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Namgung E, Ha E, Yoon S, Song Y, Lee H, Kang HJ, Han JS, Kim JM, Lee W, Lyoo IK, Kim SJ. Identifying unique subgroups in suicide risks among psychiatric outpatients. Compr Psychiatry 2024; 131:152463. [PMID: 38394926 DOI: 10.1016/j.comppsych.2024.152463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/27/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND The presence of psychiatric disorders is widely recognized as one of the primary risk factors for suicide. A significant proportion of individuals receiving outpatient psychiatric treatment exhibit varying degrees of suicidal behaviors, which may range from mild suicidal ideations to overt suicide attempts. This study aims to elucidate the transdiagnostic symptom dimensions and associated suicidal features among psychiatric outpatients. METHODS The study enrolled patients who attended the psychiatry outpatient clinic at a tertiary hospital in South Korea (n = 1, 849, age range = 18-81; 61% women). A data-driven classification methodology was employed, incorporating a broad spectrum of clinical symptoms, to delineate distinctive subgroups among psychiatric outpatients exhibiting suicidality (n = 1189). A reference group of patients without suicidality (n = 660) was included for comparative purposes to ascertain cluster-specific sociodemographic, suicide-related, and psychiatric characteristics. RESULTS Psychiatric outpatients with suicidality (n = 1189) were subdivided into three distinctive clusters: the low-suicide risk cluster (Cluster 1), the high-suicide risk externalizing cluster (Cluster 2), and the high-suicide risk internalizing cluster (Cluster 3). Relative to the reference group (n = 660), each cluster exhibited distinct attributes pertaining to suicide-related characteristics and clinical symptoms, covering domains such as anxiety, externalizing and internalizing behaviors, and feelings of hopelessness. Cluster 1, identified as the low-suicide risk group, exhibited less frequent suicidal ideation, planning, and multiple attempts. In the high-suicide risk groups, Cluster 2 displayed pronounced externalizing symptoms, whereas Cluster 3 was primarily defined by internalizing and hopelessness symptoms. Bipolar disorders were most common in Cluster 2, while depressive disorders were predominant in Cluster 3. DISCUSSION Our findings suggest the possibility of differentiating psychiatric outpatients into distinct, clinically relevant subgroups predicated on their suicide risk. This research potentially paves the way for personalizing interventions and preventive strategies that address cluster-specific characteristics, thereby mitigating suicide-related mortality among psychiatric outpatients.
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Affiliation(s)
- Eun Namgung
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Eunji Ha
- Ewha Brain Institute, Ewha Womans University, Seoul, South Korea
| | - Sujung Yoon
- Ewha Brain Institute, Ewha Womans University, Seoul, South Korea; Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul, South Korea
| | - Yumi Song
- Ewha Brain Institute, Ewha Womans University, Seoul, South Korea; Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul, South Korea
| | - Hyangwon Lee
- Ewha Brain Institute, Ewha Womans University, Seoul, South Korea; Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul, South Korea
| | - Hee-Ju Kang
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, South Korea
| | - Jung-Soo Han
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Jae-Min Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, South Korea
| | - Wonhye Lee
- Department of Psychiatry, Sungkyunkwan University College of Medicine, Samsung Medical Center, Seoul, South Korea
| | - In Kyoon Lyoo
- Ewha Brain Institute, Ewha Womans University, Seoul, South Korea; Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul, South Korea; Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, South Korea.
| | - Seog Ju Kim
- Department of Psychiatry, Sungkyunkwan University College of Medicine, Samsung Medical Center, Seoul, South Korea.
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2
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Bao B, Zahiri J, Gazestani VH, Lopez L, Xiao Y, Kim R, Wen TH, Chiang AWT, Nalabolu S, Pierce K, Robasky K, Wang T, Hoekzema K, Eichler EE, Lewis NE, Courchesne E. A predictive ensemble classifier for the gene expression diagnosis of ASD at ages 1 to 4 years. Mol Psychiatry 2023; 28:822-833. [PMID: 36266569 PMCID: PMC9908553 DOI: 10.1038/s41380-022-01826-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 09/13/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Autism Spectrum Disorder (ASD) diagnosis remains behavior-based and the median age of diagnosis is ~52 months, nearly 5 years after its first-trimester origin. Accurate and clinically-translatable early-age diagnostics do not exist due to ASD genetic and clinical heterogeneity. Here we collected clinical, diagnostic, and leukocyte RNA data from 240 ASD and typically developing (TD) toddlers (175 toddlers for training and 65 for test). To identify gene expression ASD diagnostic classifiers, we developed 42,840 models composed of 3570 gene expression feature selection sets and 12 classification methods. We found that 742 models had AUC-ROC ≥ 0.8 on both Training and Test sets. Weighted Bayesian model averaging of these 742 models yielded an ensemble classifier model with accurate performance in Training and Test gene expression datasets with ASD diagnostic classification AUC-ROC scores of 85-89% and AUC-PR scores of 84-92%. ASD toddlers with ensemble scores above and below the overall ASD ensemble mean of 0.723 (on a scale of 0 to 1) had similar diagnostic and psychometric scores, but those below this ASD ensemble mean had more prenatal risk events than TD toddlers. Ensemble model feature genes were involved in cell cycle, inflammation/immune response, transcriptional gene regulation, cytokine response, and PI3K-AKT, RAS and Wnt signaling pathways. We additionally collected targeted DNA sequencing smMIPs data on a subset of ASD risk genes from 217 of the 240 ASD and TD toddlers. This DNA sequencing found about the same percentage of SFARI Level 1 and 2 ASD risk gene mutations in TD (12 of 105) as in ASD (13 of 112) toddlers, and classification based only on the presence of mutation in these risk genes performed at a chance level of 49%. By contrast, the leukocyte ensemble gene expression classifier correctly diagnostically classified 88% of TD and ASD toddlers with ASD risk gene mutations. Our ensemble ASD gene expression classifier is diagnostically predictive and replicable across different toddler ages, races, and ethnicities; out-performs a risk gene mutation classifier; and has potential for clinical translation.
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Affiliation(s)
- Bokan Bao
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Javad Zahiri
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Vahid H Gazestani
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Yaqiong Xiao
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Center for Language and Brain, Shenzhen Institute of Neuroscience, Shenzhen, China
| | - Raphael Kim
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa H Wen
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Austin W T Chiang
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Srinivasa Nalabolu
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Kimberly Robasky
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, US
- School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Carolina Health and Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, 100191, Beijing, China
- Neuroscience Research Institute, Peking University; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, 100191, Beijing, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA.
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3
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Wang Z, Xu Y, Peng D, Gao J, Lu F. Brain functional activity-based classification of autism spectrum disorder using an attention-based graph neural network combined with gene expression. Cereb Cortex 2022; 33:6407-6419. [PMID: 36587290 DOI: 10.1093/cercor/bhac513] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 01/02/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex brain neurodevelopmental disorder related to brain activity and genetics. Most of the ASD diagnostic models perform feature selection at the group level without considering individualized information. Evidence has shown the unique topology of the individual brain has a fundamental impact on brain diseases. Thus, a data-constructing method fusing individual topological information and a corresponding classification model is crucial in ASD diagnosis and biomarker discovery. In this work, we trained an attention-based graph neural network (GNN) to perform the ASD diagnosis with the fusion of graph data. The results achieved an accuracy of 79.78%. Moreover, we found the model paid high attention to brain regions mainly involved in the social-brain circuit, default-mode network, and sensory perception network. Furthermore, by analyzing the covariation between functional magnetic resonance imaging data and gene expression, current studies detected several ASD-related genes (i.e. MUTYH, AADAT, and MAP2), and further revealed their links to image biomarkers. Our work demonstrated that the ASD diagnostic framework based on graph data and attention-based GNN could be an effective tool for ASD diagnosis. The identified functional features with high attention values may serve as imaging biomarkers for ASD.
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Affiliation(s)
- Zhengning Wang
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu 611731, PR China
| | - Yuhang Xu
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu 611731, PR China
| | - Dawei Peng
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu 611731, PR China
| | - Jingjing Gao
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu 611731, PR China
| | - Fengmei Lu
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, PR China
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4
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Moreau MM, Pietropaolo S, Ezan J, Robert BJA, Miraux S, Maître M, Cho Y, Crusio WE, Montcouquiol M, Sans N. Scribble Controls Social Motivation Behavior through the Regulation of the ERK/Mnk1 Pathway. Cells 2022; 11:cells11101601. [PMID: 35626639 PMCID: PMC9139383 DOI: 10.3390/cells11101601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Social behavior is a basic domain affected by several neurodevelopmental disorders, including ASD and a heterogeneous set of neuropsychiatric disorders. The SCRIB gene that codes for the polarity protein SCRIBBLE has been identified as a risk gene for spina bifida, the most common type of neural tube defect, found at high frequencies in autistic patients, as well as other congenital anomalies. The deletions and mutations of the 8q24.3 region encompassing SCRIB are also associated with multisyndromic and rare disorders. Nonetheless, the potential link between SCRIB and relevant social phenotypes has not been fully investigated. Hence, we show that Scribcrc/+ mice, carrying a mutated version of Scrib, displayed reduced social motivation behavior and social habituation, while other behavioral domains were unaltered. Social deficits were associated with the upregulation of ERK phosphorylation, together with increased c-Fos activity. Importantly, the social alterations were rescued by both direct and indirect pERK inhibition. These results support a link between polarity genes, social behaviors and hippocampal functionality and suggest a role for SCRIB in the etiopathology of neurodevelopmental disorders. Furthermore, our data demonstrate the crucial role of the MAPK/ERK signaling pathway in underlying social motivation behavior, thus supporting its relevance as a therapeutic target.
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Affiliation(s)
- Maïté M. Moreau
- Univ. Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077 Bordeaux, France; (J.E.); (B.J.A.R.); (M.M.); (M.M.)
- Correspondence: (M.M.M.); (N.S.)
| | - Susanna Pietropaolo
- Univ. Bordeaux, CNRS, Aquitaine Institute for Cognitive and Integrative Neurosciences, UMR5287, 33405 Bordeaux, France; (S.P.); (Y.C.); (W.E.C.)
| | - Jérôme Ezan
- Univ. Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077 Bordeaux, France; (J.E.); (B.J.A.R.); (M.M.); (M.M.)
| | - Benjamin J. A. Robert
- Univ. Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077 Bordeaux, France; (J.E.); (B.J.A.R.); (M.M.); (M.M.)
| | - Sylvain Miraux
- Univ. Bordeaux, CNRS, Centre de Résonance Magnétique des Systèmes Biologiques UMR5536, 33077 Bordeaux, France;
| | - Marlène Maître
- Univ. Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077 Bordeaux, France; (J.E.); (B.J.A.R.); (M.M.); (M.M.)
| | - Yoon Cho
- Univ. Bordeaux, CNRS, Aquitaine Institute for Cognitive and Integrative Neurosciences, UMR5287, 33405 Bordeaux, France; (S.P.); (Y.C.); (W.E.C.)
| | - Wim E. Crusio
- Univ. Bordeaux, CNRS, Aquitaine Institute for Cognitive and Integrative Neurosciences, UMR5287, 33405 Bordeaux, France; (S.P.); (Y.C.); (W.E.C.)
| | - Mireille Montcouquiol
- Univ. Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077 Bordeaux, France; (J.E.); (B.J.A.R.); (M.M.); (M.M.)
| | - Nathalie Sans
- Univ. Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077 Bordeaux, France; (J.E.); (B.J.A.R.); (M.M.); (M.M.)
- Correspondence: (M.M.M.); (N.S.)
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5
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Hsieh FF, Korsunsky I, Shih AJ, Moss MA, Chatterjee PK, Deshpande J, Xue X, Madankumar S, Kumar G, Rochelson B, Metz CN. Maternal oxytocin administration modulates gene expression in the brains of perinatal mice. J Perinat Med 2022; 50:207-218. [PMID: 34717055 DOI: 10.1515/jpm-2020-0525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 10/01/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Oxytocin (OXT) is widely used to facilitate labor. However, little is known about the effects of perinatal OXT exposure on the developing brain. We investigated the effects of maternal OXT administration on gene expression in perinatal mouse brains. METHODS Pregnant C57BL/6 mice were treated with saline or OXT at term (n=6-7/group). Dams and pups were euthanized on gestational day (GD) 18.5 after delivery by C-section. Another set of dams was treated with saline or OXT (n=6-7/group) and allowed to deliver naturally; pups were euthanized on postnatal day 9 (PND9). Perinatal/neonatal brain gene expression was determined using Illumina BeadChip Arrays and real time quantitative PCR. Differential gene expression analyses were performed. In addition, the effect of OXT on neurite outgrowth was assessed using PC12 cells. RESULTS Distinct and sex-specific gene expression patterns were identified in offspring brains following maternal OXT administration at term. The microarray data showed that female GD18.5 brains exhibited more differential changes in gene expression compared to male GD18.5 brains. Specifically, Cnot4 and Frmd4a were significantly reduced by OXT exposure in male and female GD18.5 brains, whereas Mtap1b, Srsf11, and Syn2 were significantly reduced only in female GD18.5 brains. No significant microarray differences were observed in PND9 brains. By quantitative PCR, OXT exposure reduced Oxtr expression in female and male brains on GD18.5 and PND9, respectively. PC12 cell differentiation assays revealed that OXT induced neurite outgrowth. CONCLUSIONS Prenatal OXT exposure induces sex-specific differential regulation of several nervous system-related genes and pathways with important neural functions in perinatal brains.
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Affiliation(s)
- Frances F Hsieh
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology Stamford Hospital, Stamford, CT, USA
| | - Ilya Korsunsky
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Division of Genetics, Department of Medicine at Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew J Shih
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Matthew A Moss
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Prodyot K Chatterjee
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Jaai Deshpande
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Providence Community Health Center, Providence, RI, USA
| | - Xiangying Xue
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Swati Madankumar
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Gopal Kumar
- Elmezzi Graduate School of Molecular Medicine at Northwell Health, Manhasset, NY, USA
| | - Burton Rochelson
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Christine N Metz
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Elmezzi Graduate School of Molecular Medicine at Northwell Health, Manhasset, NY, USA
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6
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Mizuno S, Hirota JN, Ishii C, Iwasaki H, Sano Y, Furuichi T. Comprehensive Profiling of Gene Expression in the Cerebral Cortex and Striatum of BTBRTF/ArtRbrc Mice Compared to C57BL/6J Mice. Front Cell Neurosci 2020; 14:595607. [PMID: 33362469 PMCID: PMC7758463 DOI: 10.3389/fncel.2020.595607] [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: 08/17/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Mouse line BTBR T+ Iptr3tf/J (hereafter referred as to BTBR/J) is a mouse strain that shows lower sociability compared to the C57BL/6J mouse strain (B6) and thus is often utilized as a model for autism spectrum disorder (ASD). In this study, we utilized another subline, BTBRTF/ArtRbrc (hereafter referred as to BTBR/R), and analyzed the associated brain transcriptome compared to B6 mice using microarray analysis, quantitative RT-PCR analysis, various bioinformatics analyses, and in situ hybridization. We focused on the cerebral cortex and the striatum, both of which are thought to be brain circuits associated with ASD symptoms. The transcriptome profiling identified 1,280 differentially expressed genes (DEGs; 974 downregulated and 306 upregulated genes, including 498 non-coding RNAs [ncRNAs]) in BTBR/R mice compared to B6 mice. Among these DEGs, 53 genes were consistent with ASD-related genes already established. Gene Ontology (GO) enrichment analysis highlighted 78 annotations (GO terms) including DNA/chromatin regulation, transcriptional/translational regulation, intercellular signaling, metabolism, immune signaling, and neurotransmitter/synaptic transmission-related terms. RNA interaction analysis revealed novel RNA–RNA networks, including 227 ASD-related genes. Weighted correlation network analysis highlighted 10 enriched modules including DNA/chromatin regulation, neurotransmitter/synaptic transmission, and transcriptional/translational regulation. Finally, the behavioral analyses showed that, compared to B6 mice, BTBR/R mice have mild but significant deficits in social novelty recognition and repetitive behavior. In addition, the BTBR/R data were comprehensively compared with those reported in the previous studies of human subjects with ASD as well as ASD animal models, including BTBR/J mice. Our results allow us to propose potentially important genes, ncRNAs, and RNA interactions. Analysis of the altered brain transcriptome data of the BTBR/R and BTBR/J sublines can contribute to the understanding of the genetic underpinnings of autism susceptibility.
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Affiliation(s)
- Shota Mizuno
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Jun-Na Hirota
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Chiaki Ishii
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Hirohide Iwasaki
- Department of Anatomy, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Yoshitake Sano
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Teiichi Furuichi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
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7
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Sun MW, Moretti S, Paskov KM, Stockham NT, Varma M, Chrisman BS, Washington PY, Jung JY, Wall DP. Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value. BMC Bioinformatics 2020; 21:356. [PMID: 32787845 PMCID: PMC7430867 DOI: 10.1186/s12859-020-03693-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/21/2020] [Indexed: 11/13/2022] Open
Abstract
Background Complex human health conditions with etiological heterogeneity like Autism Spectrum Disorder (ASD) often pose a challenge for traditional genome-wide association study approaches in defining a clear genotype to phenotype model. Coalitional game theory (CGT) is an exciting method that can consider the combinatorial effect of groups of variants working in concert to produce a phenotype. CGT has been applied to associate likely-gene-disrupting variants encoded from whole genome sequence data to ASD; however, this previous approach cannot take into account for prior biological knowledge. Here we extend CGT to incorporate a priori knowledge from biological networks through a game theoretic centrality measure based on Shapley value to rank genes by their relevance–the individual gene’s synergistic influence in a gene-to-gene interaction network. Game theoretic centrality extends the notion of Shapley value to the evaluation of a gene’s contribution to the overall connectivity of its corresponding node in a biological network. Results We implemented and applied game theoretic centrality to rank genes on whole genomes from 756 multiplex autism families. Top ranking genes with the highest game theoretic centrality in both the weighted and unweighted approaches were enriched for pathways previously associated with autism, including pathways of the immune system. Four of the selected genes HLA-A, HLA-B, HLA-G, and HLA-DRB1–have also been implicated in ASD and further support the link between ASD and the human leukocyte antigen complex. Conclusions Game theoretic centrality can prioritize influential, disease-associated genes within biological networks, and assist in the decoding of polygenic associations to complex disorders like autism.
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Affiliation(s)
- Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, USA.,Department of Pediatrics, Stanford University, Stanford, USA
| | - Stefano Moretti
- LAMSADE, CNRS, Université Paris-Dauphine, Université PSL, Paris, France
| | - Kelley M Paskov
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Nate T Stockham
- Department of Neuroscience, Stanford University, Stanford, USA
| | - Maya Varma
- Department of Computer Science, Stanford University, Stanford, USA
| | | | | | - Jae-Yoon Jung
- Department of Biomedical Data Science, Stanford University, Stanford, USA.,Department of Pediatrics, Stanford University, Stanford, USA
| | - Dennis P Wall
- Department of Biomedical Data Science, Stanford University, Stanford, USA. .,Department of Pediatrics, Stanford University, Stanford, USA. .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, United States.
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8
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Aldosary M, Al-Bakheet A, Al-Dhalaan H, Almass R, Alsagob M, Al-Younes B, AlQuait L, Mustafa OM, Bulbul M, Rahbeeni Z, Alfadhel M, Chedrawi A, Al-Hassnan Z, AlDosari M, Al-Zaidan H, Al-Muhaizea MA, AlSayed MD, Salih MA, AlShammari M, Faiyaz-Ul-Haque M, Chishti MA, Al-Harazi O, Al-Odaib A, Kaya N, Colak D. Rett Syndrome, a Neurodevelopmental Disorder, Whole-Transcriptome, and Mitochondrial Genome Multiomics Analyses Identify Novel Variations and Disease Pathways. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:160-171. [PMID: 32105570 DOI: 10.1089/omi.2019.0192] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder reported worldwide in diverse populations. RTT is diagnosed primarily in females, with clinical findings manifesting early in life. Despite the variable rates across populations, RTT has an estimated prevalence of ∼1 in 10,000 live female births. Among 215 Saudi Arabian patients with neurodevelopmental and autism spectrum disorders, we identified 33 patients with RTT who were subsequently examined by genome-wide transcriptome and mitochondrial genome variations. To the best of our knowledge, this is the first in-depth molecular and multiomics analyses of a large cohort of Saudi RTT cases with a view to informing the underlying mechanisms of this disease that impact many patients and families worldwide. The patients were unrelated, except for 2 affected sisters, and comprised of 25 classic and eight atypical RTT cases. The cases were screened for methyl-CpG binding protein 2 (MECP2), CDKL5, FOXG1, NTNG1, and mitochondrial DNA (mtDNA) variants, as well as copy number variations (CNVs) using a genome-wide experimental strategy. We found that 15 patients (13 classic and two atypical RTT) have MECP2 mutations, 2 of which were novel variants. Two patients had novel FOXG1 and CDKL5 variants (both atypical RTT). Whole mtDNA sequencing of the patients who were MECP2 negative revealed two novel mtDNA variants in two classic RTT patients. Importantly, the whole-transcriptome analysis of our RTT patients' blood and further comparison with previous expression profiling of brain tissue from patients with RTT revealed 77 significantly dysregulated genes. The gene ontology and interaction network analysis indicated potentially critical roles of MAPK9, NDUFA5, ATR, SMARCA5, RPL23, SRSF3, and mitochondrial dysfunction, oxidative stress response and MAPK signaling pathways in the pathogenesis of RTT genes. This study expands our knowledge on RTT disease networks and pathways as well as presents novel mutations and mtDNA alterations in RTT in a population sample that was not previously studied.
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Affiliation(s)
- Mazhor Aldosary
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - AlBandary Al-Bakheet
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Hesham Al-Dhalaan
- Department of Neuroscience, and King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Rawan Almass
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Maysoon Alsagob
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Banan Al-Younes
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Laila AlQuait
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Osama Mufid Mustafa
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mustafa Bulbul
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Genetics Division, Department of Pediatrics, King Abdullah Specialized Children Hospital, Riyadh, Saudi Arabia
| | - Aziza Chedrawi
- Department of Neuroscience, and King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Zuhair Al-Hassnan
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mohammed AlDosari
- Center for Pediatric Neurosciences, Cleveland Clinic, Cleveland, Ohio
| | - Hamad Al-Zaidan
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mohammad A Al-Muhaizea
- Department of Neuroscience, and King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Moeenaldeen D AlSayed
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Division of Pediatric Neurology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mai AlShammari
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | | | - Mohammad Azhar Chishti
- Department of Biochemistry, King Khalid Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Olfat Al-Harazi
- Department of Biostatistics, Epidemiology, and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ali Al-Odaib
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology, and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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9
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Duda M, Zhang H, Li HD, Wall DP, Burmeister M, Guan Y. Brain-specific functional relationship networks inform autism spectrum disorder gene prediction. Transl Psychiatry 2018; 8:56. [PMID: 29507298 PMCID: PMC5838237 DOI: 10.1038/s41398-018-0098-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/20/2017] [Accepted: 12/30/2017] [Indexed: 11/09/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neuropsychiatric disorder with strong evidence of genetic contribution, and increased research efforts have resulted in an ever-growing list of ASD candidate genes. However, only a fraction of the hundreds of nominated ASD-related genes have identified de novo or transmitted loss of function (LOF) mutations that can be directly attributed to the disorder. For this reason, a means of prioritizing candidate genes for ASD would help filter out false-positive results and allow researchers to focus on genes that are more likely to be causative. Here we constructed a machine learning model by leveraging a brain-specific functional relationship network (FRN) of genes to produce a genome-wide ranking of ASD risk genes. We rigorously validated our gene ranking using results from two independent sequencing experiments, together representing over 5000 simplex and multiplex ASD families. Finally, through functional enrichment analysis on our highly prioritized candidate gene network, we identified a small number of pathways that are key in early neural development, providing further support for their potential role in ASD.
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Affiliation(s)
- Marlena Duda
- 0000000086837370grid.214458.eDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USA
| | - Hongjiu Zhang
- 0000000086837370grid.214458.eDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USA
| | - Hong-Dong Li
- 0000000086837370grid.214458.eDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USA ,0000 0001 0379 7164grid.216417.7Center for Bioinformatics, School of Information Science and Engineering, Central South University, Changsha, China
| | - Dennis P. Wall
- 0000000419368956grid.168010.eDepartment of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA USA ,0000000419368956grid.168010.eDepartment of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Margit Burmeister
- 0000000086837370grid.214458.eDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USA ,0000000086837370grid.214458.eMolecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI USA ,0000000086837370grid.214458.eDepartment of Human Genetics, University of Michigan, Ann Arbor, MI USA ,0000000086837370grid.214458.eDepartment of Psychiatry, University of Michigan, Ann Arbor, MI USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. .,Department of Internal Medicine, Usniversity of Michigan, Ann Arbor, MI, USA. .,Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA.
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10
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Breen MS, Tylee DS, Maihofer AX, Neylan TC, Mehta D, Binder EB, Chandler SD, Hess JL, Kremen WS, Risbrough VB, Woelk CH, Baker DG, Nievergelt CM, Tsuang MT, Buxbaum JD, Glatt SJ. PTSD Blood Transcriptome Mega-Analysis: Shared Inflammatory Pathways across Biological Sex and Modes of Trauma. Neuropsychopharmacology 2018; 43:469-481. [PMID: 28925389 PMCID: PMC5770765 DOI: 10.1038/npp.2017.220] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/29/2017] [Accepted: 08/29/2017] [Indexed: 01/30/2023]
Abstract
Transcriptome-wide screens of peripheral blood during the onset and development of posttraumatic stress disorder (PTSD) indicate widespread immune dysregulation. However, little is known as to whether biological sex and the type of traumatic event influence shared or distinct biological pathways in PTSD. We performed a combined analysis of five independent PTSD blood transcriptome studies covering seven types of trauma in 229 PTSD and 311 comparison individuals to synthesize the extant data. Analyses by trauma type revealed a clear pattern of PTSD gene expression signatures distinguishing interpersonal (IP)-related traumas from combat-related traumas. Co-expression network analyses integrated all data and identified distinct gene expression perturbations across sex and modes of trauma in PTSD, including one wound-healing module downregulated in men exposed to combat traumas, one IL-12-mediated signaling module upregulated in men exposed to IP-related traumas, and two modules associated with lipid metabolism and mitogen-activated protein kinase activity upregulated in women exposed to IP-related traumas. Remarkably, a high degree of sharing of transcriptional dysregulation across sex and modes of trauma in PTSD was also observed converging on common signaling cascades, including cytokine, innate immune, and type I interferon pathways. Collectively, these findings provide a broad view of immune dysregulation in PTSD and demonstrate inflammatory pathways of molecular convergence and specificity, which may inform mechanisms and diagnostic biomarkers for the disorder.
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Affiliation(s)
- Michael S Breen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1668, New York, NY 10029, USA, Tel: +1 212 241 0242, Fax: 212 828 4221, E-mail:
| | - Daniel S Tylee
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University, Syracuse, NY, USA
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Thomas C Neylan
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA,San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Divya Mehta
- School of Psychology and Counseling, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Sharon D Chandler
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jonathan L Hess
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University, Syracuse, NY, USA
| | - William S Kremen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA,Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA,Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Christopher H Woelk
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK,Merck Exploratory Science Center, Merck Research Laboratories, Cambridge, MA, USA
| | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA,Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA,Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Ming T Tsuang
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA,Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen J Glatt
- Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), SUNY Upstate Medical University, Syracuse, NY, USA
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11
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Coalitional game theory as a promising approach to identify candidate autism genes. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018; 23:436-447. [PMID: 29218903 PMCID: PMC6055932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Despite mounting evidence for the strong role of genetics in the phenotypic manifestation of Autism Spectrum Disorder (ASD), the specific genes responsible for the variable forms of ASD remain undefined. ASD may be best explained by a combinatorial genetic model with varying epistatic interactions across many small effect mutations. Coalitional or cooperative game theory is a technique that studies the combined effects of groups of players, known as coalitions, seeking to identify players who tend to improve the performance--the relationship to a specific disease phenotype--of any coalition they join. This method has been previously shown to boost biologically informative signal in gene expression data but to-date has not been applied to the search for cooperative mutations among putative ASD genes. We describe our approach to highlight genes relevant to ASD using coalitional game theory on alteration data of 1,965 fully sequenced genomes from 756 multiplex families. Alterations were encoded into binary matrices for ASD (case) and unaffected (control) samples, indicating likely gene-disrupting, inherited mutations in altered genes. To determine individual gene contributions given an ASD phenotype, a "player" metric, referred to as the Shapley value, was calculated for each gene in the case and control cohorts. Sixty seven genes were found to have significantly elevated player scores and likely represent significant contributors to the genetic coordination underlying ASD. Using network and cross-study analysis, we found that these genes are involved in biological pathways known to be affected in the autism cases and that a subset directly interact with several genes known to have strong associations to autism. These findings suggest that coalitional game theory can be applied to large-scale genomic data to identify hidden yet influential players in complex polygenic disorders such as autism.
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12
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Diaz-Beltran L, Esteban FJ, Varma M, Ortuzk A, David M, Wall DP. Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes. BMC Genomics 2017; 18:315. [PMID: 28427329 PMCID: PMC5399393 DOI: 10.1186/s12864-017-3667-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/28/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Numerous studies have highlighted the elevated degree of comorbidity associated with autism spectrum disorder (ASD). These comorbid conditions may add further impairments to individuals with autism and are substantially more prevalent compared to neurotypical populations. These high rates of comorbidity are not surprising taking into account the overlap of symptoms that ASD shares with other pathologies. From a research perspective, this suggests common molecular mechanisms involved in these conditions. Therefore, identifying crucial genes in the overlap between ASD and these comorbid disorders may help unravel the common biological processes involved and, ultimately, shed some light in the understanding of autism etiology. RESULTS In this work, we used a two-fold systems biology approach specially focused on biological processes and gene networks to conduct a comparative analysis of autism with 31 frequently comorbid disorders in order to define a multi-disorder subcomponent of ASD and predict new genes of potential relevance to ASD etiology. We validated our predictions by determining the significance of our candidate genes in high throughput transcriptome expression profiling studies. Using prior knowledge of disease-related biological processes and the interaction networks of the disorders related to autism, we identified a set of 19 genes not previously linked to ASD that were significantly differentially regulated in individuals with autism. In addition, these genes were of potential etiologic relevance to autism, given their enriched roles in neurological processes crucial for optimal brain development and function, learning and memory, cognition and social behavior. CONCLUSIONS Taken together, our approach represents a novel perspective of autism from the point of view of related comorbid disorders and proposes a model by which prior knowledge of interaction networks may enlighten and focus the genome-wide search for autism candidate genes to better define the genetic heterogeneity of ASD.
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Affiliation(s)
- Leticia Diaz-Beltran
- Division of Systems Medicine, Department of Pediatrics, School of Medicine, Stanford University, 1265 Welch Road, Stanford, CA, 94305-5488, USA
- Division of Systems Medicine, Department of Psychiatry, Stanford University, Stanford, CA, USA
- Systems Biology Unit, Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Francisco J Esteban
- Systems Biology Unit, Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Maya Varma
- Division of Systems Medicine, Department of Pediatrics, School of Medicine, Stanford University, 1265 Welch Road, Stanford, CA, 94305-5488, USA
- Division of Systems Medicine, Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - Alp Ortuzk
- Division of Systems Medicine, Department of Pediatrics, School of Medicine, Stanford University, 1265 Welch Road, Stanford, CA, 94305-5488, USA
- Division of Systems Medicine, Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - Maude David
- Division of Systems Medicine, Department of Pediatrics, School of Medicine, Stanford University, 1265 Welch Road, Stanford, CA, 94305-5488, USA
- Division of Systems Medicine, Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - Dennis P Wall
- Division of Systems Medicine, Department of Pediatrics, School of Medicine, Stanford University, 1265 Welch Road, Stanford, CA, 94305-5488, USA.
- Division of Systems Medicine, Department of Psychiatry, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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13
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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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14
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Meguid NA, Ghozlan SAS, Mohamed MF, Ibrahim MK, Dawood RM, Din NGBE, Abdelhafez TH, Hemimi M, Awady MKE. Expression of Reactive Oxygen Species-Related Transcripts in Egyptian Children With Autism. Biomark Insights 2017; 12:1177271917691035. [PMID: 28469396 PMCID: PMC5391985 DOI: 10.1177/1177271917691035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 01/04/2017] [Indexed: 12/27/2022] Open
Abstract
The molecular basis of the pathophysiological role of oxidative stress in autism is understudied. Herein, we used polymerase chain reaction (PCR) array to analyze transcriptional pattern of 84 oxidative stress genes in peripheral blood mononuclear cell pools isolated from 32 autistic patients (16 mild/moderate and 16 severe) and 16 healthy subjects (each sample is a pool from 4 autistic patients or 4 controls). The PCR array data were further validated by quantitative real-time PCR in 80 autistic children (55 mild/moderate and 25 severe) and 60 healthy subjects. Our data revealed downregulation in GCLM, SOD2, NCF2, PRNP, and PTGS2 transcripts (1.5, 3.8, 1.2, 1.7, and 2.2, respectively;P < .05 for all) in autistic group compared with controls. In addition, TXN and FTH1 exhibited 1.4- and 1.7-fold downregulation, respectively, in severe autistic patients when compared with mild/moderate group (P = .005 and .0008, respectively). This study helps in a better understanding of the underlying biology and related genetic factors of autism, and most importantly, it presents suggested candidate biomarkers for diagnosis and prognosis purposes as well as targets for therapeutic intervention.
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Affiliation(s)
- Nagwa A Meguid
- Department of Research on Children with Special Needs, Medical Research Division, National Research Centre, Giza, Egypt
| | - Said A S Ghozlan
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - Magda F Mohamed
- Department of Chemistry (Biochemistry Branch), Faculty of Science, Cairo University, Giza, Egypt
| | - Marwa K Ibrahim
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Giza, Egypt
| | - Reham M Dawood
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Giza, Egypt
| | - Noha G Bader El Din
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Giza, Egypt
| | - Tawfeek H Abdelhafez
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Giza, Egypt
| | - Maha Hemimi
- Department of Research on Children with Special Needs, Medical Research Division, National Research Centre, Giza, Egypt
| | - Mostafa K El Awady
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Giza, Egypt
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15
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Esposito G, Burgunder JM, Dunlop J, Gorwood P, Inamdar A, Pfister SM, Pochet R, van den Bent MJ, Van Hoylandt N, Weller M, Westphal M, Wick W, Nutt D. Gene-Tailored Treatments for Brain Disorders: Challenges and Opportunities. Public Health Genomics 2016; 19:170-7. [DOI: 10.1159/000446535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Pearson BL, Simon JM, McCoy ES, Salazar G, Fragola G, Zylka MJ. Identification of chemicals that mimic transcriptional changes associated with autism, brain aging and neurodegeneration. Nat Commun 2016; 7:11173. [PMID: 27029645 PMCID: PMC4821887 DOI: 10.1038/ncomms11173] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/29/2016] [Indexed: 12/13/2022] Open
Abstract
Environmental factors, including pesticides, have been linked to autism and neurodegeneration risk using retrospective epidemiological studies. Here we sought to prospectively identify chemicals that share transcriptomic signatures with neurological disorders, by exposing mouse cortical neuron-enriched cultures to hundreds of chemicals commonly found in the environment and on food. We find that rotenone, a pesticide associated with Parkinson's disease risk, and certain fungicides, including pyraclostrobin, trifloxystrobin, famoxadone and fenamidone, produce transcriptional changes in vitro that are similar to those seen in brain samples from humans with autism, advanced age and neurodegeneration (Alzheimer's disease and Huntington's disease). These chemicals stimulate free radical production and disrupt microtubules in neurons, effects that can be reduced by pretreating with a microtubule stabilizer, an antioxidant, or with sulforaphane. Our study provides an approach to prospectively identify environmental chemicals that transcriptionally mimic autism and other brain disorders. This study presents gene expression responses of cultured brain cells to hundreds of chemicals found in the environment and in food. The authors identified chemicals that induce transcriptomic profiles that overlap those seen in human brains affected with autism, aging, and neurodegeneration.
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Affiliation(s)
- Brandon L Pearson
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, North Carolina 27599-7545, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina Chapel Hill, Chapel Hill, North Carolina 27599-7255, USA
| | - Jeremy M Simon
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, North Carolina 27599-7545, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina Chapel Hill, Chapel Hill, North Carolina 27599-7255, USA
| | - Eric S McCoy
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, North Carolina 27599-7545, USA
| | - Gabriela Salazar
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, North Carolina 27599-7545, USA
| | - Giulia Fragola
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, North Carolina 27599-7545, USA
| | - Mark J Zylka
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, North Carolina 27599-7545, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina Chapel Hill, Chapel Hill, North Carolina 27599-7255, USA
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