of 15 human tissues, RPS10P2-AS1 was expressed at higher levels than the protein-coding MACROD2 in both fetal temporal cortex and adult peripheral blood. In postmortem temporal cortex, expression of RPS10P2-AS1 was increased 7-fold in individuals with ASD (P = 0.02) and increased 8-fold in individuals with the ASD-associated rs4141463 genotype (P = 0.01). Further, RPS10P2-AS1 expression was increased in human neural progenitor cells exposed to model air pollutants, indicating that both genetic and environmental factors that contribute to ASD increased RPS10P2-AS1 expression. Overexpression of RPS10P2-AS1 in human neural progenitor cells indicated substantial changes in neuronal gene expression. These data indicate that genome-wide significant associations with ASD implicate long noncoding RNAs. Because long noncoding RNAs are more abundant in human brain than protein-coding RNAs, this class of molecules is likely to contribute to ASD risk.
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Affiliation(s)
- Stephanie M Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI, United States
| | - Kristy Lewis
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI, United States
| | - Nicole Grepo
- Center for Gene Therapy, City of Hope, Duarte, CA, United States
| | - Daniel B Campbell
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI, United States
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26
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Alonso-Gonzalez A, Calaza M, Rodriguez-Fontenla C, Carracedo A. Novel Gene-Based Analysis of ASD GWAS: Insight Into the Biological Role of Associated Genes. Front Genet 2019; 10:733. [PMID: 31447886 PMCID: PMC6696953 DOI: 10.3389/fgene.2019.00733] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/11/2019] [Indexed: 11/30/2022] Open
Abstract
Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by its significant social impact and high heritability. The latest meta-analysis of ASD GWAS (genome-wide association studies) has revealed the association of several SNPs that were replicated in additional sets of independent samples. However, summary statistics from GWAS can be used to perform a gene-based analysis (GBA). GBA allows to combine all genetic information across the gene to create a single statistic (p-value for each gene). Thus, PASCAL (Pathway scoring algorithm), a novel GBA tool, has been applied to the summary statistics from the latest meta-analysis of ASD. GBA approach (testing the gene as a unit) provides an advantage to perform an accurate insight into the biological ASD mechanisms. Therefore, a gene-network analysis and an enrichment analysis for KEGG and GO terms were carried out. GENE2FUNC was used to create gene expression heatmaps and to carry out differential expression analysis (DEA) across GTEx v7 tissues and Brainspan data. dbMDEGA was employed to perform a DEG analysis between ASD and brain control samples for the associated genes and interactors. Results: PASCAL has identified the following loci associated with ASD: XRN2, NKX2-4, PLK1S1, KCNN2, NKX2-2, CRHR1-IT1, C8orf74 and LOC644172. While some of these genes were previously reported by MAGMA (XRN2, PLK1S1, and KCNN2), PASCAL has been useful to highlight additional genes. The biological characterization of the ASD-associated genes and their interactors have demonstrated the association of several GO and KEGG terms. Moreover, DEA analysis has revealed several up- and down-regulated clusters. In addition, many of the ASD-associated genes and their interactors have shown association with ASD expression datasets. Conclusions: This study identifies several associations at a gene level in ASD. Most of them were previously reported by MAGMA. This fact proves that PASCAL is an efficient GBA tool to extract additional information from previous GWAS. In addition, this study has characterized for the first time the biological role of the ASD-associated genes across brain regions, neurodevelopmental stages, and ASD gene-expression datasets.
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Affiliation(s)
- Aitana Alonso-Gonzalez
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Calaza
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristina Rodriguez-Fontenla
- Grupo de Medicina Genómica, CIBERER, CIMUS (Centre for Research in Molecular Medicine and Chronic Diseases), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Genómica, CIBERER, CIMUS (Centre for Research in Molecular Medicine and Chronic Diseases), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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27
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Replication of previous GWAS hits suggests the association between rs4307059 near MSNP1AS and autism in a Chinese Han population. Prog Neuropsychopharmacol Biol Psychiatry 2019; 92:194-198. [PMID: 30610940 DOI: 10.1016/j.pnpbp.2018.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/08/2018] [Accepted: 12/27/2018] [Indexed: 11/22/2022]
Abstract
Autism is a complex neurodevelopmental disorder with high heritability. Previous genome-wide association studies (GWAS) demonstrated that some single-nucleotide polymorphisms (SNPs) were significantly associated with autism, while other studies focusing on these GWAS hits showed inconsistent results. Besides, the association between these variants and autism in the Chinese Han population remains unclear. Therefore, this family-based association study was performed in 640 Chinese Han autism trios to investigate the association between autism and 7 SNPs with genome-wide significance in previous GWAS (rs4307059 near MSNP1AS, rs4141463 in MACROD2, rs2535629 in ITIH3, rs11191454 in AS3MT, rs1625579 in MIR137HG, rs11191580 in NT5C2, and rs1409313 in CUEDC2). The results showed a nominal association between the T allele of rs4307059 and autism under both additive model (T>C, Z = 2.250, P = .024) and recessive model (T>C, Z = 2.109, P = .035). The findings provided evidence that rs4307059 near MSNP1AS might be a susceptibility variant for autism in the Chinese Han population.
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28
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Genome-wide profiling of long noncoding RNA expression patterns and CeRNA analysis in mouse cortical neurons infected with different strains of borna disease virus. Genes Dis 2019; 6:147-158. [PMID: 31193942 PMCID: PMC6545444 DOI: 10.1016/j.gendis.2019.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/09/2019] [Indexed: 12/05/2022] Open
Abstract
Borna disease virus 1 (BoDV-1) is neurotropic prototype of Bornaviruses causing neurological diseases and maintaining persistent infection in brain cells of mammalian species. Long non-coding RNA (lncRNA) is transcript of more than 200 nucleotides without protein-coding function regulating various biological processes as proliferation, apoptosis, cell migration and viral infection. However, regulatory of lncRNAs in BoDV-1 infection remains unknown. To identify differential expression profiles and predict functions of lncRNA in BoDV-1 infection, microarray data showed that 3528 lncRNAs and 2661 lncRNAs were differentially expressed in Strain V and Hu-H1 BoDV-infected groups compared with control groups, respectively. Gene Ontology (GO) and pathway analysis suggested that differential lncRNAs may be involved in regulation of metabolic, biological regulation, cellular process, endocytosis, viral infections and cell adhesion processes, cancer in both BoDV-infected strains. ENSMUST00000128469 was found down-regulated in both BoDV-infected groups compared with control groups consistent with microarray (p < 0.05). ceRNA analysis indicated possible interaction networks as ENSMUST00000128469/miR-22-5p, miR-206-3p, miR-302b-5p, miR-302c-3p, miR-1a-3p/Igf1. Igf1 was found up-regulated in both BoDV-infected groups compared with control groups (p < 0.05). Possible functions of predicted target mRNAs and miRNAs of ENSMUST00000128469 were involved in cell proliferation, transcriptional misregulation and proteoglycan pathways enriched in cancer. lncRNA may be involved in regulation of Hu-H1 inhibited cell proliferation and promoted apoptosis through NF-kB, JNK/MAPK signaling, BCL2 and CDK6/E2F1 pathways different from Strain V. Possible interaction networks as ENSMUST00000128469/miR-22-5p, miR-206-3p, miR-302b-5p, miR-302c-3p, miR-1a-3p/Igf1 may involve in regulation of cell proliferation, apoptosis, and cancer.
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29
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Zan XY, Li L. Construction of lncRNA-mediated ceRNA network to reveal clinically relevant lncRNA biomarkers in glioblastomas. Oncol Lett 2019; 17:4369-4374. [PMID: 30944630 PMCID: PMC6444437 DOI: 10.3892/ol.2019.10114] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 02/07/2019] [Indexed: 12/27/2022] Open
Abstract
Cross-talk between competing endogenous RNAs (ceRNAs) play key roles in tumor development. In this study, we performed exon-level expression profiling on 26 glioblastomas (GBMs) and 6 controls to identify long non-coding RNAs (lncRNAs) of GBM initiation and progression using lncRNA-mediated ceRNA network (LMCN). The mRNA and lncRNA expression data, as well as miRNA-target interactions were firstly collected. Then, we used hypergeometric test to detect the lncRNA-mRNA interactions, followed by the construction of LMCN based on Pearson correlation coefficient. With the goal of investigation of the network organization, degree distribution of LMCN was performed. Next, the synergistic, competing lncRNA modules were identified using jActiveModule plug-in of Cytoscape. Moreover, we implemented the pathway analysis for its mRNAs in the module to explore the functions of significant lncRNAs. Using the criteria of degrees >50, 8 hub genes were identified, including EPB41L4A-AS1, ZRANB2-AS2, XIST, HOTAIR, TRAF3IP2-AS1, TPT1-AS1, PVT1 and DLG1-AS1. Furthermore, 1 synergistic, competitive module was identified. In this module, lncRNAs XIST and PVT1 were also the hubs in the synergistic, competing lncRNA module. Functional annotation demonstrated that 5 pathways were identified, including cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and mTOR signaling pathway. We have successfully identified several hubs (such as XIST and PVT1) and significant pathways (for instance, cytokine-cytokine receptor interaction, and neuroactive ligand-receptor interactions) for GBM via establishing the LMCN. These findings might offer potential biomarkers to early diagnose, and predict GBM prognosis in the future.
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Affiliation(s)
- Xiang-Yang Zan
- Department of Neurosurgery, Affiliated Traditional Chinese Medical Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830000, P.R. China
| | - Luo Li
- Department of Neurosurgery, Qingdao Municipal Hospital, Qingdao, Shandong 266071, P.R. China
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30
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Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF. Environmental and Genetic Factors in Autism Spectrum Disorders: Special Emphasis on Data from Arabian Studies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16040658. [PMID: 30813406 PMCID: PMC6406800 DOI: 10.3390/ijerph16040658] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 12/28/2022]
Abstract
One of the most common neurodevelopmental disorders worldwide is autism spectrum disorder (ASD), which is characterized by language delay, impaired communication interactions, and repetitive patterns of behavior caused by environmental and genetic factors. This review aims to provide a comprehensive survey of recently published literature on ASD and especially novel insights into excitatory synaptic transmission. Even though numerous genes have been discovered that play roles in ASD, a good understanding of the pathophysiologic process of ASD is still lacking. The protein⁻protein interactions between the products of NLGN, SHANK, and NRXN synaptic genes indicate that the dysfunction in synaptic plasticity could be one reason for the development of ASD. Designing more accurate diagnostic tests for the early diagnosis of ASD would improve treatment strategies and could enhance the appropriate monitoring of prognosis. This comprehensive review describes the psychotropic and antiepileptic drugs that are currently available as effective pharmacological treatments and provides in-depth knowledge on the concepts related to clinical, diagnostic, therapeutic, and genetic perspectives of ASD. An increase in the prevalence of ASD in Gulf Cooperation Council countries is also addressed in the review. Further, the review emphasizes the need for international networking and multidimensional studies to design novel and effective treatment strategies.
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Affiliation(s)
- Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
| | - Deem N Alkuroud
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
| | - Abdulla AlSulaiman
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
| | - Abdelhamid Elaissari
- Univ Lyon, University Claude Bernard Lyon-1, CNRS, LAGEP-UMR 5007, F-69622 Lyon, France.
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
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31
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Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease. Noncoding RNA 2019; 5:ncrna5010017. [PMID: 30781588 PMCID: PMC6468922 DOI: 10.3390/ncrna5010017] [Citation(s) in RCA: 373] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
The identification of RNAs that are not translated into proteins was an important breakthrough, defining the diversity of molecules involved in eukaryotic regulation of gene expression. These non-coding RNAs can be divided into two main classes according to their length: short non-coding RNAs, such as microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). The lncRNAs in association with other molecules can coordinate several physiological processes and their dysfunction may impact in several pathologies, including cancer and infectious diseases. They can control the flux of genetic information, such as chromosome structure modulation, transcription, splicing, messenger RNA (mRNA) stability, mRNA availability, and post-translational modifications. Long non-coding RNAs present interaction domains for DNA, mRNAs, miRNAs, and proteins, depending on both sequence and secondary structure. The advent of new generation sequencing has provided evidences of putative lncRNAs existence; however, the analysis of transcriptomes for their functional characterization remains a challenge. Here, we review some important aspects of lncRNA biology, focusing on their role as regulatory elements in gene expression modulation during physiological and disease processes, with implications in host and pathogens physiology, and their role in immune response modulation.
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32
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Luo T, Liu P, Wang XY, Li LZ, Zhao LP, Huang J, Li YM, Ou JL, Peng XQ. Effect of the autism-associated lncRNA Shank2-AS on architecture and growth of neurons. J Cell Biochem 2019; 120:1754-1762. [PMID: 30160788 DOI: 10.1002/jcb.27471] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/19/2018] [Indexed: 01/24/2023]
Abstract
The pathogenic mechanism of autism is complex, and current research has shown that long noncoding RNAs (lncRNAs) may play important roles in this process. The antisense lncRNA of SH3 and multiple ankyrin repeat domains 2 (Shank2-AS) is upregulated in patients with autism spectrum disorder (ASD), whereas the expression of its sense strand gene Shank2 is downregulated. In neuronal cells, Shank2-AS and Shank2 can form a double-stranded RNA and inhibit Shank2 expression. Overexpression of Shank2-AS decreases neurite numbers and lengths, thereby inhibiting the proliferation of neuronal cells and promoting their apoptosis. Overexpression of Shank2 inhibits the abovementioned effects of Shank2-AS, and transfection of a vector containing the 10th intron of Shank2 (Shank2-AS is reverse-transcribed from this region) also blocks the function of Shank2-AS. Shank2 small interfering RNA plays a role similar to Shank2-AS. Therefore, Shank2-AS is abnormally expressed in patients with ASD and may affect the structure and growth of neurons by regulating Shank2 expression, thereby facilitating the development of ASD.
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Affiliation(s)
- Ting Luo
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China.,School of Public Health, Central South University, Changsha, China
| | - Ping Liu
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiao-Yan Wang
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Le-Zhi Li
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Li-Ping Zhao
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jin Huang
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ya-Min Li
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jin-Lan Ou
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiao-Qing Peng
- Key Laboratory of Medical Information Research (Central South University), College of Hunan Province, Changsha, China
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33
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Mehta D, Czamara D. GWAS of Behavioral Traits. Curr Top Behav Neurosci 2019; 42:1-34. [PMID: 31407241 DOI: 10.1007/7854_2019_105] [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: 06/10/2023]
Abstract
Over the past decade, genome-wide association studies (GWAS) have evolved into a powerful tool to investigate genetic risk factors for human diseases via a hypothesis-free scan of the genome. The success of GWAS for psychiatric disorders and behavioral traits have been somewhat mixed, partly owing to the complexity and heterogeneity of these traits. Significant progress has been made in the last few years in the development and implementation of complex statistical methods and algorithms incorporating GWAS. Such advanced statistical methods applied to GWAS hits in combination with incorporation of different layers of genomics data have catapulted the search for novel genes for behavioral traits and improved our understanding of the complex polygenic architecture of these traits.This chapter will give a brief overview on GWAS and statistical methods currently used in GWAS. The chapter will focus on reviewing the current literature and highlight some of the most important GWAS on psychiatric and other behavioral traits and will conclude with a discussion on future directions.
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Affiliation(s)
- Divya Mehta
- School of Psychology and Counselling, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia.
| | - Darina Czamara
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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Quesnel-Vallières M, Weatheritt RJ, Cordes SP, Blencowe BJ. Autism spectrum disorder: insights into convergent mechanisms from transcriptomics. Nat Rev Genet 2018; 20:51-63. [DOI: 10.1038/s41576-018-0066-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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35
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Cheng Y, Li Z, Manupipatpong S, Lin L, Li X, Xu T, Jiang YH, Shu Q, Wu H, Jin P. 5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder. Hum Mol Genet 2018; 27:2955-2964. [PMID: 29790956 PMCID: PMC6097011 DOI: 10.1093/hmg/ddy193] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/26/2022] Open
Abstract
Autism spectrum disorders (ASDs) include a group of syndromes characterized by impaired language, social and communication skills, in addition to restrictive behaviors or stereotypes. However, with a prevalence of 1.5% in developed countries and high comorbidity rates, no clear underlying mechanism that unifies the heterogeneous phenotypes of ASD exists. 5-hydroxymethylcytosine (5hmC) is highly enriched in the brain and recognized as an essential epigenetic mark in developmental and brain disorders. To explore the role of 5hmC in ASD, we used the genomic DNA isolated from the postmortem cerebellum of both ASD patients and age-matched controls to profile genome-wide distribution of 5hmC. We identified 797 age-dependent differentially hydroxymethylated regions (DhMRs) in the young group (age ≤ 18), while no significant DhMR was identified in the groups over 18 years of age. Pathway and disease association analyses demonstrated that the intragenic DhMRs were in the genes involved in cell-cell communication and neurological disorders. Also, we saw significant 5hmC changes in the larger group of psychiatric genes. Interestingly, we found that the predicted cis functions of non-coding intergenic DhMRs strikingly associate with ASD and intellectual disorders. A significant fraction of intergenic DhMRs overlapped with topologically associating domains. These results together suggest that 5hmC alteration is associated with ASD, particularly in the early development stage, and could contribute to the pathogenesis of ASD.
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Affiliation(s)
- Ying Cheng
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ziyi Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Sasicha Manupipatpong
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xuekun Li
- The Children’s Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Tianlei Xu
- Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Neurobiology, University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qiang Shu
- The Children’s Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Cipolla GA, de Oliveira JC, Salviano-Silva A, Lobo-Alves SC, Lemos DS, Oliveira LC, Jucoski TS, Mathias C, Pedroso GA, Zambalde EP, Gradia DF. Long Non-Coding RNAs in Multifactorial Diseases: Another Layer of Complexity. Noncoding RNA 2018; 4:E13. [PMID: 29751665 PMCID: PMC6027498 DOI: 10.3390/ncrna4020013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/13/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023] Open
Abstract
Multifactorial diseases such as cancer, cardiovascular conditions and neurological, immunological and metabolic disorders are a group of diseases caused by the combination of genetic and environmental factors. High-throughput RNA sequencing (RNA-seq) technologies have revealed that less than 2% of the genome corresponds to protein-coding genes, although most of the human genome is transcribed. The other transcripts include a large variety of non-coding RNAs (ncRNAs), and the continuous generation of RNA-seq data shows that ncRNAs are strongly deregulated and may be important players in pathological processes. A specific class of ncRNAs, the long non-coding RNAs (lncRNAs), has been intensively studied in human diseases. For clinical purposes, lncRNAs may have advantages mainly because of their specificity and differential expression patterns, as well as their ideal qualities for diagnosis and therapeutics. Multifactorial diseases are the major cause of death worldwide and many aspects of their development are not fully understood. Recent data about lncRNAs has improved our knowledge and helped risk assessment and prognosis of these pathologies. This review summarizes the involvement of some lncRNAs in the most common multifactorial diseases, with a focus on those with published functional data.
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Affiliation(s)
- Gabriel A Cipolla
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | | | | | - Sara C Lobo-Alves
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | - Debora S Lemos
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | - Luana C Oliveira
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | - Tayana S Jucoski
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | - Carolina Mathias
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | - Gabrielle A Pedroso
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | - Erika P Zambalde
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
| | - Daniela F Gradia
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil.
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Saha P, Verma S, Pathak RU, Mishra RK. Long Noncoding RNAs in Mammalian Development and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:155-198. [PMID: 28815540 DOI: 10.1007/978-981-10-5203-3_6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively. These transcripts regulate epigenetic processes and constitute an important layer of regulatory information essential for organismal development and play a causative role in diseases. The noncoding RNA-directed regulatory circuit controls complex characteristics. Sequence variations in noncoding RNAs influence evolution, quantitative traits, and disease susceptibility. This chapter presents an account on a class of such noncoding transcripts that are longer than 200 nucleotides (long noncoding RNA-lncRNA) in mammalian development and diseases.
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Affiliation(s)
- Parna Saha
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Shreekant Verma
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Rashmi U Pathak
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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38
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Zhong J, Jiang L, Huang Z, Zhang H, Cheng C, Liu H, He J, Wu J, Darwazeh R, Wu Y, Sun X. The long non-coding RNA Neat1 is an important mediator of the therapeutic effect of bexarotene on traumatic brain injury in mice. Brain Behav Immun 2017; 65:183-194. [PMID: 28483659 DOI: 10.1016/j.bbi.2017.05.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/03/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Bexarotene treatments exert neuroprotective effects on mice following traumatic brain injury (TBI). The present study aims to investigate the potential roles of the long noncoding RNA Neat1 in the neuroprotective effects of bexarotene. MATERIALS AND METHODS Adult male C57BL/6J mice (n=80) and newborn mice (within 24h after birth) (n=20) were used to generate a "controlled cortical impact" (CCI) model and harvest primary cortex neurons, respectively. The HT22 cell line and the BV2 cell line were cultured under "normal" or "oxygen/glucose-deprived" (OGD) conditions. The relationship between RXR-α and the Neat1 promoter was clarified using ChIP-qPCR and dual-luciferase reporter gene assays. The mRNA alterations induced by Neat1 knockdown were measured using next-generation RNA sequencing. Proteins were captured by Neat1, pulled down and subjected to mass spectrometry. The neurological severity score, rotarod test and water maze test were employed to measure the animals' motor and cognitive functions. RESULTS Bexarotene prominently up-regulated the Neat1 level in an RXR-α-dependent manner. Neat1 knockdown induced significant changes in mRNA expression, and the altered mRNAs were involved in many biological processes, including synapse formation and axon guidance. In primary neurons, Neat1 knockdown inhibited and Neat1 over-expression prompted axon elongation. Multiple proteins, including Pidd1, were captured by Neat1. Neat1 inhibited cell apoptosis and restricted inflammation by capturing Pidd1. The in vitro anti-apoptotic and anti-inflammatory effects of Neat1 were further confirmed in C57BL/6 mice, which resulted in better motor and cognitive function after TBI. CONCLUSION Bexarotene up-regulates the lncRNA Neat1, which inhibits apoptosis and inflammation, thereby resulting in better functional recovery in mice after TBI.
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Affiliation(s)
- Jianjun Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Li Jiang
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China.
| | - Zhijian Huang
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Hongrong Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Chongjie Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Han Liu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Junchi He
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Jingchuan Wu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Rami Darwazeh
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Yue Wu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, China.
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Tang J, Yu Y, Yang W. Long noncoding RNA and its contribution to autism spectrum disorders. CNS Neurosci Ther 2017; 23:645-656. [PMID: 28635106 PMCID: PMC6492731 DOI: 10.1111/cns.12710] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022] Open
Abstract
Recent studies have indicated that long noncoding RNAs (lncRNAs) play important roles in multiple processes, such as epigenetic regulation, gene expression regulation, development, nutrition-related and other diseases, toxic response, and response to drugs. Although the functional roles and mechanisms of several lncRNAs have been discovered, a better understanding of the vast majority of lncRNAs remains elusive. To understand the functional roles and mechanisms of lncRNAs is critical because these transcripts represent the majority of the transcriptional output of the mammalian genome. Recent studies have also suggested that lncRNAs are more abundant in the human brain and are involved in neurodevelopment and neurodevelopmental disorders, including autism spectrum disorders (ASDs). In this study, we review several known functions of lncRNAs and the potential contribution of lncRNAs to ASDs and to other genetic syndromes that have a similar clinical presentation to ASDs, such as fragile X syndrome and Rett syndrome.
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Affiliation(s)
- Jie Tang
- The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Preventive MedicineSchool of Public HealthGuangzhou Medical UniversityXinzaoPanyu DistrictGuangzhouChina
| | - Yizhen Yu
- Department of Child and Women Health CareSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wei Yang
- Department of Nutrition and Food HygieneHubei Key Laboratory of Food Nutrition and SafetyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Nutrition and Food HygieneMOE Key Lab of Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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40
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Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain. Transl Psychiatry 2017; 7:e1199. [PMID: 28786976 PMCID: PMC5611730 DOI: 10.1038/tp.2017.163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs orchestrate brain functioning via interaction with microRNA recognition elements (MRE) on target transcripts. However, the global impact of potential competition on the microRNA pool between coding and non-coding brain transcripts that share MREs with them remains unexplored. Here we report that non-coding pseudogene transcripts carrying MREs (PSG+MRE) often show duplicated origin, evolutionary conservation and higher expression in human temporal lobe neurons than comparable duplicated MRE-deficient pseudogenes (PSG-MRE). PSG+MRE participate in neuronal RNA-induced silencing complexes (RISC), indicating functional involvement. Furthermore, downregulation cell culture experiments validated bidirectional co-regulation of PSG+MRE with MRE-sharing coding transcripts, frequently not their mother genes, and with targeted microRNAs; also, PSG+MRE single-nucleotide polymorphisms associated with schizophrenia, bipolar disorder and autism, suggesting interaction with mental diseases. Our findings indicate functional roles of duplicated PSG+MRE in brain development and cognition, supporting physiological impact of the reciprocal co-regulation of PSG+MRE with MRE-sharing coding transcripts in human brain neurons.
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41
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Oswald F, Klöble P, Ruland A, Rosenkranz D, Hinz B, Butter F, Ramljak S, Zechner U, Herlyn H. The FOXP2-Driven Network in Developmental Disorders and Neurodegeneration. Front Cell Neurosci 2017; 11:212. [PMID: 28798667 PMCID: PMC5526973 DOI: 10.3389/fncel.2017.00212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/04/2017] [Indexed: 12/24/2022] Open
Abstract
The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing FOXP2 cDNA of either humans or the common chimpanzee, Rhesus monkey, and marmoset, respectively. RNA-seq led to identification of 27 genes with differential regulation under the control of human FOXP2, which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation. RT-qPCR and Western blotting indicated differential regulation of additional 13 new target genes in response to overexpression of human FOXP2. These genes may be directly regulated by FOXP2 considering numerous matches of established FOXP2-binding motifs as well as publicly available FOXP2-ChIP-seq reads within their putative promoters. Ontology analysis of the new and reproduced targets, along with their interactors in a network, revealed an enrichment of terms relating to cellular signaling and communication, metabolism and catabolism, cellular migration and differentiation, and expression regulation. Notably, terms including the words "neuron" or "axonogenesis" were also enriched. Complementary literature screening uncovered many connections to human developmental (autism spectrum disease, schizophrenia, Down syndrome, agenesis of corpus callosum, trismus-pseudocamptodactyly, ankyloglossia, facial dysmorphology) and neurodegenerative diseases and disorders (Alzheimer's, Parkinson's, and Huntington's diseases, Lewy body dementia, amyotrophic lateral sclerosis). Links to deafness and dyslexia were detected, too. Such relations existed for single proteins (e.g., DCDC2, NURR1, PHOX2B, MYH8, and MYH13) and groups of proteins which conjointly function in mRNA processing, ribosomal recruitment, cell-cell adhesion (e.g., CDH4), cytoskeleton organization, neuro-inflammation, and processing of amyloid precursor protein. Conspicuously, many links pointed to an involvement of the FOXP2-driven network in JAK/STAT signaling and the regulation of the ezrin-radixin-moesin complex. Altogether, the applied phylogenetic perspective substantiated FOXP2's importance for nervous system development, maintenance, and functioning. However, the study also disclosed new regulatory pathways that might prove to be useful for understanding the molecular background of the aforementioned developmental disorders and neurodegenerative diseases.
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Affiliation(s)
- Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center UlmUlm, Germany
| | - Patricia Klöble
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center UlmUlm, Germany
| | - André Ruland
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center UlmUlm, Germany
| | - David Rosenkranz
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-University MainzMainz, Germany
| | - Bastian Hinz
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-University MainzMainz, Germany
- Institute of Human Genetics, University Medical Center MainzMainz, Germany
| | - Falk Butter
- Institute of Molecular BiologyMainz, Germany
| | | | - Ulrich Zechner
- Institute of Human Genetics, University Medical Center MainzMainz, Germany
- Dr. Senckenbergisches Zentrum für HumangenetikFrankfurt, Germany
| | - Holger Herlyn
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-University MainzMainz, Germany
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42
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Reilly J, Gallagher L, Chen JL, Leader G, Shen S. Bio-collections in autism research. Mol Autism 2017; 8:34. [PMID: 28702161 PMCID: PMC5504648 DOI: 10.1186/s13229-017-0154-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with diverse clinical manifestations and symptoms. In the last 10 years, there have been significant advances in understanding the genetic basis for ASD, critically supported through the establishment of ASD bio-collections and application in research. Here, we summarise a selection of major ASD bio-collections and their associated findings. Collectively, these include mapping ASD candidate genes, assessing the nature and frequency of gene mutations and their association with ASD clinical subgroups, insights into related molecular pathways such as the synapses, chromatin remodelling, transcription and ASD-related brain regions. We also briefly review emerging studies on the use of induced pluripotent stem cells (iPSCs) to potentially model ASD in culture. These provide deeper insight into ASD progression during development and could generate human cell models for drug screening. Finally, we provide perspectives concerning the utilities of ASD bio-collections and limitations, and highlight considerations in setting up a new bio-collection for ASD research.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
| | - Louise Gallagher
- Trinity Translational Medicine Institute and Department of Psychiatry, Trinity Centre for Health Sciences, St. James Hospital Street, Dublin 8, Ireland
| | - June L Chen
- Department of Special Education, Faculty of Education, East China Normal University, Shanghai, 200062 China
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
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Abstract
Background Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology. Methods Two ASD cortical transcriptome datasets were re-analyzed using consensus weighted gene co-expression network analysis (WGCNA) to identify common co-expression modules across datasets. Linear mixed-effect models and Bayesian replication statistics were used to identify replicable differentially expressed modules. Eigengene network analysis was then utilized to identify between-group differences in how co-expression modules interact and cluster into hierarchical meta-modular organization. Protein-protein interaction analyses were also used to determine whether dysregulated co-expression modules show enhanced interactions. Results We find replicable evidence for 10 gene co-expression modules that are differentially expressed in ASD cortex. Rather than being independent non-interacting sources of pathology, these dysregulated co-expression modules work in synergy and physically interact at the protein level. These systems-level transcriptional signals are characterized by downregulation of synaptic processes coordinated with upregulation of immune/inflammation, response to other organism, catabolism, viral processes, translation, protein targeting and localization, cell proliferation, and vasculature development. Hierarchical organization of meta-modules (clusters of highly correlated modules) is also highly affected in ASD. Conclusions These findings highlight that dysregulation of the ASD cortical transcriptome is characterized by the dysregulation of multiple coordinated transcriptional programs producing synergistic systems-level effects that cannot be fully appreciated by studying the individual component biological processes in isolation. Electronic supplementary material The online version of this article (doi:10.1186/s13229-017-0147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael V Lombardo
- Department of Psychology and Center for Applied Neuroscience, University of Cyprus, Nicosia, Cyprus.,Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Eric Courchesne
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California, San Diego, La Jolla, CA USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA USA.,Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA USA
| | - Tiziano Pramparo
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California, San Diego, La Jolla, CA USA
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Vojinovic D, Brison N, Ahmad S, Noens I, Pappa I, Karssen LC, Tiemeier H, van Duijn CM, Peeters H, Amin N. Variants in TTC25 affect autistic trait in patients with autism spectrum disorder and general population. Eur J Hum Genet 2017; 25:982-987. [PMID: 28513607 DOI: 10.1038/ejhg.2017.82] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 04/03/2017] [Accepted: 04/13/2017] [Indexed: 12/30/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder with a complex genetic architecture. To identify genetic variants underlying ASD, we performed single-variant and gene-based genome-wide association studies using a dense genotyping array containing over 2.3 million single-nucleotide variants in a discovery sample of 160 families with at least one child affected with non-syndromic ASD using a binary (ASD yes/no) phenotype and a quantitative autistic trait. Replication of the top findings was performed in Psychiatric Genomics Consortium and Erasmus Rucphen Family (ERF) cohort study. Significant association of quantitative autistic trait was observed with the TTC25 gene at 17q21.2 (effect size=10.2, P-value=3.4 × 10-7) in the gene-based analysis. The gene also showed nominally significant association in the cohort-based ERF study (effect=1.75, P-value=0.05). Meta-analysis of discovery and replication improved the association signal (P-valuemeta=1.5 × 10-8). No genome-wide significant signal was observed in the single-variant analysis of either the binary ASD phenotype or the quantitative autistic trait. Our study has identified a novel gene TTC25 to be associated with quantitative autistic trait in patients with ASD. The replication of association in a cohort-based study and the effect estimate suggest that variants in TTC25 may also be relevant for broader ASD phenotype in the general population. TTC25 is overexpressed in frontal cortex and testis and is known to be involved in cilium movement and thus an interesting candidate gene for autistic trait.
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Affiliation(s)
- Dina Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nathalie Brison
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ilse Noens
- Leuven Autism Research (LAuRes), Leuven, Belgium.,Parenting and Special Education Research Unit, KU Leuven, Leuven, Belgium
| | - Irene Pappa
- School of Pedagogical and Educational Sciences, Erasmus University Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lennart C Karssen
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,PolyOmica, s-Hertogenbosch, The Netherlands
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center-Sophia Children's Hospital, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Leiden Academic Centre for Drug Research (LACDR), Leiden University, The Netherlands
| | - Hilde Peeters
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium.,Leuven Autism Research (LAuRes), Leuven, Belgium
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Adkins AE, Hack LM, Bigdeli TB, Williamson VS, McMichael GO, Mamdani M, Edwards A, Aliev F, Chan RF, Bhandari P, Raabe RC, Alaimo JT, Blackwell GG, Moscati AA, Poland RS, Rood B, Patterson DG, Walsh D, Whitfield JB, Zhu G, Montgomery GW, Henders AK, Martin NG, Heath AC, Madden PA, Frank J, Ridinger M, Wodarz N, Soyka M, Zill P, Ising M, Nöthen MM, Kiefer F, Rietschel M, Gelernter J, Sherva R, Koesterer R, Almasy L, Zhao H, Kranzler HR, Farrer LA, Maher BS, Prescott CA, Dick DM, Bacanu SA, Mathies LD, Davies AG, Vladimirov VI, Grotewiel M, Bowers MS, Bettinger JC, Webb BT, Miles MF, Kendler KS, Riley BP. Genomewide Association Study of Alcohol Dependence Identifies Risk Loci Altering Ethanol-Response Behaviors in Model Organisms. Alcohol Clin Exp Res 2017; 41:911-928. [PMID: 28226201 PMCID: PMC5404949 DOI: 10.1111/acer.13362] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 02/16/2017] [Indexed: 01/23/2023]
Abstract
BACKGROUND Alcohol dependence (AD) shows evidence for genetic liability, but genes influencing risk remain largely unidentified. METHODS We conducted a genomewide association study in 706 related AD cases and 1,748 unscreened population controls from Ireland. We sought replication in 15,496 samples of European descent. We used model organisms (MOs) to assess the role of orthologous genes in ethanol (EtOH)-response behaviors. We tested 1 primate-specific gene for expression differences in case/control postmortem brain tissue. RESULTS We detected significant association in COL6A3 and suggestive association in 2 previously implicated loci, KLF12 and RYR3. None of these signals are significant in replication. A suggestive signal in the long noncoding RNA LOC339975 is significant in case:control meta-analysis, but not in a population sample. Knockdown of a COL6A3 ortholog in Caenorhabditis elegans reduced EtOH sensitivity. Col6a3 expression correlated with handling-induced convulsions in mice. Loss of function of the KLF12 ortholog in C. elegans impaired development of acute functional tolerance (AFT). Klf12 expression correlated with locomotor activation following EtOH injection in mice. Loss of function of the RYR3 ortholog reduced EtOH sensitivity in C. elegans and rapid tolerance in Drosophila. The ryanodine receptor antagonist dantrolene reduced motivation to self-administer EtOH in rats. Expression of LOC339975 does not differ between cases and controls but is reduced in carriers of the associated rs11726136 allele in nucleus accumbens (NAc). CONCLUSIONS We detect association between AD and COL6A3, KLF12, RYR3, and LOC339975. Despite nonreplication of COL6A3, KLF12, and RYR3 signals, orthologs of these genes influence behavioral response to EtOH in MOs, suggesting potential involvement in human EtOH response and AD liability. The associated LOC339975 allele may influence gene expression in human NAc. Although the functions of long noncoding RNAs are poorly understood, there is mounting evidence implicating these genes in multiple brain functions and disorders.
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Affiliation(s)
- Amy E. Adkins
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Laura M. Hack
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Tim B. Bigdeli
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Vernell S. Williamson
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - G. Omari McMichael
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Mohammed Mamdani
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Alexis Edwards
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Fazil Aliev
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Robin F. Chan
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Poonam Bhandari
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Richard C. Raabe
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Joseph T. Alaimo
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - GinaMari G. Blackwell
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Arden A. Moscati
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Ryan S. Poland
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Benjamin Rood
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Diana G. Patterson
- Shaftesbury Square Hospital, 116-120 Great Victoria Street, Belfast,
BT2 7BG, United Kingdom
| | - Dermot Walsh
- Health Research Board, 67-72 Lower Mount Street, Dublin 2,
Ireland
| | | | - John B. Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Gu Zhu
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Grant W. Montgomery
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Anjali K. Henders
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Andrew C. Heath
- Department of Psychiatry, Washington University School of Medicine,
4560 Clayton Ave., Suite 1000, St. Louis, MO, 63110, USA
| | - Pamela A.F. Madden
- Department of Psychiatry, Washington University School of Medicine,
4560 Clayton Ave., Suite 1000, St. Louis, MO, 63110, USA
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute
of Mental Health, Medical Faculty Mannheim/Heidelberg University, J 5, 68159
Mannheim, Germany
| | - Monika Ridinger
- Department of Psychiatry, University Hospital Regensburg,
University of Regensburg, 93042 Regensburg, Germany
| | - Norbert Wodarz
- Department of Psychiatry, University Hospital Regensburg,
University of Regensburg, 93042 Regensburg, Germany
| | - Michael Soyka
- Privatklinik Meiringen, Willigen, 3860 Meiringen, Switzerland
- Department of Psychiatry and Psychotherapy, University of Munich,
Nussbaumstrasse 7, 80336 Munich, Germany
| | - Peter Zill
- Department of Psychiatry and Psychotherapy, University of Munich,
Nussbaumstrasse 7, 80336 Munich, Germany
| | - Marcus Ising
- Department of Molecular Psychology, Max-Planck-Institute of
Psychiatry, Kraepelinstrasse 2–10, 80804 Munich, Germany
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of
Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
- Department of Institute of Human Genetics, University of Bonn,
Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of
Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central
Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, J 5,
68159 Mannheim, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute
of Mental Health, Medical Faculty Mannheim/Heidelberg University, J 5, 68159
Mannheim, Germany
| | | | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Neurobiology, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Genetics, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Psychiatry, VA CT Healthcare Center, 950 Campbell
Avenue, West Haven, CT, 06516, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University
School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Ryan Koesterer
- Department of Medicine (Biomedical Genetics), Boston University
School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Laura Almasy
- Texas Biomedical Research Institute, Department of Genetics, P.O.
Box 760549, San Antonio, TX, 78245-0549, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Biostatistics, Yale University School of Medicine,
333 Cedar Street, New Haven, CT, 06510, USA
| | - Henry R. Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman
School of Medicine, Treatment Research Center, 3900 Chestnut Street, Philadelphia,
PA 19104, USA
- VISN 4 MIRECC, Philadelphia VA Medical Center, 3900 Woodland
Avenue, Philadelphia, PA, 19104, USA
| | - Lindsay A. Farrer
- Department of Psychiatry, VA CT Healthcare Center, 950 Campbell
Avenue, West Haven, CT, 06516, USA
- Department of Neurology, Boston University School of Medicine, 72
East Concord Street, Boston, MA, 02118, USA
- Department of Ophthalmology, Boston University School of Medicine,
72 East Concord Street, Boston, MA, 02118, USA
- Department of Genetics and Genomics, Boston University School of
Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Epidemiology and Biostatistics, Boston University
School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of
Public Health, 624 N. Broadway, 8th Floor, Baltimore, MD, 21205, USA
| | - Carol A. Prescott
- Department of Psychology, University of Southern California, SGM
501, 3620 South McClintock Ave., Los Angeles, CA, 90089-1061, USA
| | - Danielle M. Dick
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Silviu A. Bacanu
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Laura D. Mathies
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Andrew G. Davies
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Vladimir I. Vladimirov
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Lieber Institute for Brain Development, Johns Hopkins University,
855 North Wolfe Street Suite 300, Baltimore, MD, 21205, USA
- Center for Biomarker Research and Personalized Medicine, School of
Pharmacy, PO Box 980533, Virginia Commonwealth University, Richmond, VA 23298-0533,
USA
| | - Mike Grotewiel
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - M. Scott Bowers
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Jill C. Bettinger
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Bradley T. Webb
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Michael F. Miles
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Kenneth S. Kendler
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Brien P. Riley
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
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Liu YW, Xia R, Lu K, Xie M, Yang F, Sun M, De W, Wang C, Ji G. LincRNAFEZF1-AS1 represses p21 expression to promote gastric cancer proliferation through LSD1-Mediated H3K4me2 demethylation. Mol Cancer 2017; 16:39. [PMID: 28209170 PMCID: PMC5314465 DOI: 10.1186/s12943-017-0588-9] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/13/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Although the prognosis of gastric cancer patients have a favorable progression, there are some patients with unusual patterns of locoregional and systemic recurrence. Therefore, a better understanding of early molecular events of the disease is needed. Current evidences demonstrate that long noncoding RNAs (lncRNAs) may be an important class of functional regulators involved in human gastric cancers development. Our previous studies suggest that HOTAIR contributes to gastric cancer development, and the overexpression of HOTAIR predicts a poor prognosis. In this study, we investigated the characteristic of the LncRNA FEZF1-AS1 in gastric cancer. METHODS QRT-PCR was used to detect the expression of FEZF1-AS1 in gastric cancer tissues and cells. MTT assays, clonogenic survival assays and nude mouse xenograft model were used to examine the tumorigenesis function of FEZF1-AS1 in vitro and in vivo. Bioinformatics analysis were used to select downstream target genes of FEZF1-AS1. Cell cycle analysis, ChIP, RIP,RNA Pulldown assays were examined to dissect molecular mechanisms. RESULTS In this study, we reported that FEZF1-AS1, a 2564 bp RNA, was overexpressed in gastric cancer, and upregulated FEZF1-AS1 expression indicated larger tumor size and higher clinical stage; additional higher expression of FEZF1-AS1 predicted poor prognosis. Further experiments revealed that knockdown FEZF1-AS1 significantly inhibited gastric cancer cells proliferation by inducing G1 arrest and apoptosis, whereas endogenous expression FEZF1-AS1 promoted cell growth. Additionally, RIP assay and RNA-pulldown assay evidenced that FEZF1-AS1 could epigenetically repress the expression of P21 via binding with LSD1, the first discovered demethylase. ChIP assays demonstrated that LSD1 could directly bind to the promoter of P21, inducing H3K4me2 demethylation. CONCLUSION In summary, these data demonstrated that FEZF1-AS1 could act as an "oncogene" for gastric cancer partly through suppressing P21 expression; FEZF1-AS1 may be served as a candidate prognostic biomarker and target for new therapies of gastric cancer patients.
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Affiliation(s)
- Yan-Wen Liu
- Department of Oncology, Zhongda Hospital, Medical School, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Rui Xia
- Department of Laboratory, Affiliated Chest Hospital of southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Kai Lu
- Department of surgery, Affiliated the second hospital of Bengbu Medical College, Lianyungang, jiangsu, People's Republic of China
| | - Min Xie
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Fen Yang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Ming Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Wei De
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.
| | - Cailian Wang
- Department of Oncology, Zhongda Hospital, Medical School, Southeast University, Nanjing, Jiangsu, People's Republic of China.
| | - Guozhong Ji
- Department of Gastroenterology Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.
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Abstract
Long noncoding RNAs (lncRNAs) are nonprotein coding transcripts longer than 200 nucleotides. Many of these lncRNAs have regulatory functions and have recently emerged as major players in governing fundamental biological processes. Here, we review the definition, distribution, identification, databases, analysis, classification, and functions of lncRNAs. We also discuss the potential roles of lncRNAs in the etiological processes of psychiatric disorders and the implications for clinical diagnosis and treatment.
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48
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DeWitt JJ, Hecht PM, Grepo N, Wilkinson B, Evgrafov OV, Morris KV, Knowles JA, Campbell DB. Transcriptional Gene Silencing of the Autism-Associated Long Noncoding RNA MSNP1AS in Human Neural Progenitor Cells. Dev Neurosci 2016; 38:375-383. [PMID: 28030860 DOI: 10.1159/000453258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/08/2016] [Indexed: 12/21/2022] Open
Abstract
The long noncoding RNA MSNP1AS (moesin pseudogene 1, antisense) is a functional element that was previously associated with autism spectrum disorder (ASD) with genome-wide significance. Expression of MSNP1AS was increased 12-fold in the cerebral cortex of individuals with ASD and 22-fold in individuals with a genome-wide significantly associated ASD genetic marker on chromosome 5p14.1. Overexpression of MSNP1AS in human neuronal cells caused decreased expression of moesin protein, which is involved in neuronal process stability. In this study, we hypothesize that MSNP1AS knockdown impacts global transcriptome levels. We transfected the human neural progenitor cell line SK- N-SH with constructs that caused a 50% suppression of MSNP1AS expression. After 24 h, cells were harvested for total RNA isolation. Strand-specific RNA sequencing analysis indicated altered expression of 1,352 genes, including altered expression of 318 genes following correction for multiple comparisons. Expression of the OAS2 gene was increased >150-fold, a result that was validated by quantitative PCR. Gene ontology analysis of the 318 genes with altered expression following correction for multiple comparisons indicated that upregulated genes were significantly enriched for genes involved in immune response, and downregulated genes were significantly enriched for genes involved in chromatin remodeling. These data indicate multiple transcriptional and translational functions of MSNP1AS that impact ASD-relevant biological processes. Chromatin remodeling and immune response are biological processes implicated by genes with rare mutations associated with ASD. Our data suggest that the functional elements implicated by association of common genetic variants impact the same biological processes, suggesting a possible shared common molecular pathway of ASD.
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Affiliation(s)
- Jessica J DeWitt
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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49
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Gokoolparsadh A, Sutton GJ, Charamko A, Green NFO, Pardy CJ, Voineagu I. Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies. Cell Mol Life Sci 2016; 73:4517-4530. [PMID: 27405608 PMCID: PMC11108267 DOI: 10.1007/s00018-016-2304-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/16/2016] [Accepted: 07/05/2016] [Indexed: 01/07/2023]
Abstract
Autism spectrum disorder (ASD) is one of the most heritable neuropsychiatric conditions. The complex genetic landscape of the disorder includes both common and rare variants at hundreds of genetic loci. This marked heterogeneity has thus far hampered efforts to develop genetic diagnostic panels and targeted pharmacological therapies. Here, we give an overview of the current literature on the genetic basis of ASD, and review recent human brain transcriptome studies and their role in identifying convergent pathways downstream of the heterogeneous genetic variants. We also discuss emerging evidence on the involvement of non-coding genomic regions and non-coding RNAs in ASD.
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Affiliation(s)
- Akira Gokoolparsadh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Gavin J Sutton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Alexiy Charamko
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Nicole F Oldham Green
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Christopher J Pardy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia.
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50
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Reon BJ, Anaya J, Zhang Y, Mandell J, Purow B, Abounader R, Dutta A. Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis. PLoS Med 2016; 13:e1002192. [PMID: 27923049 PMCID: PMC5140055 DOI: 10.1371/journal.pmed.1002192] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/28/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Each year, over 16,000 patients die from malignant brain cancer in the US. Long noncoding RNAs (lncRNAs) have recently been shown to play critical roles in regulating neurogenesis and brain tumor progression. To better understand the role of lncRNAs in brain cancer, we performed a global analysis to identify and characterize all annotated and novel lncRNAs in both grade II and III gliomas as well as grade IV glioblastomas (glioblastoma multiforme [GBM]). METHODS AND FINDINGS We determined the expression of all lncRNAs in over 650 brain cancer and 70 normal brain tissue RNA sequencing datasets from The Cancer Genome Atlas (TCGA) and other publicly available datasets. We identified 611 induced and 677 repressed lncRNAs in glial tumors relative to normal brains. Hundreds of lncRNAs were specifically expressed in each of the three lower grade glioma (LGG) subtypes (IDH1/2 wt, IDH1/2 mut, and IDH1/2 mut 1p19q codeletion) and the four subtypes of GBMs (classical, mesenchymal, neural, and proneural). Overlap between the subtype-specific lncRNAs in GBMs and LGGs demonstrated similarities between mesenchymal GBMs and IDH1/2 wt LGGs, with 2-fold higher overlap than would be expected by random chance. Using a multivariate Cox regression survival model, we identified 584 and 282 lncRNAs that were associated with a poor and good prognosis, respectively, in GBM patients. We developed a survival algorithm for LGGs based on the expression of 64 lncRNAs that was associated with patient prognosis in a test set (hazard ratio [HR] = 2.168, 95% CI = 1.765-2.807, p < 0.001) and validation set (HR = 1.921, 95% CI = 1.333-2.767, p < 0.001) of patients from TCGA. The main limitations of this study are that further work is needed to investigate the clinical relevance of our findings, and that validation in an independent dataset is needed to determine the robustness of our survival algorithm. CONCLUSIONS This work identifies a panel of lncRNAs that appear to be prognostic in gliomas and provides a critical resource for future studies examining the role of lncRNAs in brain cancers.
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Affiliation(s)
- Brian J. Reon
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biochemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jordan Anaya
- Department of Biochemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ying Zhang
- Division of Neuro-Oncology, Neurology Department, University of Virginia Health System, Old Medical School, Charlottesville, Virginia, United States of America
| | - James Mandell
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Benjamin Purow
- Division of Neuro-Oncology, Neurology Department, University of Virginia Health System, Old Medical School, Charlottesville, Virginia, United States of America
| | - Roger Abounader
- Division of Neuro-Oncology, Neurology Department, University of Virginia Health System, Old Medical School, Charlottesville, Virginia, United States of America
| | - Anindya Dutta
- Department of Biochemistry, University of Virginia, Charlottesville, Virginia, United States of America
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