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Salemi M, Schillaci FA, Lanza G, Marchese G, Salluzzo MG, Cordella A, Caniglia S, Bruccheri MG, Truda A, Greco D, Ferri R, Romano C. Transcriptome Study in Sicilian Patients with Autism Spectrum Disorder. Biomedicines 2024; 12:1402. [PMID: 39061976 PMCID: PMC11274004 DOI: 10.3390/biomedicines12071402] [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: 04/24/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
ASD is a complex condition primarily rooted in genetics, although influenced by environmental, prenatal, and perinatal risk factors, ultimately leading to genetic and epigenetic alterations. These mechanisms may manifest as inflammatory, oxidative stress, hypoxic, or ischemic damage. To elucidate potential variances in gene expression in ASD, a transcriptome analysis of peripheral blood mononuclear cells was conducted via RNA-seq on 12 ASD patients and 13 healthy controls, all of Sicilian ancestry to minimize environmental confounds. A total of 733 different statistically significant genes were identified between the two cohorts. Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO) terms were employed to explore the pathways influenced by differentially expressed mRNAs. GSEA revealed GO pathways strongly associated with ASD, namely the GO Biological Process term "Response to Oxygen-Containing Compound". Additionally, the GO Cellular Component pathway "Mitochondrion" stood out among other pathways, with differentially expressed genes predominantly affiliated with this specific pathway, implicating the involvement of different mitochondrial functions in ASD. Among the differentially expressed genes, FPR2 was particularly highlighted, belonging to three GO pathways. FPR2 can modulate pro-inflammatory responses, with its intracellular cascades triggering the activation of several kinases, thus suggesting its potential utility as a biomarker of pro-inflammatory processes in ASD.
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Affiliation(s)
- Michele Salemi
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
| | - Francesca A. Schillaci
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
| | - Giuseppe Lanza
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
- Department of Surgery and Medical—Surgical Specialties, University of Catania, 95124 Catania, Italy
| | - Giovanna Marchese
- Genomix4Life S.r.l., 84081 Baronissi, Italy; (G.M.); (A.C.); (A.T.)
- Genome Research Center for Health—CRGS, 84081 Baronissi, Italy
| | - Maria Grazia Salluzzo
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
| | - Angela Cordella
- Genomix4Life S.r.l., 84081 Baronissi, Italy; (G.M.); (A.C.); (A.T.)
- Genome Research Center for Health—CRGS, 84081 Baronissi, Italy
| | - Salvatore Caniglia
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
| | - Maria Grazia Bruccheri
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
| | - Anna Truda
- Genomix4Life S.r.l., 84081 Baronissi, Italy; (G.M.); (A.C.); (A.T.)
- Genome Research Center for Health—CRGS, 84081 Baronissi, Italy
| | - Donatella Greco
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
| | - Raffaele Ferri
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
| | - Corrado Romano
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.A.S.); (G.L.); (M.G.S.); (S.C.); (M.G.B.); (D.G.); (R.F.); (C.R.)
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95124 Catania, Italy
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Mostafavi Abdolmaleky H, Alam R, Nohesara S, Deth RC, Zhou JR. iPSC-Derived Astrocytes and Neurons Replicate Brain Gene Expression, Epigenetic, Cell Morphology and Connectivity Alterations Found in Autism. Cells 2024; 13:1095. [PMID: 38994948 PMCID: PMC11240613 DOI: 10.3390/cells13131095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024] Open
Abstract
Excessive inflammatory reactions and oxidative stress are well-recognized molecular findings in autism and these processes can affect or be affected by the epigenetic landscape. Nonetheless, adequate therapeutics are unavailable, as patient-specific brain molecular markers for individualized therapies remain challenging. METHODS We used iPSC-derived neurons and astrocytes of patients with autism vs. controls (5/group) to examine whether they replicate the postmortem brain expression/epigenetic alterations of autism. Additionally, DNA methylation of 10 postmortem brain samples (5/group) was analyzed for genes affected in PSC-derived cells. RESULTS We found hyperexpression of TGFB1, TGFB2, IL6 and IFI16 and decreased expression of HAP1, SIRT1, NURR1, RELN, GPX1, EN2, SLC1A2 and SLC1A3 in the astrocytes of patients with autism, along with DNA hypomethylation of TGFB2, IL6, TNFA and EN2 gene promoters and a decrease in HAP1 promoter 5-hydroxymethylation in the astrocytes of patients with autism. In neurons, HAP1 and IL6 expression trended alike. While HAP1 promoter was hypermethylated in neurons, IFI16 and SLC1A3 promoters were hypomethylated and TGFB2 exhibited increased promoter 5-hydroxymethlation. We also found a reduction in neuronal arborization, spine size, growth rate, and migration, but increased astrocyte size and a reduced growth rate in autism. In postmortem brain samples, we found DNA hypomethylation of TGFB2 and IFI16 promoter regions, but DNA hypermethylation of HAP1 and SLC1A2 promoters in autism. CONCLUSION Autism-associated expression/epigenetic alterations in iPSC-derived cells replicated those reported in the literature, making them appropriate surrogates to study disease pathogenesis or patient-specific therapeutics.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Reza Alam
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Richard C Deth
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Abstract
Autism is often considered to reflect categorically 'different brains'. Neuropsychological research on autism spectrum disorder (ASD) however, has struggled to define this difference, or derive clear-cut boundaries between autism and non-autism. Consequently, restructuring or disbanding the ASD diagnosis is becoming increasingly advocated within research. Nonetheless, autism now exists as a salient social construction, of which 'difference' is a key facet. Clinical and educational professionals must influence this cautiously, as changes to autism's social construction may counterproductively affect the quality of life of autistic people. This paper therefore reviews ASD's value as both neuropsychological and social constructs. Although lacking neuropsychological validity, the autism label may be beneficial for autistic self-identity, reduction of stigma, and administering support. Whilst a shift away from case-control ASD research is warranted, lay notions of 'different brains' may be preserved.
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Affiliation(s)
- Daniel Crawshaw
- School of Psychology, University of Nottingham, University Park, Nottingham, UK
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Jiang M, Lu T, Yang K, Li X, Zhao L, Zhang D, Li J, Wang L. Autism spectrum disorder research: knowledge mapping of progress and focus between 2011 and 2022. Front Psychiatry 2023; 14:1096769. [PMID: 37181872 PMCID: PMC10168184 DOI: 10.3389/fpsyt.2023.1096769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Background In recent years, a large number of studies have focused on autism spectrum disorder (ASD). The present study used bibliometric analysis to describe the state of ASD research over the past decade and identify its trends and research fronts. Methods Studies on ASD published from 2011 to 2022 were obtained from the Web of Science Core Collection (WoSCC). Bibliometrix, CiteSpace, and VOSviewer were used for bibliometric analysis. Results A total of 57,108 studies were included in the systematic search, and articles were published in more than 6,000 journals. The number of publications increased by 181.7% (2,623 in 2011 and 7,390 in 2021). The articles in the field of genetics are widely cited in immunology, clinical research, and psychological research. Keywords co-occurrence analysis revealed that "causative mechanisms," "clinical features," and "intervention features" were the three main clusters of ASD research. Over the past decade, genetic variants associated with ASD have gained increasing attention, and immune dysbiosis and gut microbiota are the new development frontiers after 2015. Conclusion This study uses a bibliometric approach to visualize and quantitatively describe autism research over the last decade. Neuroscience, genetics, brain imaging studies, and gut microbiome studies improve our understanding of autism. In addition, the microbe-gut-brain axis may be an exciting research direction for ASD in the future. Therefore, through visual analysis of autism literature, this paper shows the development process, research hotspots, and cutting-edge trends in this field to provide theoretical reference for the development of autism in the future.
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Affiliation(s)
- Miaomiao Jiang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Tianlan Lu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Kang Yang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Xianjing Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Liyang Zhao
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Dai Zhang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- Translational Medicine Center of Chinese Institute for Brain Research, Beijing, China
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation (IBRR), South China Normal University, Guangzhou, China
| | - Jun Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Lifang Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
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Hess JL, Quinn TP, Zhang C, Hearn GC, Chen S, Kong SW, Cairns M, Tsuang MT, Faraone SV, Glatt SJ. BrainGENIE: The Brain Gene Expression and Network Imputation Engine. Transl Psychiatry 2023; 13:98. [PMID: 36949060 PMCID: PMC10033657 DOI: 10.1038/s41398-023-02390-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/24/2023] Open
Abstract
In vivo experimental analysis of human brain tissue poses substantial challenges and ethical concerns. To address this problem, we developed a computational method called the Brain Gene Expression and Network-Imputation Engine (BrainGENIE) that leverages peripheral-blood transcriptomes to predict brain tissue-specific gene-expression levels. Paired blood-brain transcriptomic data collected by the Genotype-Tissue Expression (GTEx) Project was used to train BrainGENIE models to predict gene-expression levels in ten distinct brain regions using whole-blood gene-expression profiles. The performance of BrainGENIE was compared to PrediXcan, a popular method for imputing gene expression levels from genotypes. BrainGENIE significantly predicted brain tissue-specific expression levels for 2947-11,816 genes (false-discovery rate-adjusted p < 0.05), including many transcripts that cannot be predicted significantly by a transcriptome-imputation method such as PrediXcan. BrainGENIE recapitulated measured diagnosis-related gene-expression changes in the brain for autism, bipolar disorder, and schizophrenia better than direct correlations from blood and predictions from PrediXcan. We developed a convenient software toolset for deploying BrainGENIE, and provide recommendations for how best to implement models. BrainGENIE complements and, in some ways, outperforms existing transcriptome-imputation tools, providing biologically meaningful predictions and opening new research avenues.
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Affiliation(s)
- Jonathan L Hess
- Department of Psychiatry & Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA
| | - Thomas P Quinn
- Applied Artificial Intelligence Institute (A2I2), Deakin University, Geelong, Australia
| | - Chunling Zhang
- Department of Neuroscience & Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA
| | - Gentry C Hearn
- Department of Neuroscience & Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA
| | - Samuel Chen
- Department of Psychiatry & Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Murray Cairns
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, Australia
- Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Australia
| | - Ming T Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
- Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, MA, USA
| | - Stephen V Faraone
- Department of Psychiatry & Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA
- Department of Neuroscience & Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stephen J Glatt
- Department of Psychiatry & Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA.
- Department of Neuroscience & Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, USA.
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Voinsky I, Zoabi Y, Shomron N, Harel M, Cassuto H, Tam J, Rose S, Scheck AC, Karim MA, Frye RE, Aran A, Gurwitz D. Blood RNA Sequencing Indicates Upregulated BATF2 and LY6E and Downregulated ISG15 and MT2A Expression in Children with Autism Spectrum Disorder. Int J Mol Sci 2022; 23:ijms23179843. [PMID: 36077244 PMCID: PMC9456089 DOI: 10.3390/ijms23179843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in over 100 genes are implicated in autism spectrum disorder (ASD). DNA SNPs, CNVs, and epigenomic modifications also contribute to ASD. Transcriptomics analysis of blood samples may offer clues for pathways dysregulated in ASD. To expand and validate published findings of RNA-sequencing (RNA-seq) studies, we performed RNA-seq of whole blood samples from an Israeli discovery cohort of eight children with ASD compared with nine age- and sex-matched neurotypical children. This revealed 10 genes with differential expression. Using quantitative real-time PCR, we compared RNAs from whole blood samples of 73 Israeli and American children with ASD and 26 matched neurotypical children for the 10 dysregulated genes detected by RNA-seq. This revealed higher expression levels of the pro-inflammatory transcripts BATF2 and LY6E and lower expression levels of the anti-inflammatory transcripts ISG15 and MT2A in the ASD compared to neurotypical children. BATF2 was recently reported as upregulated in blood samples of Japanese adults with ASD. Our findings support an involvement of these genes in ASD phenotypes, independent of age and ethnicity. Upregulation of BATF2 and downregulation of ISG15 and MT2A were reported to reduce cancer risk. Implications of the dysregulated genes for pro-inflammatory phenotypes, immunity, and cancer risk in ASD are discussed.
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Affiliation(s)
- Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yazeed Zoabi
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moria Harel
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
| | | | - Joseph Tam
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR 72205, USA
| | - Adrienne C. Scheck
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Mohammad A. Karim
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Richard E. Frye
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
- Rossignol Medical Center, Phoenix, AZ 85050, USA
| | - Adi Aran
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Correspondence: (A.A.); (D.G.)
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (A.A.); (D.G.)
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Duke CG, Bach SV, Revanna JS, Sultan FA, Southern NT, Davis MN, Carullo NVN, Bauman AJ, Phillips RA, Day JJ. An Improved CRISPR/dCas9 Interference Tool for Neuronal Gene Suppression. Front Genome Ed 2021; 2:9. [PMID: 34713218 PMCID: PMC8525373 DOI: 10.3389/fgeed.2020.00009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/03/2020] [Indexed: 01/01/2023] Open
Abstract
The expression of genetic material governs brain development, differentiation, and function, and targeted manipulation of gene expression is required to understand contributions of gene function to health and disease states. Although recent improvements in CRISPR/dCas9 interference (CRISPRi) technology have enabled targeted transcriptional repression at selected genomic sites, integrating these techniques for use in non-dividing neuronal systems remains challenging. Previously, we optimized a dual lentivirus expression system to express CRISPR-based activation machinery in post-mitotic neurons. Here we used a similar strategy to adapt an improved dCas9-KRAB-MeCP2 repression system for robust transcriptional inhibition in neurons. We find that lentiviral delivery of a dCas9-KRAB-MeCP2 construct driven by the neuron-selective human synapsin promoter enabled transgene expression in primary rat neurons. Next, we demonstrate transcriptional repression using CRISPR sgRNAs targeting diverse gene promoters, and show superiority of this system in neurons compared to existing RNA interference methods for robust transcript specific manipulation at the complex Brain-derived neurotrophic factor (Bdnf) gene. Our findings advance this improved CRISPRi technology for use in neuronal systems for the first time, potentially enabling improved ability to manipulate gene expression states in the nervous system.
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Affiliation(s)
- Corey G Duke
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Svitlana V Bach
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jasmin S Revanna
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Faraz A Sultan
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nicholas T Southern
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - M Natalie Davis
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nancy V N Carullo
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Allison J Bauman
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Robert A Phillips
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
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Napoli E, Flores A, Mansuri Y, Hagerman RJ, Giulivi C. Sulforaphane improves mitochondrial metabolism in fibroblasts from patients with fragile X-associated tremor and ataxia syndrome. Neurobiol Dis 2021; 157:105427. [PMID: 34153466 PMCID: PMC8475276 DOI: 10.1016/j.nbd.2021.105427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 02/09/2023] Open
Abstract
CGG expansions between 55 and 200 in the 5'-untranslated region of the fragile-X mental retardation gene (FMR1) increase the risk of developing the late-onset debilitating neuromuscular disease Fragile X-Associated Tremor/Ataxia Syndrome (FXTAS). While the science behind this mutation, as a paradigm for RNA-mediated nucleotide triplet repeat expansion diseases, has progressed rapidly, no treatment has proven effective at delaying the onset or decreasing morbidity, especially at later stages of the disease. Here, we demonstrated the beneficial effect of the phytochemical sulforaphane (SFN), exerted through NRF2-dependent and independent manner, on pathways relevant to brain function, bioenergetics, unfolded protein response, proteosome, antioxidant defenses, and iron metabolism in fibroblasts from FXTAS-affected subjects at all disease stages. This study paves the way for future clinical studies with SFN in the treatment of FXTAS, substantiated by the established use of this agent in clinical trials of diseases with NRF2 dysregulation and in which age is the leading risk factor.
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Affiliation(s)
- Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Amanda Flores
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616;,Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Yasmeen Mansuri
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Randi J. Hagerman
- Department of Pediatrics, University of California Davis Medical Center, Sacramento, CA;,Medical Investigations of Neurodevelopmental Disorders (M.I.N.D.) Institute, University of California Davis, CA 95817
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, United States of America; Medical Investigations of Neurodevelopmental Disorders (M.I.N.D.) Institute, University of California Davis, CA 95817, USA.
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9
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Schmidt RJ, Liang D, Busgang SA, Curtin P, Giulivi C. Maternal Plasma Metabolic Profile Demarcates a Role for Neuroinflammation in Non-Typical Development of Children. Metabolites 2021; 11:545. [PMID: 34436486 PMCID: PMC8400060 DOI: 10.3390/metabo11080545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/16/2022] Open
Abstract
Maternal and cord plasma metabolomics were used to elucidate biological pathways associated with increased diagnosis risk for autism spectrum disorders (ASD). Metabolome-wide associations were assessed in both maternal and umbilical cord plasma in relation to diagnoses of ASD and other non-typical development (Non-TD) compared to typical development (TD) in the Markers of Autism risk in Babies: Learning Early Signs (MARBLES) cohort study of children born to mothers who already have at least one child with ASD. Analyses were stratified by sample matrix type, machine mode, and annotation confidence level. Dimensionality reduction techniques were used [i.e, principal component analysis (PCA) and random subset weighted quantile sum regression (WQSRS)] to minimize the high multiple comparison burden. With WQSRS, a metabolite mixture obtained from the negative mode of maternal plasma decreased the odds of Non-TD compared to TD. These metabolites, all related to the prostaglandin pathway, underscored the relevance of neuroinflammation status. No other significant findings were observed. Dimensionality reduction strategies provided confirming evidence that a set of maternal plasma metabolites are important in distinguishing Non-TD compared to TD diagnosis. A lower risk for Non-TD was linked to anti-inflammatory elements, thereby linking neuroinflammation to detrimental brain function consistent with studies ranging from neurodevelopment to neurodegeneration.
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Affiliation(s)
- Rebecca J. Schmidt
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA 95616, USA;
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, School of Medicine, University of California Davis, Sacramento, CA 95817, USA
| | - Donghai Liang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - Stefanie A. Busgang
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (S.A.B.); (P.C.)
| | - Paul Curtin
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (S.A.B.); (P.C.)
| | - Cecilia Giulivi
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, School of Medicine, University of California Davis, Sacramento, CA 95817, USA
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
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The Potential Use of Peripheral Blood Mononuclear Cells as Biomarkers for Treatment Response and Outcome Prediction in Psychiatry: A Systematic Review. Mol Diagn Ther 2021; 25:283-299. [PMID: 33978935 DOI: 10.1007/s40291-021-00516-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Psychiatric disorders have a major impact on the global burden of disease while therapeutic interventions remain insufficient to adequately treat a large number of patients. Regrettably, the efficacy of several psychopharmacological treatment regimens becomes apparent only after 4-6 weeks, and at this point, a significant number of patients present as non-responsive. As such, many patients go weeks/months without appropriate treatment or symptom management. Adequate biomarkers for treatment success and outcome prediction are thus urgently needed. OBJECTIVE With this systematic review, we provide an overview of the use of peripheral blood mononuclear cells (PBMCs) and their signaling pathways in evaluating and/or predicting the effectiveness of different treatment regimens in the course of psychiatric illnesses. We highlight PBMC characteristics that (i) reflect treatment presence, (ii) allow differentiation of responders from non-responders, and (iii) prove predictive at baseline with regard to treatment outcome for a broad range of psychiatric intervention strategies. REVIEW METHODS A PubMed database search was performed to extract papers investigating the relation between any type of PBMC characteristic and treatment presence and/or outcome in patients suffering from severe mental illness. Criteria for eligibility were: written in English; psychiatric diagnosis based on DSM-III-R or newer; PBMC isolation via gradient centrifugation; comparison between treated and untreated patients via PBMC features; sample size ≥ n = 5 per experimental group. Papers not researching in vivo treatment effects between patients and healthy controls, non-clinical trials, and non-hypothesis-/data-driven (e.g., -omics designs) approaches were excluded. DATA SYNTHESIS Twenty-nine original articles were included and qualitatively summarized. Antidepressant and antipsychotic treatments were mostly reflected by intracellular inflammatory markers while intervention with mood stabilizers was evidenced through cell maturation pathways. Lastly, cell viability parameters mirrored predominantly non-pharmacological therapeutic strategies. As for response prediction, PBMC (subtype) counts and telomerase activity seemed most promising for antidepressant treatment outcome determination; full length brain-derived neurotrophic factor (BDNF)/truncated BDNF were shown to be most apt to prognosticate antipsychotic treatment. CONCLUSIONS We conclude that, although inherent limitations to and heterogeneity in study designs in combination with the scarce number of original studies hamper unambiguous identification, several PBMC characteristics-mostly related to inflammatory pathways and cell viability-indeed show promise towards establishment as clinically relevant treatment biomarkers.
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11
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Jangjoo M, Goodman SJ, Choufani S, Trost B, Scherer SW, Kelley E, Ayub M, Nicolson R, Georgiades S, Crosbie J, Schachar R, Anagnostou E, Grunebaum E, Weksberg R. An Epigenetically Distinct Subset of Children With Autism Spectrum Disorder Resulting From Differences in Blood Cell Composition. Front Neurol 2021; 12:612817. [PMID: 33935932 PMCID: PMC8085304 DOI: 10.3389/fneur.2021.612817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/23/2022] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that often involves impaired cognition, communication difficulties and restrictive, repetitive behaviors. ASD is extremely heterogeneous both clinically and etiologically, which represents one of the greatest challenges in studying the molecular underpinnings of ASD. While hundreds of ASD-associated genes have been identified that confer varying degrees of risk, no single gene variant accounts for >1% of ASD cases. Notably, a large number of ASD-risk genes function as epigenetic regulators, indicating potential epigenetic dysregulation in ASD. As such, we compared genome-wide DNA methylation (DNAm) in the blood of children with ASD (n = 265) to samples from age- and sex-matched, neurotypical controls (n = 122) using the Illumina Infinium HumanMethylation450 arrays. Results: While DNAm patterns did not distinctly separate ASD cases from controls, our analysis identified an epigenetically unique subset of ASD cases (n = 32); these individuals exhibited significant differential methylation from both controls than the remaining ASD cases. The CpG sites at which this subset was differentially methylated mapped to known ASD risk genes that encode proteins of the nervous and immune systems. Moreover, the observed DNAm differences were attributable to altered blood cell composition, i.e., lower granulocyte proportion and granulocyte-to-lymphocyte ratio in the ASD subset, as compared to the remaining ASD cases and controls. This ASD subset did not differ from the rest of the ASD cases in the frequency or type of high-risk genomic variants. Conclusion: Within our ASD cohort, we identified a subset of individuals that exhibit differential methylation from both controls and the remaining ASD group tightly associated with shifts in immune cell type proportions. This is an important feature that should be assessed in all epigenetic studies of blood cells in ASD. This finding also builds on past reports of changes in the immune systems of children with ASD, supporting the potential role of altered immunological mechanisms in the complex pathophysiology of ASD. The discovery of significant molecular and immunological features in subgroups of individuals with ASD may allow clinicians to better stratify patients, facilitating personalized interventions and improved outcomes.
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Affiliation(s)
- Maryam Jangjoo
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J. Goodman
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Brett Trost
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W. Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Elizabeth Kelley
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Muhammad Ayub
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON, Canada
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Russell Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Eyal Grunebaum
- Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada
- Division of Immunology and Allergy, The Hospital for Sick Children, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
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12
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Hewitson L, Mathews JA, Devlin M, Schutte C, Lee J, German DC. Blood biomarker discovery for autism spectrum disorder: A proteomic analysis. PLoS One 2021; 16:e0246581. [PMID: 33626076 PMCID: PMC7904196 DOI: 10.1371/journal.pone.0246581] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication and social interaction and restricted, repetitive patterns of behavior, interests, or activities. Given the lack of specific pharmacological therapy for ASD and the clinical heterogeneity of the disorder, current biomarker research efforts are geared mainly toward identifying markers for determining ASD risk or for assisting with a diagnosis. A wide range of putative biological markers for ASD is currently being investigated. Proteomic analyses indicate that the levels of many proteins in plasma/serum are altered in ASD, suggesting that a panel of proteins may provide a blood biomarker for ASD. Serum samples from 76 boys with ASD and 78 typically developing (TD) boys, 18 months-8 years of age, were analyzed to identify possible early biological markers for ASD. Proteomic analysis of serum was performed using SomaLogic’s SOMAScanTM assay 1.3K platform. A total of 1,125 proteins were analyzed. There were 86 downregulated proteins and 52 upregulated proteins in ASD (FDR < 0.05). Combining three different algorithms, we found a panel of 9 proteins that identified ASD with an area under the curve (AUC) = 0.8599±0.0640, with specificity and sensitivity of 0.8217±0.1178 and 0.835±0.1176, respectively. All 9 proteins were significantly different in ASD compared with TD boys, and were significantly correlated with ASD severity as measured by ADOS total scores. Using machine learning methods, a panel of serum proteins was identified that may be useful as a blood biomarker for ASD in boys. Further verification of the protein biomarker panel with independent test sets is warranted.
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Affiliation(s)
- Laura Hewitson
- The Johnson Center for Child Health and Development, Austin, TX, United States of America
| | - Jeremy A Mathews
- Departments of Mathematical Sciences and Biological Sciences, Bioinformatics & Computational Biology Program, University of Texas at Dallas, Dallas, TX, United States of America
| | - Morgan Devlin
- The Johnson Center for Child Health and Development, Austin, TX, United States of America
| | - Claire Schutte
- The Johnson Center for Child Health and Development, Austin, TX, United States of America
| | - Jeon Lee
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Dwight C German
- Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX, United States of America
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13
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Early screening of autism spectrum disorder using cry features. PLoS One 2020; 15:e0241690. [PMID: 33301502 PMCID: PMC7728261 DOI: 10.1371/journal.pone.0241690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 10/19/2020] [Indexed: 12/05/2022] Open
Abstract
The increase in the number of children with autism and the importance of early autism intervention has prompted researchers to perform automatic and early autism screening. Consequently, in the present paper, a cry-based screening approach for children with Autism Spectrum Disorder (ASD) is introduced which would provide both early and automatic screening. During the study, we realized that ASD specific features are not necessarily observable in all children with ASD and in all instances collected from each child. Therefore, we proposed a new classification approach to be able to determine such features and their corresponding instances. To test the proposed approach a set of data relating to children between 18 to 53 months which had been recorded using high-quality voice recording devices and typical smartphones at various locations such as homes and daycares was studied. Then, after preprocessing, the approach was used to train a classifier, using data for 10 boys with ASD and 10 Typically Developed (TD) boys. The trained classifier was tested on the data of 14 boys and 7 girls with ASD and 14 TD boys and 7 TD girls. The sensitivity, specificity, and precision of the proposed approach for boys were 85.71%, 100%, and 92.85%, respectively. These measures were 71.42%, 100%, and 85.71% for girls, respectively. It was shown that the proposed approach outperforms the common classification methods. Furthermore, it demonstrated better results than the studies which used voice features for screening ASD. To pilot the practicality of the proposed approach for early autism screening, the trained classifier was tested on 57 participants between 10 to 18 months. These 57 participants consisted of 28 boys and 29 girls and the results were very encouraging for the use of the approach in early ASD screening.
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14
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Hu VW, Bi C. Phenotypic Subtyping and Re-analyses of Existing Transcriptomic Data from Autistic Probands in Simplex Families Reveal Differentially Expressed and ASD Trait-Associated Genes. Front Neurol 2020; 11:578972. [PMID: 33281715 PMCID: PMC7689346 DOI: 10.3389/fneur.2020.578972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 12/25/2022] Open
Abstract
Autism spectrum disorder (ASD) describes a collection of neurodevelopmental disorders characterized by core symptoms that include social communication deficits and repetitive, stereotyped behaviors often coupled with restricted interests. Primary challenges to understanding and treating ASD are the genetic and phenotypic heterogeneity of cases that complicates all omics analyses as well as a lack of information on relationships among genes, pathways, and autistic traits. In this study, we re-analyze existing transcriptomic data from simplex families by subtyping individuals with ASD according to multivariate cluster analyses of clinical ADI-R scores that encompass a broad range of behavioral symptoms. We also correlate multiple ASD traits, such as deficits in verbal and non-verbal communication, play and social skills, ritualistic behaviors, and savant skills, with expression profiles using Weighted Gene Correlation Network Analyses (WGCNA). Our results show that subtyping greatly enhances the ability to identify differentially expressed genes involved in specific canonical pathways and biological functions associated with ASD within each phenotypic subgroup. Moreover, using WGCNA, we identify gene modules that correlate significantly with specific ASD traits. Network prediction analyses of the genes in these modules reveal canonical pathways as well as neurological functions and disorders relevant to the pathobiology of ASD. Finally, we compare the WGCNA-derived data on autistic traits in simplex families with analogous data from multiplex families using transcriptomic data from our previous studies. The comparison reveals overlapping trait-associated pathways as well as upstream regulators of the module-associated genes that may serve as useful targets for a precision medicine approach to ASD.
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Affiliation(s)
- Valerie W Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Chongfeng Bi
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
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15
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Zhu Y, Mordaunt CE, Durbin-Johnson BP, Caudill MA, Malysheva OV, Miller JW, Green R, James SJ, Melnyk SB, Fallin MD, Hertz-Picciotto I, Schmidt RJ, LaSalle JM. Expression Changes in Epigenetic Gene Pathways Associated With One-Carbon Nutritional Metabolites in Maternal Blood From Pregnancies Resulting in Autism and Non-Typical Neurodevelopment. Autism Res 2020; 14:11-28. [PMID: 33159718 PMCID: PMC7894157 DOI: 10.1002/aur.2428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
The prenatal period is a critical window for the development of autism spectrum disorder (ASD). The relationship between prenatal nutrients and gestational gene expression in mothers of children later diagnosed with ASD or non-typical development (Non-TD) is poorly understood. Maternal blood collected prospectively during pregnancy provides insights into the effects of nutrition, particularly one-carbon metabolites, on gene pathways and neurodevelopment. Genome-wide transcriptomes were measured with microarrays in 300 maternal blood samples in Markers of Autism Risk in Babies-Learning Early Signs. Sixteen different one-carbon metabolites, including folic acid, betaine, 5'-methyltretrahydrofolate (5-MeTHF), and dimethylglycine (DMG) were measured. Differential expression analysis and weighted gene correlation network analysis (WGCNA) were used to compare gene expression between children later diagnosed as typical development (TD), Non-TD and ASD, and to one-carbon metabolites. Using differential gene expression analysis, six transcripts (TGR-AS1, SQSTM1, HLA-C, and RFESD) were associated with child outcomes (ASD, Non-TD, and TD) with genome-wide significance. Genes nominally differentially expressed between ASD and TD significantly overlapped with seven high confidence ASD genes. WGCNA identified co-expressed gene modules significantly correlated with 5-MeTHF, folic acid, DMG, and betaine. A module enriched in DNA methylation functions showed a suggestive protective association with folic acid/5-MeTHF concentrations and ASD risk. Maternal plasma betaine and DMG concentrations were associated with a block of co-expressed genes enriched for adaptive immune, histone modification, and RNA processing functions. These results suggest that the prenatal maternal blood transcriptome is a sensitive indicator of gestational one-carbon metabolite status and changes relevant to children's later neurodevelopmental outcomes. LAY SUMMARY: Pregnancy is a time when maternal nutrition could interact with genetic risk for autism spectrum disorder. Blood samples collected during pregnancy from mothers who had a prior child with autism were examined for gene expression and nutrient metabolites, then compared to the diagnosis of the child at age three. Expression differences in gene pathways related to the immune system and gene regulation were observed for pregnancies of children with autism and non-typical neurodevelopment and were associated with maternal nutrients.
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Affiliation(s)
- Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and Perinatal Origins of Disparities Center, University of California, Davis, California, USA.,MIND Institute, School of Medicine, University of California, Davis, California, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, and Perinatal Origins of Disparities Center, University of California, Davis, California, USA.,MIND Institute, School of Medicine, University of California, Davis, California, USA
| | | | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Olga V Malysheva
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Joshua W Miller
- Department of Nutritional Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ralph Green
- Department of Pathology and Laboratory Medicine, University of California Davis School of Medicine, Sacramento, California, USA
| | - S Jill James
- Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Stepan B Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Irva Hertz-Picciotto
- MIND Institute, School of Medicine, University of California, Davis, California, USA.,Department of Public Health Sciences, University of California, Davis, California, USA
| | - Rebecca J Schmidt
- MIND Institute, School of Medicine, University of California, Davis, California, USA.,Department of Public Health Sciences, University of California, Davis, California, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and Perinatal Origins of Disparities Center, University of California, Davis, California, USA.,MIND Institute, School of Medicine, University of California, Davis, California, USA
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16
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Comprehensive Analysis of RNA-Seq Gene Expression Profiling of Brain Transcriptomes Reveals Novel Genes, Regulators, and Pathways in Autism Spectrum Disorder. Brain Sci 2020; 10:brainsci10100747. [PMID: 33080834 PMCID: PMC7603078 DOI: 10.3390/brainsci10100747] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental disorder with deficits in social communication ability and repetitive behavior. The pathophysiological events involved in the brain of this complex disease are still unclear. METHODS In this study, we aimed to profile the gene expression signatures of brain cortex of ASD patients, by using two publicly available RNA-seq studies, in order to discover new ASD-related genes. RESULTS We detected 1567 differentially expressed genes (DEGs) by meta-analysis, where 1194 were upregulated and 373 were downregulated genes. Several ASD-related genes previously reported were also identified. Our meta-analysis identified 235 new DEGs that were not detected using the individual RNA-seq studies used. Some of those genes, including seven DEGs (PAK1, DNAH17, DOCK8, DAPP1, PCDHAC2, and ERBIN, SLC7A7), have been confirmed in previous reports to be associated with ASD. Gene Ontology (GO) and pathways analysis showed several molecular pathways enriched by the DEGs, namely, osteoclast differentiation, TNF signaling pathway, complement and coagulation cascade. Topological analysis of protein-protein interaction of the ASD brain cortex revealed proteomics hub gene signatures: MYC, TP53, HDAC1, CDK2, BAG3, CDKN1A, GABARAPL1, EZH2, VIM, and TRAF1. We also identified the transcriptional factors (TFs) regulating DEGs, namely, FOXC1, GATA2, YY1, FOXL1, USF2, NFIC, NFKB1, E2F1, TFAP2A, HINFP. CONCLUSION Novel core genes and molecular signatures involved with ASD were identified by our meta-analysis.
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Ventura G, Calvano CD, Porcelli V, Palmieri L, De Giacomo A, Xu Y, Goodacre R, Palmisano F, Cataldi TRI. Phospholipidomics of peripheral blood mononuclear cells (PBMCs): the tricky case of children with autism spectrum disorder (ASD) and their healthy siblings. Anal Bioanal Chem 2020; 412:6859-6874. [DOI: 10.1007/s00216-020-02817-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022]
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18
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Vargason T, Grivas G, Hollowood-Jones KL, Hahn J. Towards a Multivariate Biomarker-Based Diagnosis of Autism Spectrum Disorder: Review and Discussion of Recent Advancements. Semin Pediatr Neurol 2020; 34:100803. [PMID: 32446437 PMCID: PMC7248126 DOI: 10.1016/j.spen.2020.100803] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An ever-evolving understanding of autism spectrum disorder (ASD) pathophysiology necessitates that diagnostic standards also evolve from being observation-based to include quantifiable clinical measurements. The multisystem nature of ASD motivates the use of multivariate methods of statistical analysis over common univariate approaches for discovering clinical biomarkers relevant to this goal. In addition to characterization of important behavioral patterns for improving current diagnostic instruments, multivariate analyses to date have allowed for thorough investigation of neuroimaging-based, genetic, and metabolic abnormalities in individuals with ASD. This review highlights current research using multivariate statistical analyses to quantify the value of these behavioral and physiological markers for ASD diagnosis. A detailed discussion of a blood-based diagnostic test for ASD using specific metabolite concentrations is also provided. The advancement of ASD biomarker research promises to provide earlier and more accurate diagnoses of the disorder.
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Affiliation(s)
- Troy Vargason
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY
| | - Genevieve Grivas
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY
| | - Kathryn L Hollowood-Jones
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY
| | - Juergen Hahn
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY.
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19
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Transcriptome signatures from discordant sibling pairs reveal changes in peripheral blood immune cell composition in Autism Spectrum Disorder. Transl Psychiatry 2020; 10:106. [PMID: 32291385 PMCID: PMC7156413 DOI: 10.1038/s41398-020-0778-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022] Open
Abstract
Notwithstanding several research efforts in the past years, robust and replicable molecular signatures for autism spectrum disorders from peripheral blood remain elusive. The available literature on blood transcriptome in ASD suggests that through accurate experimental design it is possible to extract important information on the disease pathophysiology at the peripheral level. Here we exploit the availability of a resource for molecular biomarkers in ASD, the Italian Autism Network (ITAN) collection, for the investigation of transcriptomic signatures in ASD based on a discordant sibling pair design. Whole blood samples from 75 discordant sibling pairs selected from the ITAN network where submitted to RNASeq analysis and data analyzed by complementary approaches. Overall, differences in gene expression between affected and unaffected siblings were small. In order to assess the contribution of differences in the relative proportion of blood cells between discordant siblings, we have applied two different cell deconvolution algorithms, showing that the observed molecular signatures mainly reflect changes in peripheral blood immune cell composition, in particular NK cells. The results obtained by the cell deconvolution approach are supported by the analysis performed by WGCNA. Our report describes the largest differential gene expression profiling in peripheral blood of ASD subjects and controls conducted by RNASeq. The observed signatures are consistent with the hypothesis of immune alterations in autism and an increased risk of developing autism in subjects exposed to prenatal infections or stress. Our study also points to a potential role of NMUR1, HMGB3, and PTPRN2 in ASD.
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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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21
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Ansel A, Posen Y, Ellis R, Deutsch L, Zisman PD, Gesundheit B. Biomarkers for Autism Spectrum Disorders (ASD): A Meta-analysis. Rambam Maimonides Med J 2019; 10:RMMJ.10375. [PMID: 31675302 PMCID: PMC6824829 DOI: 10.5041/rmmj.10375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE To compare the reported accuracy and sensitivity of the various modalities used to diagnose autism spectrum disorders (ASD) in efforts to help focus further biomarker research on the most promising methods for early diagnosis. METHODS The Medline scientific literature database was searched to identify publications assessing potential clinical ASD biomarkers. Reports were categorized by the modality used to assess the putative markers, including protein, genetic, metabolic, or objective imaging methods. The reported sensitivity, specificity, area under the curve, and overall agreement were summarized and analyzed to determine weighted averages for each diagnostic modality. Heterogeneity was measured using the I2 test. RESULTS Of the 71 papers included in this analysis, each belonging to one of five modalities, protein-based followed by metabolite-based markers provided the highest diagnostic accuracy, each with a pooled overall agreement of 83.3% and respective weighted area under the curve (AUC) of 89.5% and 88.3%. Sensitivity provided by protein markers was highest (85.5%), while metabolic (85.9%) and protein markers (84.7%) had the highest specificity. Other modalities showed degrees of sensitivity, specificity, and overall agreements in the range of 73%-80%. CONCLUSIONS Each modality provided for diagnostic accuracy and specificity similar or slightly higher than those reported for the gold-standard Autism Diagnostic Observation Schedule (ADOS) instrument. Further studies are required to identify the most predictive markers within each modality and to evaluate biological pathways or clustering with possible etiological relevance. Analyses will also be necessary to determine the potential of these novel biomarkers in diagnosing pediatric patients, thereby enabling early intervention.
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Affiliation(s)
| | - Yehudit Posen
- Cell-El Therapeutics Ltd, Jerusalem, Israel
- PSW Ltd, Rehovot, Israel
| | - Ronald Ellis
- Cell-El Therapeutics Ltd, Jerusalem, Israel
- Biotech & Biopharma Consulting, Jerusalem, Israel
| | - Lisa Deutsch
- Biostats Statistical Consulting Ltd, Modiin, Israel
| | | | - Benjamin Gesundheit
- Cell-El Therapeutics Ltd, Jerusalem, Israel
- To whom correspondence should be addressed. E-mail:
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22
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Mordaunt CE, Park BY, Bakulski KM, Feinberg JI, Croen LA, Ladd-Acosta C, Newschaffer CJ, Volk HE, Ozonoff S, Hertz-Picciotto I, LaSalle JM, Schmidt RJ, Fallin MD. A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood. Mol Autism 2019; 10:36. [PMID: 31673306 PMCID: PMC6814108 DOI: 10.1186/s13229-019-0287-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/08/2019] [Indexed: 12/17/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects more than 1% of children in the USA. ASD risk is thought to arise from both genetic and environmental factors, with the perinatal period as a critical window. Understanding early transcriptional changes in ASD would assist in clarifying disease pathogenesis and identifying biomarkers. However, little is known about umbilical cord blood gene expression profiles in babies later diagnosed with ASD compared to non-typically developing and non-ASD (Non-TD) or typically developing (TD) children. Methods Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in RNA from cord blood samples from both the Markers of Autism Risk in Babies-Learning Early Signs (MARBLES) and the Early Autism Risk Longitudinal Investigation (EARLI) high-risk pregnancy cohorts that enroll younger siblings of a child previously diagnosed with ASD. Younger siblings were diagnosed based on assessments at 36 months, and 59 ASD, 92 Non-TD, and 120 TD subjects were included. Using both differential expression analysis and weighted gene correlation network analysis, gene expression between ASD and TD, and between Non-TD and TD, was compared within each study and via meta-analysis. Results While cord blood gene expression differences comparing either ASD or Non-TD to TD did not reach genome-wide significance, 172 genes were nominally differentially expressed between ASD and TD cord blood (log2(fold change) > 0.1, p < 0.01). These genes were significantly enriched for functions in xenobiotic metabolism, chromatin regulation, and systemic lupus erythematosus (FDR q < 0.05). In contrast, 66 genes were nominally differentially expressed between Non-TD and TD, including 8 genes that were also differentially expressed in ASD. Gene coexpression modules were significantly correlated with demographic factors and cell type proportions. Limitations ASD-associated gene expression differences identified in this study are subtle, as cord blood is not the main affected tissue, it is composed of many cell types, and ASD is a heterogeneous disorder. Conclusions This is the first study to identify gene expression differences in cord blood specific to ASD through a meta-analysis across two prospective pregnancy cohorts. The enriched gene pathways support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology.
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Affiliation(s)
- Charles E Mordaunt
- 1Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Bo Y Park
- 2Department of Public Health, California State University, Fullerton, CA USA
| | - Kelly M Bakulski
- 3Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Jason I Feinberg
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Lisa A Croen
- 5Division of Research and Autism Research Program, Kaiser Permanente Northern California, Oakland, CA USA
| | | | - Craig J Newschaffer
- 6Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA USA
| | - Heather E Volk
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Sally Ozonoff
- 7Psychiatry and Behavioral Sciences and MIND Institute, University of California, Davis, CA USA
| | - Irva Hertz-Picciotto
- 8Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - Janine M LaSalle
- 1Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Rebecca J Schmidt
- 8Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - M Daniele Fallin
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
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23
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Ross JL, Bloy L, Roberts TP, Miller J, Xing C, Silverman L, Zinn AR. Y chromosome gene copy number and lack of autism phenotype in a male with an isodicentric Y chromosome and absent NLGN4Y expression. Am J Med Genet B Neuropsychiatr Genet 2019; 180:471-482. [PMID: 31161682 PMCID: PMC6730649 DOI: 10.1002/ajmg.b.32745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/26/2019] [Accepted: 05/01/2019] [Indexed: 11/10/2022]
Abstract
We describe a unique male with a dicentric Y chromosome whose phenotype was compared to that of males with 47,XYY (XYY). The male Y-chromosome aneuploidy XYY is associated with physical, behavioral/cognitive phenotypes, and autism spectrum disorders. We hypothesize that increased risk for these phenotypes is caused by increased copy number/overexpression of Y-encoded genes. Specifically, an extra copy of the neuroligin gene NLGN4Y might elevate the risk of autism in boys with XYY. We present a unique male with the karyotype 46,X,idic(Y)(q11.22), which includes duplication of the Y short arm and proximal long arm and deletion of the distal long arm, evaluated his physical, behavioral/cognitive, and neuroimaging/magnetoencephalography (MEG) phenotypes, and measured blood RNA expression of Y genes. The proband had tall stature and cognitive function within the typical range, without autism features. His blood RNA showed twofold increase in expression of Yp genes versus XY controls, and absent expression of deleted Yq genes, including NLGN4Y. The M100 latencies were similar to findings in typically developing males. In summary, the proband had overexpression of a subset of Yp genes, absent NLGN4Y expression, without ASD findings or XYY-MEG latency findings. These results are consistent with a role for NLGN4Y overexpression in the etiology of behavioral phenotypes associated with XYY. Further investigation of NLGN4Y as an ASD risk gene in XYY is warranted. The genotype and phenotype(s) of this subject may also provide insight into how Y chromosome genes contribute to normal male development and the male predominance in ASD.
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Affiliation(s)
- Judith L. Ross
- Department of Pediatrics, Nemours DuPont Hospital for Children, Thomas Jefferson University, Philadelphia, PA 19107
| | - Luke Bloy
- Lurie Family Foundations MEG Imaging Center, Department of Radiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA, 19104
| | - Timothy P.L. Roberts
- Lurie Family Foundations MEG Imaging Center, Department of Radiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA, 19104
| | - Judith Miller
- CHOP Center for Autism Research, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19146
| | - Chao Xing
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390,Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390,Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, 75390
| | | | - Andrew R. Zinn
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390
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24
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Quinn TP, Lee SC, Venkatesh S, Nguyen T. Improving the classification of neuropsychiatric conditions using gene ontology terms as features. Am J Med Genet B Neuropsychiatr Genet 2019; 180:508-518. [PMID: 31025483 DOI: 10.1002/ajmg.b.32727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/14/2019] [Accepted: 03/08/2019] [Indexed: 11/11/2022]
Abstract
Although neuropsychiatric disorders have an established genetic background, their molecular foundations remain elusive. This has prompted many investigators to search for explanatory biomarkers that can predict clinical outcomes. One approach uses machine learning to classify patients based on blood mRNA expression. However, these endeavors typically fail to achieve the high level of performance, stability, and generalizability required for clinical translation. Moreover, these classifiers can lack interpretability because not all genes have relevance to researchers. For this study, we hypothesized that annotation-based classifiers can improve classification performance, stability, generalizability, and interpretability. To this end, we evaluated the models of four classification algorithms on six neuropsychiatric data sets using four annotation databases. Our results suggest that the Gene Ontology Biological Process database can transform gene expression into an annotation-based feature space that is accurate and stable. We also show how annotation features can improve the interpretability of classifiers: as annotations are used to assign biological importance to genes, the biological importance of annotation-based features are the features themselves. In evaluating the annotation features, we find that top ranked annotations tend contain top ranked genes, suggesting that the most predictive annotations are a superset of the most predictive genes. Based on this, and the fact that annotations are used routinely to assign biological importance to genetic data, we recommend transforming gene-level expression into annotation-level expression prior to the classification of neuropsychiatric conditions.
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Affiliation(s)
- Thomas P Quinn
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, Victoria, Australia.,Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia.,Bioinformatics Core Research Group, Deakin University, Geelong, Victoria, Australia
| | - Samuel C Lee
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, Victoria, Australia
| | - Svetha Venkatesh
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, Victoria, Australia
| | - Thin Nguyen
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, Victoria, Australia
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25
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Lee SC, Quinn TP, Lai J, Kong SW, Hertz-Picciotto I, Glatt SJ, Crowley TM, Venkatesh S, Nguyen T. Solving for X: Evidence for sex-specific autism biomarkers across multiple transcriptomic studies. Am J Med Genet B Neuropsychiatr Genet 2019; 180:377-389. [PMID: 30520558 PMCID: PMC6551334 DOI: 10.1002/ajmg.b.32701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/20/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is a markedly heterogeneous condition with a varied phenotypic presentation. Its high concordance among siblings, as well as its clear association with specific genetic disorders, both point to a strong genetic etiology. However, the molecular basis of ASD is still poorly understood, although recent studies point to the existence of sex-specific ASD pathophysiologies and biomarkers. Despite this, little is known about how exactly sex influences the gene expression signatures of ASD probands. In an effort to identify sex-dependent biomarkers and characterize their function, we present an analysis of a single paired-end postmortem brain RNA-Seq data set and a meta-analysis of six blood-based microarray data sets. Here, we identify several genes with sex-dependent dysregulation, and many more with sex-independent dysregulation. Moreover, through pathway analysis, we find that these sex-independent biomarkers have substantially different biological roles than the sex-dependent biomarkers, and that some of these pathways are ubiquitously dysregulated in both postmortem brain and blood. We conclude by synthesizing the discovered biomarker profiles with the extant literature, by highlighting the advantage of studying sex-specific dysregulation directly, and by making a call for new transcriptomic data that comprise large female cohorts.
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Affiliation(s)
- Samuel C. Lee
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, 3220, Australia
| | - Thomas P. Quinn
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, 3220, Australia
- Centre for Molecular and Medical Research, Deakin University, Geelong, 3220, Australia
- Bioinformatics Core Research Group, Deakin University, Geelong, 3220, Australia
| | - Jerry Lai
- Deakin eResearch, Deakin University, Geelong, 3220, Australia | Intersect Australia, Sydney, 2000, Australia
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, USA | Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and UC Davis MIND Institute, School of Medicine, Davis, California
| | - Stephen J. Glatt
- Psychiatric Genetic Epidemiology and Neurobiology Laboratory (PsychGENe Lab) | SUNY Upstate Medical University, Syracuse, NY, USA
| | - Tamsyn M. Crowley
- Centre for Molecular and Medical Research, Deakin University, Geelong, 3220, Australia
- Bioinformatics Core Research Group, Deakin University, Geelong, 3220, Australia
- Poultry Hub Australia, University of New England, Armidale, New South Wales, 2351, Australia
| | - Svetha Venkatesh
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, 3220, Australia
| | - Thin Nguyen
- Centre for Pattern Recognition and Data Analytics (PRaDA), Deakin University, Geelong, 3220, Australia
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26
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Shen L, Feng C, Zhang K, Chen Y, Gao Y, Ke J, Chen X, Lin J, Li C, Iqbal J, Zhao Y, Wang W. Proteomics Study of Peripheral Blood Mononuclear Cells (PBMCs) in Autistic Children. Front Cell Neurosci 2019; 13:105. [PMID: 30941018 PMCID: PMC6433831 DOI: 10.3389/fncel.2019.00105] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022] Open
Abstract
Autism is one of the most common neurological developmental disorder associated with social isolation and restricted interests in children. The etiology of this disorder is still unknown. There is neither any confirmed laboratory test nor any effective therapeutic strategy to diagnose or cure it. To search for biomarkers for early detection and exploration of the disease mechanisms, here, we investigated the protein expression signatures of peripheral blood mononuclear cells (PBMCs) in autistic children compared with healthy controls by using isobaric tags for relative and absolute quantitation (iTRAQ) proteomics approach. The results showed a total of 41 proteins as differentially expressed in autistic group as compared to control. These proteins are found associated with metabolic pathways, endoplasmic reticulum (ER) stress and protein folding, endocytosis, immune and inflammatory response, plasma lipoprotein particle organization, and cell adhesion. Among these, 17 proteins (13 up-regulated and four down-regulated) are found to be linked with mitochondria. Eight proteins including three already reported proteins in our previous studies were selected to be verified. Five already reported autism associated pro-inflammatory cytokines [interferon-γ (IFN-γ), interleukin-1β (IL-1β), IL-6, IL-12, and tumor necrosis factor-α (TNF-α)] were detected in plasma by enzyme-linked immunosorbent assay (ELISA) analysis. The results were consistent with proteomic results and reports from previous literature. These results proposed that PBMCs from autistic children might be activated, and ER stress, unfolded protein response (UPR), acute-phase response (APR), inflammatory response, and endocytosis may be involved in autism occurrence. These reported proteins may serve as potential biomarkers for early diagnosis of autism. More specifically, simultaneous detection of three proteins [complement C3 (C3), calreticulin (CALR), and SERPINA1] in the plasma and PBMCs could increase the authenticity of detection.
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Affiliation(s)
- Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Kaoyuan Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Youjiao Chen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
- Xiang Ya Changde Hospital, Changde, China
| | - Yan Gao
- Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Junyan Ke
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Xinqian Chen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Jing Lin
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Cuihua Li
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Javed Iqbal
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Yuxi Zhao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Weibin Wang
- School of Art, Shenzhen University, Shenzhen, China
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27
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Shen L, Zhao Y, Zhang H, Feng C, Gao Y, Zhao D, Xia S, Hong Q, Iqbal J, Liu XK, Yao F. Advances in Biomarker Studies in Autism Spectrum Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:207-233. [PMID: 30747425 DOI: 10.1007/978-3-030-05542-4_11] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorder (ASD) is a neurological and developmental condition that begins early in childhood and lasts throughout life. The epidemiology of ASD is continuously increasing all over the world with huge social and economical burdens. As the etiology of autism is not completely understood, there is still no medication available for the treatment of this disorder. However, some behavioral interventions are available to improve the core and associated symptoms of autism, particularly when initiated at an early stage. Thus, there is an increasing demand for finding biomarkers for ASD. Although diagnostic biomarkers have not yet been established, research efforts have been carried out in neuroimaging and biological analyses including genomics and gene testing, proteomics, metabolomics, transcriptomics, and studies of the immune system, inflammation, and microRNAs. Here, we will review the current progress in these fields and focus on new methods, developments, research strategies, and studies of blood-based biomarkers.
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Affiliation(s)
- Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China.
| | - Yuxi Zhao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Yan Gao
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Danqing Zhao
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, People's Republic of China
| | - Sijian Xia
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Qi Hong
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Javed Iqbal
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Xu Kun Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Fang Yao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
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28
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Oxidative Stress in Autistic Children Alters Erythrocyte Shape in the Absence of Quantitative Protein Alterations and of Loss of Membrane Phospholipid Asymmetry. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:6430601. [PMID: 30607218 PMCID: PMC6252219 DOI: 10.1155/2018/6430601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/20/2018] [Indexed: 12/29/2022]
Abstract
Red blood cells (RBCs) from people affected by autism spectrum disorders (ASDs) are a target of oxidative stress. By scanning electron microscopy, we analyzed RBC morphology from 22 ASD children and show here that only 47.5 ± 3.33% of RBC displayed the typical biconcave shape, as opposed to 87.5 ± 1.3% (mean ± SD) of RBC from 21 sex- and age-matched healthy typically developing (TD) controls. Codocytes and star-shaped cells accounted for about 30% of all abnormally shaped ASD erythrocytes. RBC shape alterations were independent of the anticoagulant used (Na2-EDTA or heparin) and of different handling procedures preceding glutaraldehyde fixation, thus suggesting that they were not artefactual. Incubation for 24 h in the presence of antioxidants restored normal morphology in most erythrocytes from ASD patients. By Coomassie staining, as well as Western blotting analysis of relevant proteins playing a key role in the membrane-cytoskeleton organization, we were unable to find differences in RBC ghost composition between ASD and normal subjects. Phosphatidylserine (PS) exposure towards the extracellular membrane domain was examined in both basal and erythroptosis-inducing conditions. No differences were found between ASD and TD samples except when the aminophospholipid translocase was blocked by N-ethylmaleimide, upon which an increased amount of PS was found to face the outer membrane in RBC from ASD. These complex data are discussed in the light of the current understanding of the mode by which oxidative stress might affect erythrocyte shape in ASD and in other pathological conditions.
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29
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Singh S, Yazdani U, Gadad B, Zaman S, Hynan LS, Roatch N, Schutte C, Marti CN, Hewitson L, German DC. Serum thyroid-stimulating hormone and interleukin-8 levels in boys with autism spectrum disorder. J Neuroinflammation 2017; 14:113. [PMID: 28577577 PMCID: PMC5457729 DOI: 10.1186/s12974-017-0888-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/24/2017] [Indexed: 12/14/2022] Open
Abstract
Background Autism spectrum disorder (ASD) affects approximately 1 in 68 children in the USA. An ASD blood biomarker may enable early diagnosis and/or identification of new therapeutic targets. Serum samples from ASD and typically developing (TD) boys (n = 30/group) were screened for differences in 110 proteins using a multiplex immunoassay. Results Eleven proteins were found that together could confirm ASD with modest accuracy using multiple training and test sets. Two of the 11 proteins identified here were further tested using a different detection platform and with a larger sample of ASD and TD boys. The two proteins, thyroid-stimulating hormone (TSH) and interleukin-8 (IL-8), have been previously identified as putative biomarkers for ASD. TSH levels were significantly lower in ASD boys, whereas IL-8 levels were significantly elevated. The diagnostic accuracy for ASD based upon TSH or IL-8 levels alone varied from 74 to 76%, but using both proteins together, the diagnostic accuracy increased to 82%. In addition, TSH levels were negatively correlated with the Autism Diagnostic Observation Schedule subdomain scores. Conclusions These data suggest that a panel of proteins may be useful as a putative blood biomarker for ASD.
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Affiliation(s)
- Sarika Singh
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9070, USA.,Present Address: Toxicology Division, CSIR-CDRI, Lucknow, 226021, Uttar Pradesh, India
| | - Umar Yazdani
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9070, USA
| | - Bharathi Gadad
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9070, USA
| | - Sayed Zaman
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9070, USA
| | - Linda S Hynan
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9070, USA.,Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Nichole Roatch
- The Johnson Center for Child Health and Development, 1700 Rio Grande St., Austin, TX, 78701, USA
| | - Claire Schutte
- The Johnson Center for Child Health and Development, 1700 Rio Grande St., Austin, TX, 78701, USA
| | | | - Laura Hewitson
- The Johnson Center for Child Health and Development, 1700 Rio Grande St., Austin, TX, 78701, USA
| | - Dwight C German
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9070, USA.
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30
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Negi SK, Guda C. Global gene expression profiling of healthy human brain and its application in studying neurological disorders. Sci Rep 2017; 7:897. [PMID: 28420888 PMCID: PMC5429860 DOI: 10.1038/s41598-017-00952-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/20/2017] [Indexed: 12/31/2022] Open
Abstract
Brain function is governed by precise regulation of gene expression across its anatomically distinct structures; however, the expression patterns of genes across hundreds of brain structures are not clearly understood. Here, we describe a gene expression model, which is representative of the healthy human brain transcriptome by using data from the Allen Brain Atlas. Our in-depth gene expression profiling revealed that 84% of genes are expressed in at least one of the 190 brain structures studied. Hierarchical clustering based on gene expression profiles delineated brain regions into structurally tiered spatial groups and we observed striking enrichment for region-specific processes. Further, weighted co-expression network analysis identified 19 robust modules of highly correlated genes enriched with functional associations for neurogenesis, dopamine signaling, immune regulation and behavior. Also, structural distribution maps of major neurotransmission systems in the brain were generated. Finally, we developed a supervised classification model, which achieved 84% and 81% accuracies for predicting autism- and Parkinson’s-implicated genes, respectively, using our expression model as a baseline. This study represents the first use of global gene expression profiling from healthy human brain to develop a disease gene prediction model and this generic methodology can be applied to study any neurological disorder.
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Affiliation(s)
- Simarjeet K Negi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA. .,Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA. .,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA. .,Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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31
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Tylee DS, Hess JL, Quinn TP, Barve R, Huang H, Zhang-James Y, Chang J, Stamova BS, Sharp FR, Hertz-Picciotto I, Faraone SV, Kong SW, Glatt SJ. Blood transcriptomic comparison of individuals with and without autism spectrum disorder: A combined-samples mega-analysis. Am J Med Genet B Neuropsychiatr Genet 2017; 174:181-201. [PMID: 27862943 PMCID: PMC5499528 DOI: 10.1002/ajmg.b.32511] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/21/2016] [Indexed: 12/25/2022]
Abstract
Blood-based microarray studies comparing individuals affected with autism spectrum disorder (ASD) and typically developing individuals help characterize differences in circulating immune cell functions and offer potential biomarker signal. We sought to combine the subject-level data from previously published studies by mega-analysis to increase the statistical power. We identified studies that compared ex vivo blood or lymphocytes from ASD-affected individuals and unrelated comparison subjects using Affymetrix or Illumina array platforms. Raw microarray data and clinical meta-data were obtained from seven studies, totaling 626 affected and 447 comparison subjects. Microarray data were processed using uniform methods. Covariate-controlled mixed-effect linear models were used to identify gene transcripts and co-expression network modules that were significantly associated with diagnostic status. Permutation-based gene-set analysis was used to identify functionally related sets of genes that were over- and under-expressed among ASD samples. Our results were consistent with diminished interferon-, EGF-, PDGF-, PI3K-AKT-mTOR-, and RAS-MAPK-signaling cascades, and increased ribosomal translation and NK-cell related activity in ASD. We explored evidence for sex-differences in the ASD-related transcriptomic signature. We also demonstrated that machine-learning classifiers using blood transcriptome data perform with moderate accuracy when data are combined across studies. Comparing our results with those from blood-based studies of protein biomarkers (e.g., cytokines and trophic factors), we propose that ASD may feature decoupling between certain circulating signaling proteins (higher in ASD samples) and the transcriptional cascades which they typically elicit within circulating immune cells (lower in ASD samples). These findings provide insight into ASD-related transcriptional differences in circulating immune cells. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel S. Tylee
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Jonathan L. Hess
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Thomas P. Quinn
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Rahul Barve
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yanli Zhang-James
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Jeffrey Chang
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, U.S.A
| | - Boryana S. Stamova
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, USA
| | - Frank R. Sharp
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and UC Davis MIND Institute, School of Medicine, Davis, CA
| | - Stephen V. Faraone
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A,K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA, U.S.A
| | - Stephen J. Glatt
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A,To whom correspondence should be addressed: SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, Phone: (315) 464-7742,
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Oh DH, Kim IB, Kim SH, Ahn DH. Predicting Autism Spectrum Disorder Using Blood-based Gene Expression Signatures and Machine Learning. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2017; 15:47-52. [PMID: 28138110 PMCID: PMC5290715 DOI: 10.9758/cpn.2017.15.1.47] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/18/2016] [Accepted: 08/09/2016] [Indexed: 01/11/2023]
Abstract
Objective The aim of this study was to identify a transcriptomic signature that could be used to classify subjects with autism spectrum disorder (ASD) compared to controls on the basis of blood gene expression profiles. The gene expression profiles could ultimately be used as diagnostic biomarkers for ASD. Methods We used the published microarray data (GSE26415) from the Gene Expression Omnibus database, which included 21 young adults with ASD and 21 age- and sex-matched unaffected controls. Nineteen differentially expressed probes were identified from a training dataset (n=26, 13 ASD cases and 13 controls) using the limma package in R language (adjusted p value <0.05) and were further analyzed in a test dataset (n=16, 8 ASD cases and 8 controls) using machine learning algorithms. Results Hierarchical cluster analysis showed that subjects with ASD were relatively well-discriminated from controls. Based on the support vector machine and K-nearest neighbors analysis, validation of 19-DE probes with a test dataset resulted in an overall class prediction accuracy of 93.8% as well as a sensitivity and specificity of 100% and 87.5%, respectively. Conclusion The results of our exploratory study suggest that the gene expression profiles identified from the peripheral blood samples of young adults with ASD can be used to identify a biological signature for ASD. Further study using a larger cohort and more homogeneous datasets is required to improve the diagnostic accuracy.
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Affiliation(s)
- Dong Hoon Oh
- Institute for Health and Society, Hanyang University, Seoul, Korea
| | - Il Bin Kim
- Translational Neurogenetics Laboratory, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Seok Hyeon Kim
- Department of Psychiatry and Institute of Mental Health, Hanyang University College of Medicine, Seoul, Korea
| | - Dong Hyun Ahn
- Department of Psychiatry and Institute of Mental Health, Hanyang University College of Medicine, Seoul, Korea
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Sivanesan S, Tan A, Jeyaraj R, Lam J, Gole M, Hardan A, Ashkan K, Rajadas J. Pharmaceuticals and Stem Cells in Autism Spectrum Disorders: Wishful Thinking? World Neurosurg 2017; 98:659-672. [DOI: 10.1016/j.wneu.2016.09.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
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Ansel A, Rosenzweig JP, Zisman PD, Melamed M, Gesundheit B. Variation in Gene Expression in Autism Spectrum Disorders: An Extensive Review of Transcriptomic Studies. Front Neurosci 2017; 10:601. [PMID: 28105001 PMCID: PMC5214812 DOI: 10.3389/fnins.2016.00601] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023] Open
Abstract
Autism spectrum disorders (ASDs) are a group of complex neurodevelopmental conditions that present in early childhood and have a current estimated prevalence of about 1 in 68 US children, 1 in 42 boys. ASDs are heterogeneous, and arise from epigenetic, genetic and environmental origins, yet, the exact etiology of ASDs still remains unknown. Individuals with ASDs are characterized by having deficits in social interaction, impaired communication and a range of stereotyped and repetitive behaviors. Currently, a diagnosis of ASD is based solely on behavioral assessments and phenotype. Hundreds of diverse ASD susceptibility genes have been identified, yet none of the mutations found account for more than a small subset of autism cases. Therefore, a genetic diagnosis is not yet possible for the majority of the ASD population. The susceptibility genes that have been identified are involved in a wide and varied range of biological functions. Since the genetics of ASDs is so diverse, information on genome function as provided by transcriptomic data is essential to further our understanding. Gene expression studies have been extremely useful in comparing groups of individuals with ASD and control samples in order to measure which genes (or group of genes) are dysregulated in the ASD group. Transcriptomic studies are essential as a key link between measuring protein levels and analyzing genetic information. This review of recent autism gene expression studies highlights genes that are expressed in the brain, immune system, and processes such as cell metabolism and embryology. Various biological processes have been shown to be implicated with ASD individuals as well as differences in gene expression levels between different types of biological tissues. Some studies use gene expression to attempt to separate autism into different subtypes. An updated list of genes shown to be significantly dysregulated in individuals with autism from all recent ASD expression studies will help further research isolate any patterns useful for diagnosis or understanding the mechanisms involved. The functional relevance of transcriptomic studies as a method of classifying and diagnosing ASD cannot be underestimated despite the possible limitations of transcriptomic studies.
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Niu T, Li J, Wang J, Ma JZ, Li MD. Identification of Novel Signal Transduction, Immune Function, and Oxidative Stress Genes and Pathways by Topiramate for Treatment of Methamphetamine Dependence Based on Secondary Outcomes. Front Psychiatry 2017; 8:271. [PMID: 29321746 PMCID: PMC5733474 DOI: 10.3389/fpsyt.2017.00271] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Topiramate (TPM) is suggested to be a promising medication for treatment of methamphetamine (METH) dependence, but the molecular basis remains to be elucidated. METHODS Among 140 METH-dependent participants randomly assigned to receive either TPM (N = 69) or placebo (N = 71) in a previously conducted randomized controlled trial, 50 TPM- and 49 placebo-treated participants had a total 212 RNA samples available at baseline, week 8, and week 12 time points. Following our primary analysis of gene expression data, we reanalyzed the microarray expression data based on a latent class analysis of binary secondary outcomes during weeks 1-12 that provided a classification of 21 responders and 31 non-responders with consistent responses at both time points. RESULTS Based on secondary outcomes, 1,381, 576, 905, and 711 differentially expressed genes at nominal P values < 0.05 were identified in responders versus non-responders for week 8 TPM, week 8 placebo, week 12 TPM, and week 12 placebo groups, respectively. Among 1,381 genes identified in week 8 TPM responders, 359 genes were identified in both week 8 and week 12 TPM groups, of which 300 genes were exclusively detected in TPM responders. Of them, 32 genes had nominal P values < 5 × 10-3 at either week 8 or week 12 and false discovery rates < 0.15 at both time points with consistent directions of gene expression changes, which include GABARAPL1, GPR155, and IL15RA in GABA receptor signaling that represent direct targets for TPM. Analyses of these 300 genes revealed 7 enriched pathways belonging to neuronal function/synaptic plasticity, signal transduction, inflammation/immune function, and oxidative stress response categories. No pathways were enriched for 72 genes exclusively detected in both week 8 and week 12 placebo groups. CONCLUSION This secondary analysis study of gene expression data from a TPM clinical trial not only yielded consistent results with those of primary analysis but also identified additional new genes and pathways on TPM response to METH addiction.
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Affiliation(s)
- Tianhua Niu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Jingjing Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China
| | - Ju Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China.,School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Jennie Z Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China.,Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China.,Institute of Neuroimmune Pharmacology, Seton Hall University, South Orange, NJ, United States
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Ovenden ES, Drögemöller BI, van der Merwe L, Chiliza B, Asmal L, Emsley RA, Warnich L. Fine-mapping of antipsychotic response genome-wide association studies reveals novel regulatory mechanisms. Pharmacogenomics 2017; 18:105-120. [DOI: 10.2217/pgs-2016-0108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aim: Noncoding variation has demonstrated regulatory effects on disease treatment outcomes. This study investigated the potential functionality of previously implicated noncoding variants on schizophrenia treatment response. Materials & methods: Predicted regulatory potential of variation identified from antipsychotic response genome-wide association studies was determined. Prioritized variants were assessed for association(s) with treatment outcomes in a South African first episode schizophrenia cohort (n = 103). Results: Bioinformatic and association results implicated a relationship between regulatory variants, expression of MANBA, COL9A2 and NFKB1, and treatment response. Three SNPs were associated with poor outcomes (rs230493: p = 1.88 × 10-6; rs3774959: p = 1.75 × 10-5; and rs230504: p = 1.48 × 10-4). Conclusion: This study has thoroughly investigated previous GWAS to pinpoint variants that may play a causal role in poor schizophrenia treatment outcomes, and provides potential candidate genes for further study in the field of antipsychotic response.
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Affiliation(s)
- Ellen S Ovenden
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Lize van der Merwe
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Bonginkosi Chiliza
- Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa
| | - Laila Asmal
- Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa
| | - Robin A Emsley
- Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa
| | - Louise Warnich
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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Mitra AK, Dodge J, Van Ness J, Sokeye I, Van Ness B. A de novo splice site mutation in EHMT1 resulting in Kleefstra syndrome with pharmacogenomics screening and behavior therapy for regressive behaviors. Mol Genet Genomic Med 2016; 5:130-140. [PMID: 28361099 PMCID: PMC5370220 DOI: 10.1002/mgg3.265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/24/2016] [Accepted: 11/01/2016] [Indexed: 12/18/2022] Open
Abstract
Background Kleefstra syndrome (KS) is a rare autosomal dominant developmental disability, caused by microdeletions or intragenic mutations within the epigenetic regulator gene EHMT1 (euchromatic histone lysine N‐methyltransferase 1). In addition to common features of autism, young adult regressive behaviors have been reported. However, the genetic downstream effects of the reported deletions or mutations on KS phenotype have not yet been completely explored. While genetic backgrounds affecting drug metabolism can have a profound effect on therapeutic interventions, pharmacogenomic variations are seldom considered in directing psychotropic therapies. Methods In this report, we used next‐generation sequencing (exome sequencing and high‐throughput RNA sequencing) in a patient and his parents to identify causative genetic variants followed by pharmacogenomics‐guided clinical decision‐making for making positive changes toward his treatment strategies. The patient had an early autism diagnosis and showed significant regressive behaviors and physical aberrations at age 23. Results Exome sequencing identified a novel, de novo splice site variant NM_024757.4: c.2750‐1G>T in EHMT1, a candidate gene for Kleefstra syndrome, in the patient that results in exon skipping and downstream frameshift and termination. Gene expression results from the patient showed, when compared to his parents, there was a significant decreased expression of several reported gene variants associated with autism risk. Further, using a pharmacogenomics genotyping panel, we discovered that the patient had the CYP2D6 nonfunctioning variant genotype *4/*4 that results in very low metabolic activity on a number of psychotropic drugs, including fluvoxamine which he was prescribed. As reported here, a change in psychotropic drugs and intense behavior therapies resulted in a significant reversal of the regressive behaviors and physical aberrations. Conclusion These results demonstrate an individualized approach that integrated genetic information and behavior therapies, resulting in a dramatic improvement in regressive behaviors associated with KS.
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Affiliation(s)
- Amit Kumar Mitra
- Department of Genetics, Cell Biology & Development University of Minnesota Minneapolis Minnesota
| | | | - Jody Van Ness
- Eyebox Tools, Inc.MinneapolisMinnesota; Present address: Jody Van Ness, Institute for Community IntegrationUniversity of MinnesotaMinneapolisMinnesota
| | | | - Brian Van Ness
- Department of Genetics, Cell Biology & Development University of Minnesota Minneapolis Minnesota
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Insights into psychosis risk from leukocyte microRNA expression. Transl Psychiatry 2016; 6:e981. [PMID: 27959328 PMCID: PMC5290334 DOI: 10.1038/tp.2016.148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 06/17/2016] [Accepted: 06/30/2016] [Indexed: 11/11/2022] Open
Abstract
Dysregulation of immune system functions has been implicated in schizophrenia, suggesting that immune cells may be involved in the development of the disorder. With the goal of a biomarker assay for psychosis risk, we performed small RNA sequencing on RNA isolated from circulating immune cells. We compared baseline microRNA (miRNA) expression for persons who were unaffected (n=27) or who, over a subsequent 2-year period, were at clinical high risk but did not progress to psychosis (n=37), or were at high risk and did progress to psychosis (n=30). A greedy algorithm process led to selection of five miRNAs that when summed with +1 weights distinguished progressed from nonprogressed subjects with an area under the receiver operating characteristic curve of 0.86. Of the five, miR-941 is human-specific with incompletely understood functions, but the other four are prominent in multiple immune system pathways. Three of those four are downregulated in progressed vs. nonprogressed subjects (with weight -1 in a classifier function that increases with risk); all three have also been independently reported as downregulated in monocytes from schizophrenia patients vs. unaffected subjects. Importantly, these findings passed stringent randomization tests that minimized the risk of conclusions arising by chance. Regarding miRNA-miRNA correlations over the three groups, progressed subjects were found to have much weaker miRNA orchestration than nonprogressed or unaffected subjects. If independently verified, the leukocytic miRNA biomarker assay might improve accuracy of psychosis high-risk assessments and eventually help rationalize preventative intervention decisions.
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Walker SJ, Beavers DP, Fortunato J, Krigsman A. A Putative Blood-Based Biomarker for Autism Spectrum Disorder-Associated Ileocolitis. Sci Rep 2016; 6:35820. [PMID: 27767057 PMCID: PMC5073317 DOI: 10.1038/srep35820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/06/2016] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal symptoms are common in children with autism spectrum disorder (ASD). A significant proportion of children with ASD and gastrointestinal symptoms have histologic evidence of ileocolitis (inflammation of the terminal ileum and/or colon). We previously reported the molecular characterization of gastrointestinal biopsy tissue from ASD children with ileocolitis (ASDIC+) compared to anatomically similar inflamed tissue from typically developing children with inflammatory bowel disease (IBD; i.e. Crohn’s disease or ulcerative colitis) and typically developing children with gastrointestinal symptoms but no evidence of gastrointestinal mucosal inflammation (TDIC−). ASDIC+ children had a gene expression profile that, while primarily overlapping with known IBD, had distinctive differences. The present study confirms these findings and replicates this molecular characterization in a second cohort of cases (ASDIC+) and controls (TDIC−). In these two separate case/control mucosal-based cohorts, we have demonstrated overlap of 59 differentially expressed transcripts (DETs) unique to inflamed ileocolonic tissue from symptomatic ASDIC+ children. We now report that 9 of these 59 transcripts are also differentially expressed in the peripheral blood of the second cohort of ASDIC+ children. This set of transcripts represents a putative blood-based biomarker for ASD-associated ileocolonic inflammation.
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Affiliation(s)
- Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston Salem, NC, USA
| | - Daniel P Beavers
- Department of Biostatistical Sciences, Public Health Sciences, Wake Forest University Health Sciences, Winston Salem, NC, USA
| | - John Fortunato
- Pediatric Gastroenterology, Hepatology, and Nutrition, Ann &Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Arthur Krigsman
- Pediatric Gastroenterology Resources, 148 Beach 9th Street, Suite 2B, Far Rockaway, NY, USA
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Hess JL, Tylee DS, Barve R, de Jong S, Ophoff RA, Kumarasinghe N, Tooney P, Schall U, Gardiner E, Beveridge NJ, Scott RJ, Yasawardene S, Perera A, Mendis J, Carr V, Kelly B, Cairns M, Tsuang MT, Glatt SJ. Transcriptome-wide mega-analyses reveal joint dysregulation of immunologic genes and transcription regulators in brain and blood in schizophrenia. Schizophr Res 2016; 176:114-124. [PMID: 27450777 PMCID: PMC5026943 DOI: 10.1016/j.schres.2016.07.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 12/18/2022]
Abstract
The application of microarray technology in schizophrenia research was heralded as paradigm-shifting, as it allowed for high-throughput assessment of cell and tissue function. This technology was widely adopted, initially in studies of postmortem brain tissue, and later in studies of peripheral blood. The collective body of schizophrenia microarray literature contains apparent inconsistencies between studies, with failures to replicate top hits, in part due to small sample sizes, cohort-specific effects, differences in array types, and other confounders. In an attempt to summarize existing studies of schizophrenia cases and non-related comparison subjects, we performed two mega-analyses of a combined set of microarray data from postmortem prefrontal cortices (n=315) and from ex-vivo blood tissues (n=578). We adjusted regression models per gene to remove non-significant covariates, providing best-estimates of transcripts dysregulated in schizophrenia. We also examined dysregulation of functionally related gene sets and gene co-expression modules, and assessed enrichment of cell types and genetic risk factors. The identities of the most significantly dysregulated genes were largely distinct for each tissue, but the findings indicated common emergent biological functions (e.g. immunity) and regulatory factors (e.g., predicted targets of transcription factors and miRNA species across tissues). Our network-based analyses converged upon similar patterns of heightened innate immune gene expression in both brain and blood in schizophrenia. We also constructed generalizable machine-learning classifiers using the blood-based microarray data. Our study provides an informative atlas for future pathophysiologic and biomarker studies of schizophrenia.
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Affiliation(s)
- Jonathan L Hess
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Syracuse, NY, USA; Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, Syracuse, NY, USA; SUNY Upstate Medical University, Syracuse, NY, USA
| | - Daniel S Tylee
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Syracuse, NY, USA; Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, Syracuse, NY, USA; SUNY Upstate Medical University, Syracuse, NY, USA
| | - Rahul Barve
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Syracuse, NY, USA; Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, Syracuse, NY, USA; SUNY Upstate Medical University, Syracuse, NY, USA
| | - Simone de Jong
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, USA; MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, USA; Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nishantha Kumarasinghe
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia; Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka; Schizophrenia Research Institute, Sydney, New South Wales, Australia; Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Paul Tooney
- Schizophrenia Research Institute, Sydney, New South Wales, Australia; School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Hunter Medical Research Institute, Newcastle, Australia; Centre for Translational Neuroscience & Mental Health, University of Newcastle, Callaghan, Newcastle, Australia
| | - Ulrich Schall
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia; Schizophrenia Research Institute, Sydney, New South Wales, Australia; Hunter Medical Research Institute, Newcastle, Australia; Centre for Translational Neuroscience & Mental Health, University of Newcastle, Callaghan, Newcastle, Australia
| | - Erin Gardiner
- Schizophrenia Research Institute, Sydney, New South Wales, Australia; School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Centre for Translational Neuroscience & Mental Health, University of Newcastle, Callaghan, Newcastle, Australia
| | - Natalie Jane Beveridge
- Schizophrenia Research Institute, Sydney, New South Wales, Australia; School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Centre for Translational Neuroscience & Mental Health, University of Newcastle, Callaghan, Newcastle, Australia
| | - Rodney J Scott
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Hunter Medical Research Institute, Newcastle, Australia
| | - Surangi Yasawardene
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Antionette Perera
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Jayan Mendis
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Vaughan Carr
- Schizophrenia Research Institute, Sydney, New South Wales, Australia; School of Psychiatry, University of New South Wales, Kensington, New South Wales, Australia
| | - Brian Kelly
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia; Hunter Medical Research Institute, Newcastle, Australia; Centre for Translational Neuroscience & Mental Health, University of Newcastle, Callaghan, Newcastle, Australia
| | - Murray Cairns
- Schizophrenia Research Institute, Sydney, New South Wales, Australia; School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Hunter Medical Research Institute, Newcastle, Australia; Centre for Translational Neuroscience & Mental Health, University of Newcastle, Callaghan, Newcastle, Australia
| | - Ming T Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, USA
| | - Stephen J Glatt
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Syracuse, NY, USA; Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, Syracuse, NY, USA; SUNY Upstate Medical University, Syracuse, NY, USA.
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Tylee DS, Espinoza AJ, Hess JL, Tahir MA, McCoy SY, Rim JK, Dhimal T, Cohen OS, Glatt SJ. RNA sequencing of transformed lymphoblastoid cells from siblings discordant for autism spectrum disorders reveals transcriptomic and functional alterations: Evidence for sex-specific effects. Autism Res 2016; 10:439-455. [DOI: 10.1002/aur.1679] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/07/2016] [Accepted: 07/01/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel S. Tylee
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
| | - Alfred J. Espinoza
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
| | - Jonathan L. Hess
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
| | - Muhammad A. Tahir
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
| | - Sarah Y. McCoy
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
| | - Joshua K. Rim
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
| | - Totadri Dhimal
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
| | - Ori S. Cohen
- Department of Neuroscience; The Scripps Research Institute; Jupiter Florida
| | - Stephen J. Glatt
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University; Syracuse New York
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Abstract
Abstract
ASD research is at an important crossroads. The ASD diagnosis is important for assigning a child to early behavioral intervention and explaining a child’s condition. But ASD research has not provided a diagnosis-specific medical treatment, or a consistent early predictor, or a unified life course. If the ASD diagnosis also lacks biological and construct validity, a shift away from studying ASD-defined samples would be warranted. Consequently, this paper reviews recent findings for the neurobiological validity of ASD, the construct validity of ASD diagnostic criteria, and the construct validity of ASD spectrum features. The findings reviewed indicate that the ASD diagnosis lacks biological and construct validity. The paper concludes with proposals for research going forward.
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Napoli E, Song G, Schneider A, Hagerman R, Eldeeb MAAA, Azarang A, Tassone F, Giulivi C. Warburg effect linked to cognitive-executive deficits in FMR1 premutation. FASEB J 2016; 30:3334-3351. [PMID: 27335370 DOI: 10.1096/fj.201600315r] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/14/2016] [Indexed: 11/11/2022]
Abstract
A 55-200 CGG repeat expansion in the 5'-UTR of the fragile X mental retardation 1 (FMR1) gene is known as a premutation. Some carriers are affected by the neurodegenerative disorder fragile X-associated tremor/ataxia syndrome (FXTAS), primary ovarian insufficiency, and neurobehavioral impairments. Based on the mitochondrial dysfunction observed in fibroblasts and brain samples from carriers, as well as in neurons and brains from a mouse model of the premutation, we evaluated the presence of the Warburg effect in peripheral blood mononuclear cells (PBMCs) from 30 premutation carriers with either a rebalance of the metabolism [increasing glycolysis while decreasing oxidative phosphorylation (oxphos)] or a metabolic amplification (increasing glycolysis while maintaining/increasing oxphos). Deficits in oxphos-more pronounced in FXTAS-affected subjects-were accompanied by a shift toward glycolysis, suggesting increased glycolysis despite aerobic conditions. Differential proteomics extended these findings, unveiling a decreased antioxidant response, translation, and disrupted extracellular matrix and cytoskeleton organization with activation of prosenescence pathways. Lower bioenergetics segregated with increased incidence of low executive function, tremors, below-average IQ, and FXTAS. The combination of functional and proteomic data unveiled new mechanisms related to energy production in the premutation, showing the potential of being applicable to other psychiatric disorders to identify endophenotype-specific responses relevant to neurobiology.-Napoli, E., Song, G., Schneider, A., Hagerman, R., Eldeeb, M. A. A. A., Azarang, A., Tassone, F., Giulivi, C. Warburg effect linked to cognitive-executive deficits in FMR1 premutation.
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Affiliation(s)
- Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Gyu Song
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Andrea Schneider
- Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, Davis, California, USA; Department of Pediatrics, University of California Davis Medical Center, Sacramento California, USA; and
| | - Randi Hagerman
- Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, Davis, California, USA; Department of Pediatrics, University of California Davis Medical Center, Sacramento California, USA; and
| | - Marwa Abd Al Azaim Eldeeb
- Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, Davis, California, USA
| | - Atoosa Azarang
- Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, Davis, California, USA
| | - Flora Tassone
- Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, Davis, California, USA; Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, California, USA
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA; Department of Pediatrics, University of California Davis Medical Center, Sacramento California, USA; and
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Pierce K, Marinero S, Hazin R, McKenna B, Barnes CC, Malige A. Eye Tracking Reveals Abnormal Visual Preference for Geometric Images as an Early Biomarker of an Autism Spectrum Disorder Subtype Associated With Increased Symptom Severity. Biol Psychiatry 2016; 79:657-66. [PMID: 25981170 PMCID: PMC4600640 DOI: 10.1016/j.biopsych.2015.03.032] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 03/13/2015] [Accepted: 03/14/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Clinically and biologically, autism spectrum disorder (ASD) is heterogeneous. Unusual patterns of visual preference as indexed by eye tracking are hallmarks; however, whether they can be used to define an early biomarker of ASD as a whole or leveraged to define a subtype is unclear. To begin to examine this issue, large cohorts are required. METHODS A sample of 334 toddlers from six distinct groups (115 toddlers with ASD, 20 toddlers with ASD features, 57 toddlers with developmental delay, 53 toddlers with other conditions [e.g., premature birth, prenatal drug exposure], 64 toddlers with typical development, and 25 unaffected toddlers with siblings with ASD) was studied. Toddlers watched a movie containing geometric and social images. Fixation duration and number of saccades within each area of interest and validation statistics for this independent sample were computed. Next, to maximize power, data from our previous study (n = 110) were added for a total of 444 subjects. A subset of toddlers repeated the eye-tracking procedure. RESULTS As in the original study, a subset of toddlers with ASD fixated on geometric images >69% of the time. Using this cutoff, sensitivity for ASD was 21%, specificity was 98%, and positive predictive value was 86%. Toddlers with ASD who strongly preferred geometric images had 1) worse cognitive, language, and social skills relative to toddlers with ASD who strongly preferred social images and 2) fewer saccades when viewing geometric images. Unaffected siblings of ASD probands did not show evidence of heightened preference for geometric images. Test-retest reliability was good. Examination of age effects suggested that this test may not be appropriate with children >4 years old. CONCLUSIONS Enhanced visual preference for geometric repetition may be an early developmental biomarker of an ASD subtype with more severe symptoms.
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Affiliation(s)
- Karen Pierce
- Department of Neurosciences, University of California, San Diego, La Jolla, California..
| | - Steven Marinero
- Department of Neurosciences, University of California, San Diego, La Jolla, California
| | - Roxana Hazin
- Department of Neurosciences, University of California, San Diego, La Jolla, California
| | - Benjamin McKenna
- Department of Psychiatry, University of California, San Diego, La Jolla, California
| | - Cynthia Carter Barnes
- Department of Neurosciences, University of California, San Diego, La Jolla, California
| | - Ajith Malige
- Department of Neurosciences, University of California, San Diego, La Jolla, California
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Miyata S, Kurachi M, Okano Y, Sakurai N, Kobayashi A, Harada K, Yamagata H, Matsuo K, Takahashi K, Narita K, Fukuda M, Ishizaki Y, Mikuni M. Blood Transcriptomic Markers in Patients with Late-Onset Major Depressive Disorder. PLoS One 2016; 11:e0150262. [PMID: 26926397 PMCID: PMC4771207 DOI: 10.1371/journal.pone.0150262] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/11/2016] [Indexed: 01/09/2023] Open
Abstract
We investigated transcriptomic markers of late-onset major depressive disorder (LOD; onset age of first depressive episode ≥ 50 years) from the genes expressed in blood cells and identified state-dependent transcriptomic markers in these patients. We assessed the genes expressed in blood cells by microarray and found that the expression levels of 3,066 probes were state-dependently changed in the blood cells of patients with LOD. To select potential candidates from those probes, we assessed the genes expressed in the blood of an animal model of depression, ovariectomized female mice exposed to chronic ultra-mild stress, by microarray and cross-matched the differentially expressed genes between the patients and the model mice. We identified 14 differentially expressed genes that were similarly changed in both patients and the model mice. By assessing statistical significance using real-time quantitative PCR (RT-qPCR), the following 4 genes were selected as candidates: cell death-inducing DFFA-like effector c (CIDEC), ribonuclease 1 (RNASE1), solute carrier family 36 member-1 (SLC36A1), and serine/threonine/tyrosine interacting-like 1 (STYXL1). The discriminating ability of these 4 candidate genes was evaluated in an independent cohort that was validated. Among them, CIDEC showed the greatest discriminant validity (sensitivity 91.3% and specificity 87.5%). Thus, these 4 biomarkers should be helpful for properly diagnosing LOD.
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Affiliation(s)
- Shigeo Miyata
- Departments of Psychiatry and Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
- * E-mail:
| | - Masashi Kurachi
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Yoshiko Okano
- Departments of Psychiatry and Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Noriko Sakurai
- Departments of Psychiatry and Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Ayumi Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Kenichiro Harada
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Hirotaka Yamagata
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Koji Matsuo
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Keisuke Takahashi
- Departments of Psychiatry and Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Kosuke Narita
- Departments of Psychiatry and Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Masato Fukuda
- Departments of Psychiatry and Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Yasuki Ishizaki
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Masahiko Mikuni
- Departments of Psychiatry and Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
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46
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Higdon R, Earl RK, Stanberry L, Hudac CM, Montague E, Stewart E, Janko I, Choiniere J, Broomall W, Kolker N, Bernier RA, Kolker E. The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:197-208. [PMID: 25831060 DOI: 10.1089/omi.2015.0020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Complex diseases are caused by a combination of genetic and environmental factors, creating a difficult challenge for diagnosis and defining subtypes. This review article describes how distinct disease subtypes can be identified through integration and analysis of clinical and multi-omics data. A broad shift toward molecular subtyping of disease using genetic and omics data has yielded successful results in cancer and other complex diseases. To determine molecular subtypes, patients are first classified by applying clustering methods to different types of omics data, then these results are integrated with clinical data to characterize distinct disease subtypes. An example of this molecular-data-first approach is in research on Autism Spectrum Disorder (ASD), a spectrum of social communication disorders marked by tremendous etiological and phenotypic heterogeneity. In the case of ASD, omics data such as exome sequences and gene and protein expression data are combined with clinical data such as psychometric testing and imaging to enable subtype identification. Novel ASD subtypes have been proposed, such as CHD8, using this molecular subtyping approach. Broader use of molecular subtyping in complex disease research is impeded by data heterogeneity, diversity of standards, and ineffective analysis tools. The future of molecular subtyping for ASD and other complex diseases calls for an integrated resource to identify disease mechanisms, classify new patients, and inform effective treatment options. This in turn will empower and accelerate precision medicine and personalized healthcare.
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Affiliation(s)
- Roger Higdon
- 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
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47
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Wang Y, Zhao X, Ju W, Flory M, Zhong J, Jiang S, Wang P, Dong X, Tao X, Chen Q, Shen C, Zhong M, Yu Y, Brown WT, Zhong N. Genome-wide differential expression of synaptic long noncoding RNAs in autism spectrum disorder. Transl Psychiatry 2015; 5:e660. [PMID: 26485544 PMCID: PMC4930123 DOI: 10.1038/tp.2015.144] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 07/06/2015] [Accepted: 07/27/2015] [Indexed: 12/19/2022] Open
Abstract
A genome-wide differential expression of long noncoding RNAs (lncRNAs) was identified in blood specimens of autism spectrum disorder (ASD). A total of 3929 lncRNAs were found to be differentially expressed in ASD peripheral leukocytes, including 2407 that were upregulated and 1522 that were downregulated. Simultaneously, 2591 messenger RNAs (mRNAs), including 1789 upregulated and 821 downregulated, were also identified in ASD leukocytes. Functional pathway analysis of these lncRNAs revealed neurological pathways of the synaptic vesicle cycling, long-term depression and long-term potentiation to be primarily involved. Thirteen synaptic lncRNAs, including nine upregulated and four downregulated, and 19 synaptic mRNAs, including 12 upregulated and seven downregulated, were identified as being differentially expressed in ASD. Our identification of differential expression of synaptic lncRNAs and mRNAs suggested that synaptic vesicle transportation and cycling are important for the delivery of synaptosomal protein(s) between presynaptic and postsynaptic membranes in ASD. Finding of 19 lncRNAs, which are the antisense, bi-directional and intergenic, of HOX genes may lead us to investigate the role of HOX genes involved in the development of ASD. Discovery of the lncRNAs of SHANK2-AS and BDNF-AS, the natural antisense of genes SHANK2 and BDNF, respectively, indicates that in addition to gene mutations, deregulation of lncRNAs on ASD-causing gene loci presents a new approach for exploring possible epigenetic mechanisms underlying ASD. Our study also opened a new avenue for exploring the use of lncRNA(s) as biomarker(s) for the early detection of ASD.
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Affiliation(s)
- Y Wang
- Department of Child Health Care, Shanghai
Children's Hospital, Shanghai Jiaotong University,
Shanghai, China
- Chinese Alliance of Translational
Medicine for Maternal and Children's Health, Beijing,
China
| | - X Zhao
- Chinese Alliance of Translational
Medicine for Maternal and Children's Health, Beijing,
China
- Peking University Center of Medical
Genetics, Beijing, China
| | - W Ju
- Department of Human Genetics, New York
State Institute for Basic Research in Developmental Disabilities,
Staten Island, NY, USA
| | - M Flory
- Department of Human Genetics, New York
State Institute for Basic Research in Developmental Disabilities,
Staten Island, NY, USA
| | - J Zhong
- Student volunteer, Hunter College High
School, New York, NY, USA
| | - S Jiang
- Department of Obstetrics and Gynecology,
Nanfang Hospital, Southern Medical University, Guangzhou,
China
| | - P Wang
- Chinese Alliance of Translational
Medicine for Maternal and Children's Health, Beijing,
China
- Peking University Center of Medical
Genetics, Beijing, China
| | - X Dong
- Department of Child Health Care, Shanghai
Children's Hospital, Shanghai Jiaotong University,
Shanghai, China
- Chinese Alliance of Translational
Medicine for Maternal and Children's Health, Beijing,
China
| | - X Tao
- Chinese Alliance of Translational
Medicine for Maternal and Children's Health, Beijing,
China
- Peking University Center of Medical
Genetics, Beijing, China
| | - Q Chen
- Department of Obstetrics and Gynecology,
Nanfang Hospital, Southern Medical University, Guangzhou,
China
| | - C Shen
- Chinese Alliance of Translational
Medicine for Maternal and Children's Health, Beijing,
China
- Peking University Center of Medical
Genetics, Beijing, China
| | - M Zhong
- Department of Obstetrics and Gynecology,
Nanfang Hospital, Southern Medical University, Guangzhou,
China
| | - Y Yu
- Department of Obstetrics and Gynecology,
Nanfang Hospital, Southern Medical University, Guangzhou,
China
| | - W T Brown
- Department of Human Genetics, New York
State Institute for Basic Research in Developmental Disabilities,
Staten Island, NY, USA
| | - N Zhong
- Department of Child Health Care, Shanghai
Children's Hospital, Shanghai Jiaotong University,
Shanghai, China
- Chinese Alliance of Translational
Medicine for Maternal and Children's Health, Beijing,
China
- Peking University Center of Medical
Genetics, Beijing, China
- Department of Human Genetics, New York
State Institute for Basic Research in Developmental Disabilities,
Staten Island, NY, USA
- Department of Obstetrics and Gynecology,
Nanfang Hospital, Southern Medical University, Guangzhou,
China
- March of Dimes Global Network for
Maternal and Infant Health, White Plains, NY,
USA
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48
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Duda M, Wall DP. Rising interdisciplinary collaborations refine our understanding of autisms and give hope to more personalized solutions. Per Med 2015; 12:359-369. [PMID: 29771659 DOI: 10.2217/pme.15.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Autism is heterogeneous, complex and arguably a condition of many conditions. Both the number of researchers and the number of research collaborations in the field of autism have been growing at unprecedented rates. Interdisciplinary collaborations have increased more than eightfold since the year 2000. In fact, most - if not all - areas of autism research are starting to converge, and these convergences are leading not only to a richer research network but also to a causal network for autism. This network can, and likely will, decode the many forms of autism into its various subcomponents, enabling increasingly more personalized approaches for both the detection and treatment of those different forms of autism.
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Affiliation(s)
- Marlena Duda
- Department of Pediatrics & Psychiatry (by courtesy), Division of Systems Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dennis P Wall
- Department of Pediatrics & Psychiatry (by courtesy), Division of Systems Medicine, Stanford University, Stanford, CA 94305, USA
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49
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Napoli E, Tassone F, Wong S, Angkustsiri K, Simon TJ, Song G, Giulivi C. Mitochondrial Citrate Transporter-dependent Metabolic Signature in the 22q11.2 Deletion Syndrome. J Biol Chem 2015. [PMID: 26221035 DOI: 10.1074/jbc.m115.672360] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The congenital disorder 22q11.2 deletion syndrome (22qDS), characterized by a hemizygous deletion of 1.5-3 Mb on chromosome 22 at locus 11.2, is the most common microdeletion disorder (estimated prevalence of 1 in 4000) and the second risk factor for schizophrenia. Nine of ∼30 genes involved in 22qDS have the potential of disrupting mitochondrial metabolism (COMT, UFD1L, DGCR8, MRPL40, PRODH, SLC25A1, TXNRD2, T10, and ZDHHC8). Deficits in bioenergetics during early postnatal brain development could set the basis for a disrupted neuronal metabolism or synaptic signaling, partly explaining the higher incidence in developmental and behavioral deficits in these individuals. Here, we investigated whether mitochondrial outcomes and metabolites from 22qDS children segregated with the altered dosage of one or several of these mitochondrial genes contributing to 22qDS etiology and/or morbidity. Plasma metabolomics, lymphocytic mitochondrial outcomes, and epigenetics (histone H3 Lys-4 trimethylation and 5-methylcytosine) were evaluated in samples from 11 22qDS children and 13 age- and sex-matched neurotypically developing controls. Metabolite differences between 22qDS children and controls reflected a shift from oxidative phosphorylation to glycolysis (higher lactate/pyruvate ratios) accompanied by an increase in reductive carboxylation of α-ketoglutarate (increased concentrations of 2-hydroxyglutaric acid, cholesterol, and fatty acids). Altered metabolism in 22qDS reflected a critical role for the haploinsufficiency of the mitochondrial citrate transporter SLC25A1, further enhanced by HIF-1α, MYC, and metabolite controls. This comprehensive profiling served to clarify the biochemistry of this disease underlying its broad, complex phenotype.
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Affiliation(s)
- Eleonora Napoli
- From the Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, California 95616
| | - Flora Tassone
- the Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, the Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, California 95817
| | - Sarah Wong
- From the Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, California 95616
| | - Kathleen Angkustsiri
- the Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, the Department of Pediatrics, and
| | - Tony J Simon
- the Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, the Department of Psychiatry, UC Davis Medical Center, Sacramento, California 95817, and
| | - Gyu Song
- From the Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, California 95616
| | - Cecilia Giulivi
- From the Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, California 95616, the Medical Investigations of Neurodevelopmental Disorders (MIND) Institute,
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50
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Loke YJ, Hannan AJ, Craig JM. The Role of Epigenetic Change in Autism Spectrum Disorders. Front Neurol 2015; 6:107. [PMID: 26074864 PMCID: PMC4443738 DOI: 10.3389/fneur.2015.00107] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/28/2015] [Indexed: 12/14/2022] Open
Abstract
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders characterized by problems with social communication, social interaction, and repetitive or restricted behaviors. ASD are comorbid with other disorders including attention deficit hyperactivity disorder, epilepsy, Rett syndrome, and Fragile X syndrome. Neither the genetic nor the environmental components have been characterized well enough to aid diagnosis or treatment of non-syndromic ASD. However, genome-wide association studies have amassed evidence suggesting involvement of hundreds of genes and a variety of associated genetic pathways. Recently, investigators have turned to epigenetics, a prime mediator of environmental effects on genomes and phenotype, to characterize changes in ASD that constitute a molecular level on top of DNA sequence. Though in their infancy, such studies have the potential to increase our understanding of the etiology of ASD and may assist in the development of biomarkers for its prediction, diagnosis, prognosis, and eventually in its prevention and intervention. This review focuses on the first few epigenome-wide association studies of ASD and discusses future directions.
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Affiliation(s)
- Yuk Jing Loke
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne , Parkville, VIC , Australia
| | - Anthony John Hannan
- Melbourne Brain Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne , Parkville, VIC , Australia
| | - Jeffrey Mark Craig
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne , Parkville, VIC , Australia
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