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Camussi D, Naef V, Brogi L, Della Vecchia S, Marchese M, Nicoletti F, Santorelli FM, Licitra R. Delving into the Complexity of Valproate-Induced Autism Spectrum Disorder: The Use of Zebrafish Models. Cells 2024; 13:1349. [PMID: 39195239 DOI: 10.3390/cells13161349] [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: 07/13/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024] Open
Abstract
Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental condition with several identified risk factors, both genetic and non-genetic. Among these, prenatal exposure to valproic acid (VPA) has been extensively associated with the development of the disorder. The zebrafish, a cost- and time-effective model, is useful for studying ASD features. Using validated VPA-induced ASD zebrafish models, we aimed to provide new insights into VPA exposure effects during embryonic development and to identify new potential biomarkers associated with ASD-like features. Dose-response analyses were performed in vivo to study larval phenotypes and mechanisms underlying neuroinflammation, mitochondrial dysfunction, oxidative stress, microglial cell status, and motor behaviour. Wild-type and transgenic Tg(mpeg1:EGFP) zebrafish were water-exposed to VPA doses (5 to 500 µM) from 6 to 120 h post-fertilisation (hpf). Embryos and larvae were monitored daily to assess survival and hatching rates, and numerous analyses and tests were conducted from 24 to 120 hpf. VPA doses higher than 50 µM worsened survival and hatching rates, while doses of 25 µM or more altered morphology, microglial status, and larval behaviours. VPA 50 µM also affected mRNA expression of inflammatory cytokines and neurogenesis-related genes, mitochondrial respiration, and reactive oxygen species accumulation. The study confirmed that VPA alters brain homeostasis, synaptic interconnections, and neurogenesis-related signalling pathways, contributing to ASD aetiopathogenesis. Further studies are essential to identify novel ASD biomarkers for developing new drug targets and tailored therapeutic interventions for ASD.
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Affiliation(s)
- Diletta Camussi
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
| | - Valentina Naef
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
| | - Letizia Brogi
- Bio@SNS, Department of Neurosciences, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Stefania Della Vecchia
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
| | - Maria Marchese
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
| | - Ferdinando Nicoletti
- Department of Physiology and Pharmacology Vittorio Erspamer, "La Sapienza" University of Rome, 00185 Rome, Italy
- IRCSS Neuromed, "La Sapienza" University of Rome, 86077 Pozzilli, Italy
| | - Filippo M Santorelli
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
| | - Rosario Licitra
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
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Dickie EW, Ameis SH, Boileau I, Diaconescu AO, Felsky D, Goldstein BI, Gonçalves V, Griffiths JD, Haltigan JD, Husain MO, Rubin-Kahana DS, Iftikhar M, Jani M, Lai MC, Lin HY, MacIntosh BJ, Wheeler AL, Vasdev N, Vieira E, Ahmadzadeh G, Heyland L, Mohan A, Ogunsanya F, Oliver LD, Zhu C, Wong JKY, Charlton C, Truong J, Yu L, Kelly R, Cleverley K, Courtney DB, Foussias G, Hawke LD, Hill S, Kozloff N, Polillo A, Rotenberg M, Quilty LC, Tempelaar W, Wang W, Nikolova YS, Voineskos AN. Neuroimaging and Biosample Collection in the Toronto Adolescent and Youth Cohort Study: Rationale, Methods, and Early Data. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2024; 9:275-284. [PMID: 37979944 DOI: 10.1016/j.bpsc.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND The Toronto Adolescent and Youth (TAY) Cohort Study will characterize the neurobiological trajectories of psychosis spectrum symptoms, functioning, and suicidality (i.e., suicidal thoughts and behaviors) in youth seeking mental health care. Here, we present the neuroimaging and biosample component of the protocol. We also present feasibility and quality control metrics for the baseline sample collected thus far. METHODS The current study includes youths (ages 11-24 years) who were referred to child and youth mental health services within a large tertiary care center in Toronto, Ontario, Canada, with target recruitment of 1500 participants. Participants were offered the opportunity to provide any or all of the following: 1) 1-hour magnetic resonance imaging (MRI) scan (electroencephalography if ineligible for or declined MRI), 2) blood sample for genomic and proteomic data (or saliva if blood collection was declined or not feasible) and urine sample, and 3) heart rate recording to assess respiratory sinus arrhythmia. RESULTS Of the first 417 participants who consented to participate between May 4, 2021, and February 2, 2023, 412 agreed to participate in the imaging and biosample protocol. Of these, 334 completed imaging, 341 provided a biosample, 338 completed respiratory sinus arrhythmia, and 316 completed all 3. Following quality control, data usability was high (MRI: T1-weighted 99%, diffusion-weighted imaging 99%, arterial spin labeling 90%, resting-state functional MRI 95%, task functional MRI 90%; electroencephalography: 83%; respiratory sinus arrhythmia: 99%). CONCLUSIONS The high consent rates, good completion rates, and high data usability reported here demonstrate the feasibility of collecting and using brain imaging and biosamples in a large clinical cohort of youths seeking mental health care.
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Affiliation(s)
- Erin W Dickie
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie H Ameis
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Isabelle Boileau
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andreea O Diaconescu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Felsky
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin I Goldstein
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Gonçalves
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John D Griffiths
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John D Haltigan
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad O Husain
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dafna S Rubin-Kahana
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Myera Iftikhar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Melanie Jani
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom; National Taiwan University Hospital and College of Medicine, Taiwan
| | - Hsiang-Yuan Lin
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Bradley J MacIntosh
- Sunnybrook Research Institute, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Oslo University Hospital, Oslo, Norway
| | - Anne L Wheeler
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Hospital for Sick Children, Neurosciences and Mental Health, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Neil Vasdev
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erica Vieira
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ghazaleh Ahmadzadeh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Lindsay Heyland
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Acadia University, Wolfville, Nova Scotia, Canada
| | - Akshay Mohan
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Feyi Ogunsanya
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychology, Western University, London, Ontario, Canada
| | - Lindsay D Oliver
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Cherrie Zhu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Sinai Health, Toronto, Ontario, Canada
| | - Jimmy K Y Wong
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Colleen Charlton
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Jennifer Truong
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Lujia Yu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Rachel Kelly
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Kristin Cleverley
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Darren B Courtney
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - George Foussias
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lisa D Hawke
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sean Hill
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Nicole Kozloff
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alexia Polillo
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Martin Rotenberg
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lena C Quilty
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Wanda Tempelaar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Wei Wang
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Yuliya S Nikolova
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aristotle N Voineskos
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Liao X, Chen M, Li Y. The glial perspective of autism spectrum disorder convergent evidence from postmortem brain and PET studies. Front Neuroendocrinol 2023; 70:101064. [PMID: 36889545 DOI: 10.1016/j.yfrne.2023.101064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/12/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Abstract
OBJECTIVE The present study aimed to systematically and quantitatively review evidence derived from both postmortem brain and PET studies to explore the pathological role of glia induced neuroinflammation in the pathogenesis of ASD, and discuss the implications of these findings in relation to disease pathogenesis and therapeutic strategies. METHOD An online databases search was performed to collate postmortem studies and PET studies regarding glia induced neuroinflammation in ASD as compared to controls. Two authors independently conducted the literature search, study selection and data extraction. The discrepancies generated in these processes was resolved through robust discussions among all authors. RESULT The literature search yielded the identification of 619 records, from which 22 postmortem studies and 3 PET studies were identified as eligible for the qualitative synthesis. Meta-analysis of postmortem studies reported increased microglial number and microglia density as well as increased GFAP protein expression and GFAP mRNA expression in ASD subjects as compared to controls. Three PET studies produced different outcomes and emphasized different details, with one reported increased and two reported decreased TSPO expression in ASD subjects as compared to controls. CONCLUSION Both postmortem evidences and PET studies converged to support the involvement of glia induced neuroinflammation in the pathogenesis of ASD. The limited number of included studies along with the considerable heterogeneity of these studies prevented the development of firm conclusions and challenged the explanation of variability. Future research should prioritize the replication of current studies and the validation of current observations.
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Affiliation(s)
- Xiaoli Liao
- Xiangya Nursing School, Central South University, Changsha, Hunan, China; Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Miao Chen
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yamin Li
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Hall MB, Willis DE, Rodriguez EL, Schwarz JM. Maternal immune activation as an epidemiological risk factor for neurodevelopmental disorders: Considerations of timing, severity, individual differences, and sex in human and rodent studies. Front Neurosci 2023; 17:1135559. [PMID: 37123361 PMCID: PMC10133487 DOI: 10.3389/fnins.2023.1135559] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
Epidemiological evidence suggests that one's risk of being diagnosed with a neurodevelopmental disorder (NDD)-such as autism, ADHD, or schizophrenia-increases significantly if their mother had a viral or bacterial infection during the first or second trimester of pregnancy. Despite this well-known data, little is known about how developing neural systems are perturbed by events such as early-life immune activation. One theory is that the maternal immune response disrupts neural processes important for typical fetal and postnatal development, which can subsequently result in specific and overlapping behavioral phenotypes in offspring, characteristic of NDDs. As such, rodent models of maternal immune activation (MIA) have been useful in elucidating neural mechanisms that may become dysregulated by MIA. This review will start with an up-to-date and in-depth, critical summary of epidemiological data in humans, examining the association between different types of MIA and NDD outcomes in offspring. Thereafter, we will summarize common rodent models of MIA and discuss their relevance to the human epidemiological data. Finally, we will highlight other factors that may interact with or impact MIA and its associated risk for NDDs, and emphasize the importance for researchers to consider these when designing future human and rodent studies. These points to consider include: the sex of the offspring, the developmental timing of the immune challenge, and other factors that may contribute to individual variability in neural and behavioral responses to MIA, such as genetics, parental age, the gut microbiome, prenatal stress, and placental buffering.
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5
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Ismail E, Gad W, Hashem M. HEC-ASD: a hybrid ensemble-based classification model for predicting autism spectrum disorder disease genes. BMC Bioinformatics 2022; 23:554. [PMID: 36544099 PMCID: PMC9768984 DOI: 10.1186/s12859-022-05099-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Autism spectrum disorder (ASD) is the most prevalent disease today. The causes of its infection may be attributed to genetic causes by 80% and environmental causes by 20%. In spite of this, the majority of the current research is concerned with environmental causes, and the least proportion with the genetic causes of the disease. Autism is a complex disease, which makes it difficult to identify the genes that cause the disease. METHODS Hybrid ensemble-based classification (HEC-ASD) model for predicting ASD genes using gradient boosting machines is proposed. The proposed model utilizes gene ontology (GO) to construct a gene functional similarity matrix using hybrid gene similarity (HGS) method. HGS measures the semantic similarity between genes effectively. It combines the graph-based method, such as Wang method with the number of directed children's nodes of gene term from GO. Moreover, an ensemble gradient boosting classifier is adapted to enhance the prediction of genes forming a robust classification model. RESULTS The proposed model is evaluated using the Simons Foundation Autism Research Initiative (SFARI) gene database. The experimental results are promising as they improve the classification performance for predicting ASD genes. The results are compared with other approaches that used gene regulatory network (GRN), protein to protein interaction network (PPI), or GO. The HEC-ASD model reaches the highest prediction accuracy of 0.88% using ensemble learning classifiers. CONCLUSION The proposed model demonstrates that ensemble learning technique using gradient boosting is effective in predicting autism spectrum disorder genes. Moreover, the HEC-ASD model utilized GO rather than using PPI network and GRN.
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Affiliation(s)
- Eman Ismail
- grid.7269.a0000 0004 0621 1570Information Systems Department, Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt
| | - Walaa Gad
- grid.7269.a0000 0004 0621 1570Information Systems Department, Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt
| | - Mohamed Hashem
- grid.7269.a0000 0004 0621 1570Information Systems Department, Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt
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6
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The role of maternal immune activation in the immunological and neurological pathogenesis of autism. JOURNAL OF NEURORESTORATOLOGY 2022. [DOI: 10.1016/j.jnrt.2022.100030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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7
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Anne A, Saxena S, Mohan KN. Genome-wide methylation analysis of post-mortem cerebellum samples supports the role of peroxisomes in autism spectrum disorder. Epigenomics 2022; 14:1015-1027. [PMID: 36154275 DOI: 10.2217/epi-2022-0184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We tested the hypothesis that a subset of patients with autism spectrum disorder (ASD) contains candidate genes with high DNA methylation differences (effective values) that potentially affect one of the two alleles. Materials & methods: Genome-wide DNA methylation comparisons were made on cerebellum samples from 30 patients and 45 controls. Results: 12 genes with high effective values, including GSDMD, MMACHC, SLC6A5 and NKX6-2, implicated in ASD and other neuropsychiatric disorders were identified. Monoallelic promoter methylation and downregulation were observed for SERHL (serine hydrolase-like) and CAT (catalase) genes associated with peroxisome function. Conclusion: These data are consistent with the hypothesis implicating impaired peroxisome function/biogenesis for ASD. A similar approach holds promise for identifying rare epimutations in ASD and other complex disorders.
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Affiliation(s)
- Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Sonal Saxena
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
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8
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Hyperbaric Oxygen Therapy Alleviates Social Behavior Dysfunction and Neuroinflammation in a Mouse Model for Autism Spectrum Disorders. Int J Mol Sci 2022; 23:ijms231911077. [PMID: 36232395 PMCID: PMC9570008 DOI: 10.3390/ijms231911077] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder (NDD) characterized by impaired social communication and repetitive behavior, among other symptoms. ASD is highly heritable, with SHANK3 being one of the high-risk genes for ASD. In recent years, knowledge has been growing regarding the neuroplasticity effect induced by hyperbaric oxygen therapy (HBOT) and its potential use for ASD. Here, we characterized the effect of HBOT on a mouse model for ASD with the human genetic condition of InsG3680 mutation in the Shank3 gene. As compared to placebo, HBOT improved social behavior and reduced neuroinflammation in the cortex of the InsG3680(+/+) mice. Specifically, HBOT induced upregulation of Insulin-like growth factor 1 (Igf1) expression levels and reduced the number of Iba1-positive cells in the mouse model for ASD compared to placebo control. Together, our research suggests that HBOT has the potential to improve the clinical outcome of ASD by ameliorating some of the core pathophysiological processes responsible for the development of the disorder.
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Purushotham SS, Reddy NMN, D'Souza MN, Choudhury NR, Ganguly A, Gopalakrishna N, Muddashetty R, Clement JP. A perspective on molecular signalling dysfunction, its clinical relevance and therapeutics in autism spectrum disorder. Exp Brain Res 2022; 240:2525-2567. [PMID: 36063192 DOI: 10.1007/s00221-022-06448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are neurodevelopmental disorders that have become a primary clinical and social concern, with a prevalence of 2-3% in the population. Neuronal function and behaviour undergo significant malleability during the critical period of development that is found to be impaired in ID/ASD. Human genome sequencing studies have revealed many genetic variations associated with ASD/ID that are further verified by many approaches, including many mouse and other models. These models have facilitated the identification of fundamental mechanisms underlying the pathogenesis of ASD/ID, and several studies have proposed converging molecular pathways in ASD/ID. However, linking the mechanisms of the pathogenic genes and their molecular characteristics that lead to ID/ASD has progressed slowly, hampering the development of potential therapeutic strategies. This review discusses the possibility of recognising the common molecular causes for most ASD/ID based on studies from the available models that may enable a better therapeutic strategy to treat ID/ASD. We also reviewed the potential biomarkers to detect ASD/ID at early stages that may aid in diagnosis and initiating medical treatment, the concerns with drug failure in clinical trials, and developing therapeutic strategies that can be applied beyond a particular mutation associated with ASD/ID.
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Affiliation(s)
- Sushmitha S Purushotham
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Neeharika M N Reddy
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Michelle Ninochka D'Souza
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - Nilpawan Roy Choudhury
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Anusa Ganguly
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Niharika Gopalakrishna
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Ravi Muddashetty
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - James P Clement
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India.
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10
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Papale LA, Madrid A, Zhang Q, Chen K, Sak L, Keleş S, Alisch RS. Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders. Genome Res 2022; 32:266-279. [PMID: 34949667 PMCID: PMC8805724 DOI: 10.1101/gr.276137.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/22/2021] [Indexed: 11/25/2022]
Abstract
Mouse knockouts of Cntnap2 show altered neurodevelopmental behavior, deficits in striatal GABAergic signaling, and a genome-wide disruption of an environmentally sensitive DNA methylation modification (5-hydroxymethylcytosine [5hmC]) in the orthologs of a significant number of genes implicated in human neurodevelopmental disorders. We tested adult Cntnap2 heterozygous mice (Cntnap2 +/-; lacking behavioral or neuropathological abnormalities) subjected to a prenatal stress and found that prenatally stressed Cntnap2 +/- female mice show repetitive behaviors and altered sociability, similar to the homozygote phenotype. Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that are correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull-down data indicated that 5hmC abundance alters the binding of the transcription factor CLOCK near the promoters of these genes (e.g., Palld, Gigyf1, and Fry), providing a mechanistic role for 5hmC in gene regulation. Together, these data support gene-by-environment hypotheses for the origins of mental illness and provide a means to identify the elusive factors contributing to complex human diseases.
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Affiliation(s)
- Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Qi Zhang
- Department Mathematics and Statistics, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Kailei Chen
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Lara Sak
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Sündüz Keleş
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
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11
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Nassir N, Bankapur A, Samara B, Ali A, Ahmed A, Inuwa IM, Zarrei M, Safizadeh Shabestari SA, AlBanna A, Howe JL, Berdiev BK, Scherer SW, Woodbury-Smith M, Uddin M. Single-cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss-of-function variants regulating glial cells. Hum Genomics 2021; 15:68. [PMID: 34802461 PMCID: PMC8607722 DOI: 10.1186/s40246-021-00368-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from the point of view of 'brain to behaviour' pathogenic mechanisms, remains largely unknown. METHODS We undertook a study to investigate patterns of spatiotemporal and cell type expression of ASD-implicated genes by integrating large-scale brain single-cell transcriptomes (> million cells) and de novo loss-of-function (LOF) ASD variants (impacting 852 genes from 40,122 cases). RESULTS We identified multiple single-cell clusters from three distinct developmental human brain regions (anterior cingulate cortex, middle temporal gyrus and primary visual cortex) that evidenced high evolutionary constraint through enrichment for brain critical exons and high pLI genes. These clusters also showed significant enrichment with ASD loss-of-function variant genes (p < 5.23 × 10-11) that are transcriptionally highly active in prenatal brain regions (visual cortex and dorsolateral prefrontal cortex). Mapping ASD de novo LOF variant genes into large-scale human and mouse brain single-cell transcriptome analysis demonstrate enrichment of such genes into neuronal subtypes and are also enriched for subtype of non-neuronal glial cell types (astrocyte, p < 6.40 × 10-11, oligodendrocyte, p < 1.31 × 10-09). CONCLUSION Among the ASD genes enriched with pathogenic de novo LOF variants (i.e. KANK1, PLXNB1), a subgroup has restricted transcriptional regulation in non-neuronal cell types that are evolutionarily conserved. This association strongly suggests the involvement of subtype of non-neuronal glial cells in the pathogenesis of ASD and the need to explore other biological pathways for this disorder.
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Affiliation(s)
- Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Asma Bankapur
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Bisan Samara
- Biomedical Engineering Department, McGill University, Montréal, QC, Canada
| | - Abdulrahman Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Awab Ahmed
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Ibrahim M Inuwa
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Mehdi Zarrei
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Ammar AlBanna
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.,The Mental Health Center of Excellence, Al Jalila Children's Speciality Hospital, Dubai, UAE
| | - Jennifer L Howe
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bakhrom K Berdiev
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Stephen W Scherer
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada.,Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE. .,Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada.
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12
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Carulli D, de Winter F, Verhaagen J. Semaphorins in Adult Nervous System Plasticity and Disease. Front Synaptic Neurosci 2021; 13:672891. [PMID: 34045951 PMCID: PMC8148045 DOI: 10.3389/fnsyn.2021.672891] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
Semaphorins, originally discovered as guidance cues for developing axons, are involved in many processes that shape the nervous system during development, from neuronal proliferation and migration to neuritogenesis and synapse formation. Interestingly, the expression of many Semaphorins persists after development. For instance, Semaphorin 3A is a component of perineuronal nets, the extracellular matrix structures enwrapping certain types of neurons in the adult CNS, which contribute to the closure of the critical period for plasticity. Semaphorin 3G and 4C play a crucial role in the control of adult hippocampal connectivity and memory processes, and Semaphorin 5A and 7A regulate adult neurogenesis. This evidence points to a role of Semaphorins in the regulation of adult neuronal plasticity. In this review, we address the distribution of Semaphorins in the adult nervous system and we discuss their function in physiological and pathological processes.
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Affiliation(s)
- Daniela Carulli
- Laboratory for Neuroregeneration, Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, Amsterdam, Netherlands
- Department of Neuroscience Rita Levi-Montalcini and Neuroscience Institute Cavalieri Ottolenghi, University of Turin, Turin, Italy
| | - Fred de Winter
- Laboratory for Neuroregeneration, Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, Amsterdam, Netherlands
| | - Joost Verhaagen
- Laboratory for Neuroregeneration, Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, Amsterdam, Netherlands
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13
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Griesi-Oliveira K, Fogo MS, Pinto BGG, Alves AY, Suzuki AM, Morales AG, Ezquina S, Sosa OJ, Sutton GJ, Sunaga-Franze DY, Bueno AP, Seabra G, Sardinha L, Costa SS, Rosenberg C, Zachi EC, Sertie AL, Martins-de-Souza D, Reis EM, Voineagu I, Passos-Bueno MR. Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder. Mol Psychiatry 2021; 26:1589-1605. [PMID: 32060413 PMCID: PMC8159745 DOI: 10.1038/s41380-020-0669-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/11/2019] [Accepted: 01/28/2020] [Indexed: 01/02/2023]
Abstract
Evaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question, but larger cohorts and different ASD endophenotypes still need to be investigated. Moreover, whether changes seen in this in vitro model reflect previous findings in ASD postmortem brains and how consistent they are across the studies remain underexplored questions. We examined the transcriptome of iPSC-derived neuronal cells from a normocephalic ASD cohort composed mostly of high-functioning individuals and from non-ASD individuals. ASD patients presented expression dysregulation of a module of co-expressed genes involved in protein synthesis in neuronal progenitor cells (NPC), and a module of genes related to synapse/neurotransmission and a module related to translation in neurons. Proteomic analysis in NPC revealed potential molecular links between the modules dysregulated in NPC and in neurons. Remarkably, the comparison of our results to a series of transcriptome studies revealed that the module related to synapse has been consistently found as upregulated in iPSC-derived neurons-which has an expression profile more closely related to fetal brain-while downregulated in postmortem brain tissue, indicating a reliable association of this network to the disease and suggesting that its dysregulation might occur in different directions across development in ASD individuals. Therefore, the expression pattern of this network might be used as biomarker for ASD and should be experimentally explored as a therapeutic target.
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Affiliation(s)
- K Griesi-Oliveira
- Hospital Israelita Albert Einstein, São Paulo, Brazil.
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - M S Fogo
- Hospital Israelita Albert Einstein, São Paulo, Brazil
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - B G G Pinto
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - A Y Alves
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - A M Suzuki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - A G Morales
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - S Ezquina
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - O J Sosa
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - G J Sutton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - D Y Sunaga-Franze
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - A P Bueno
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - G Seabra
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - L Sardinha
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - S S Costa
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - C Rosenberg
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - E C Zachi
- Núcleo de Neurociências e Comportamento, Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil
| | - A L Sertie
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - D Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), São Paulo, Brazil
- Experimental Medicine Research Cluster (EMC), University of Campinas, Campinas, Brazil
| | - E M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - I Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - M R Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
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14
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Prem S, Millonig JH, DiCicco-Bloom E. Dysregulation of Neurite Outgrowth and Cell Migration in Autism and Other Neurodevelopmental Disorders. ADVANCES IN NEUROBIOLOGY 2020; 25:109-153. [PMID: 32578146 DOI: 10.1007/978-3-030-45493-7_5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite decades of study, elucidation of the underlying etiology of complex developmental disorders such as autism spectrum disorder (ASD), schizophrenia (SCZ), intellectual disability (ID), and bipolar disorder (BPD) has been hampered by the inability to study human neurons, the heterogeneity of these disorders, and the relevance of animal model systems. Moreover, a majority of these developmental disorders have multifactorial or idiopathic (unknown) causes making them difficult to model using traditional methods of genetic alteration. Examination of the brains of individuals with ASD and other developmental disorders in both post-mortem and MRI studies shows defects that are suggestive of dysregulation of embryonic and early postnatal development. For ASD, more recent genetic studies have also suggested that risk genes largely converge upon the developing human cerebral cortex between weeks 8 and 24 in utero. Yet, an overwhelming majority of studies in autism rodent models have focused on postnatal development or adult synaptic transmission defects in autism related circuits. Thus, studies looking at early developmental processes such as proliferation, cell migration, and early differentiation, which are essential to build the brain, are largely lacking. Yet, interestingly, a few studies that did assess early neurodevelopment found that alterations in brain structure and function associated with neurodevelopmental disorders (NDDs) begin as early as the initial formation and patterning of the neural tube. By the early to mid-2000s, the derivation of human embryonic stem cells (hESCs) and later induced pluripotent stem cells (iPSCs) allowed us to study living human neural cells in culture for the first time. Specifically, iPSCs gave us the unprecedented ability to study cells derived from individuals with idiopathic disorders. Studies indicate that iPSC-derived neural cells, whether precursors or "matured" neurons, largely resemble cortical cells of embryonic humans from weeks 8 to 24. Thus, these cells are an excellent model to study early human neurodevelopment, particularly in the context of genetically complex diseases. Indeed, since 2011, numerous studies have assessed developmental phenotypes in neurons derived from individuals with both genetic and idiopathic forms of ASD and other NDDs. However, while iPSC-derived neurons are fetal in nature, they are post-mitotic and thus cannot be used to study developmental processes that occur before terminal differentiation. Moreover, it is important to note that during the 8-24-week window of human neurodevelopment, neural precursor cells are actively undergoing proliferation, migration, and early differentiation to form the basic cytoarchitecture of the brain. Thus, by studying NPCs specifically, we could gain insight into how early neurodevelopmental processes contribute to the pathogenesis of NDDs. Indeed, a few studies have explored NPC phenotypes in NDDs and have uncovered dysregulations in cell proliferation. Yet, few studies have explored migration and early differentiation phenotypes of NPCs in NDDs. In this chapter, we will discuss cell migration and neurite outgrowth and the role of these processes in neurodevelopment and NDDs. We will begin by reviewing the processes that are important in early neurodevelopment and early cortical development. We will then delve into the roles of neurite outgrowth and cell migration in the formation of the brain and how errors in these processes affect brain development. We also provide review of a few key molecules that are involved in the regulation of neurite outgrowth and migration while discussing how dysregulations in these molecules can lead to abnormalities in brain structure and function thereby highlighting their contribution to pathogenesis of NDDs. Then we will discuss whether neurite outgrowth, migration, and the molecules that regulate these processes are associated with ASD. Lastly, we will review the utility of iPSCs in modeling NDDs and discuss future goals for the study of NDDs using this technology.
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Affiliation(s)
- Smrithi Prem
- Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - James H Millonig
- Department of Neuroscience and Cell Biology, Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Emanuel DiCicco-Bloom
- Department of Neuroscience and Cell Biology/Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.
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15
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Analyzing the Potential Biological Determinants of Autism Spectrum Disorder: From Neuroinflammation to the Kynurenine Pathway. Brain Sci 2020; 10:brainsci10090631. [PMID: 32932826 PMCID: PMC7563403 DOI: 10.3390/brainsci10090631] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022] Open
Abstract
Autism Spectrum Disorder (ASD) etiopathogenesis is still unclear and no effective preventive and treatment measures have been identified. Research has focused on the potential role of neuroinflammation and the Kynurenine pathway; here we review the nature of these interactions. Pre-natal or neonatal infections would induce microglial activation, with secondary consequences on behavior, cognition and neurotransmitter networks. Peripherally, higher levels of pro-inflammatory cytokines and anti-brain antibodies have been identified. Increased frequency of autoimmune diseases, allergies, and recurring infections have been demonstrated both in autistic patients and in their relatives. Genetic studies have also identified some important polymorphisms in chromosome loci related to the human leukocyte antigen (HLA) system. The persistence of immune-inflammatory deregulation would lead to mitochondrial dysfunction and oxidative stress, creating a self-sustaining cytotoxic loop. Chronic inflammation activates the Kynurenine pathway with an increase in neurotoxic metabolites and excitotoxicity, causing long-term changes in the glutamatergic system, trophic support and synaptic function. Furthermore, overactivation of the Kynurenine branch induces depletion of melatonin and serotonin, worsening ASD symptoms. Thus, in genetically predisposed subjects, aberrant neurodevelopment may derive from a complex interplay between inflammatory processes, mitochondrial dysfunction, oxidative stress and Kynurenine pathway overexpression. To validate this hypothesis a new translational research approach is necessary.
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16
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Ragusa M, Santagati M, Mirabella F, Lauretta G, Cirnigliaro M, Brex D, Barbagallo C, Domini CN, Gulisano M, Barone R, Trovato L, Oliveri S, Mongelli G, Spitale A, Barbagallo D, Di Pietro C, Stefani S, Rizzo R, Purrello M. Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children. Int J Mol Sci 2020; 21:ijms21176203. [PMID: 32867322 PMCID: PMC7504581 DOI: 10.3390/ijms21176203] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/16/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Recent evidence has demonstrated that salivary molecules, as well as bacterial populations, can be perturbed by several pathological conditions, including neuro-psychiatric diseases. This relationship between brain functionality and saliva composition could be exploited to unveil new pathological mechanisms of elusive diseases, such as Autistic Spectrum Disorder (ASD). We performed a combined approach of miRNA expression profiling by NanoString technology, followed by validation experiments in qPCR, and 16S rRNA microbiome analysis on saliva from 53 ASD and 27 neurologically unaffected control (NUC) children. MiR-29a-3p and miR-141-3p were upregulated, while miR-16-5p, let-7b-5p, and miR-451a were downregulated in ASD compared to NUCs. Microbiome analysis on the same subjects revealed that Rothia, Filifactor, Actinobacillus, Weeksellaceae, Ralstonia, Pasteurellaceae, and Aggregatibacter increased their abundance in ASD patients, while Tannerella, Moryella and TM7-3 decreased. Variations of both miRNAs and microbes were statistically associated to different neuropsychological scores related to anomalies in social interaction and communication. Among miRNA/bacteria associations, the most relevant was the negative correlation between salivary miR-141-3p expression and Tannerella abundance. MiRNA and microbiome dysregulations found in the saliva of ASD children are potentially associated with cognitive impairments of the subjects. Furthermore, a potential cross-talking between circulating miRNAs and resident bacteria could occur in saliva of ASD.
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Affiliation(s)
- Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
- Oasi Research Institute—IRCCS, 94018 Troina, Italy
| | - Maria Santagati
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Federica Mirabella
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Giovanni Lauretta
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Matilde Cirnigliaro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Duilia Brex
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Carla Noemi Domini
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Mariangela Gulisano
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Rita Barone
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Laura Trovato
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Salvatore Oliveri
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Gino Mongelli
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
- Bio-nanotech Research and Innovation Tower (BRIT), University of Catania, 95123 Catania, Italy
| | - Ambra Spitale
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Renata Rizzo
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
- Correspondence:
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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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FunVar: A systematic pipeline to unravel the convergence patterns of genetic variants in ASD, a paradigmatic complex disease. J Biomed Inform 2019; 98:103273. [PMID: 31454647 DOI: 10.1016/j.jbi.2019.103273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 07/28/2019] [Accepted: 08/24/2019] [Indexed: 11/22/2022]
Abstract
In recent years, the technological advances for capturing genetic variation in large populations led to the identification of large numbers of putative or disease-causing variants. However, their mechanistic understanding is lagging far behind and has posed new challenges regarding their relevance for disease phenotypes, particularly for common complex disorders. In this study, we propose a systematic pipeline to infer biological meaning from genetic variants, namely rare Copy Number Variants (CNVs). The pipeline consists of three modules that seek to (1) improve genetic data quality by excluding low confidence CNVs, (2) identify disrupted biological processes, and (3) aggregate similar enriched biological processes terms using semantic similarity. The proposed pipeline was applied to CNVs from individuals diagnosed with Autism Spectrum Disorder (ASD). We found that rare CNVs disrupting brain expressed genes dysregulated a wide range of biological processes, such as nervous system development and protein polyubiquitination. The disrupted biological processes identified in ASD patients were in accordance with previous findings. This coherence with literature indicates the feasibility of the proposed pipeline in interpreting the biological role of genetic variants in complex disease development. The suggested pipeline is easily adjustable at each step and its independence from any specific dataset and software makes it an effective tool in analyzing existing genetic resources. The FunVar pipeline is available at https://github.com/lasigeBioTM/FunVar and includes pre and post processing steps to effectively interpret biological mechanisms of putative disease causing genetic variants.
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19
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Mazón-Cabrera R, Vandormael P, Somers V. Antigenic Targets of Patient and Maternal Autoantibodies in Autism Spectrum Disorder. Front Immunol 2019; 10:1474. [PMID: 31379804 PMCID: PMC6659315 DOI: 10.3389/fimmu.2019.01474] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/13/2019] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder whose behavioral symptoms become apparent in early childhood. The underlying pathophysiological mechanisms are only partially understood and the clinical manifestations are heterogeneous in nature, which poses a major challenge for diagnosis, prognosis and intervention. In the last years, an important role of a dysregulated immune system in ASD has emerged, but the mechanisms connecting this to a disruption of brain development are still largely unknown. Although ASD is not considered as a typical autoimmune disease, self-reactive antibodies or autoantibodies against a wide variety of targets have been found in a subset of ASD patients. In addition, autoantibodies reactive to fetal brain proteins have also been described in the prenatal stage of neurodevelopment, where they can be transferred from the mother to the fetus by transplacental transport. In this review, we give an extensive overview of the antibodies described in ASD according to their target antigens, their different origins, and timing of exposure during neurodevelopment.
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Affiliation(s)
| | | | - Veerle Somers
- Biomedical Research Institute, Faculty of Medicine and Life Science, Hasselt University, Diepenbeek, Belgium
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20
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Siu MT, Butcher DT, Turinsky AL, Cytrynbaum C, Stavropoulos DJ, Walker S, Caluseriu O, Carter M, Lou Y, Nicolson R, Georgiades S, Szatmari P, Anagnostou E, Scherer SW, Choufani S, Brudno M, Weksberg R. Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants. Clin Epigenetics 2019; 11:103. [PMID: 31311581 PMCID: PMC6636171 DOI: 10.1186/s13148-019-0684-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 05/15/2019] [Indexed: 12/19/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a common and etiologically heterogeneous neurodevelopmental disorder. Although many genetic causes have been identified (> 200 ASD-risk genes), no single gene variant accounts for > 1% of all ASD cases. A role for epigenetic mechanisms in ASD etiology is supported by the fact that many ASD-risk genes function as epigenetic regulators and evidence that epigenetic dysregulation can interrupt normal brain development. Gene-specific DNAm profiles have been shown to assist in the interpretation of variants of unknown significance. Therefore, we investigated the epigenome in patients with ASD or two of the most common genomic variants conferring increased risk for ASD. Genome-wide DNA methylation (DNAm) was assessed using the Illumina Infinium HumanMethylation450 and MethylationEPIC arrays in blood from individuals with ASD of heterogeneous, undefined etiology (n = 52), and individuals with 16p11.2 deletions (16p11.2del, n = 9) or pathogenic variants in the chromatin modifier CHD8 (CHD8+/−, n = 7). Results DNAm patterns did not clearly distinguish heterogeneous ASD cases from controls. However, the homogeneous genetically-defined 16p11.2del and CHD8+/− subgroups each exhibited unique DNAm signatures that distinguished 16p11.2del or CHD8+/− individuals from each other and from heterogeneous ASD and control groups with high sensitivity and specificity. These signatures also classified additional 16p11.2del (n = 9) and CHD8 (n = 13) variants as pathogenic or benign. Our findings that DNAm alterations in each signature target unique genes in relevant biological pathways including neural development support their functional relevance. Furthermore, genes identified in our CHD8+/− DNAm signature in blood overlapped differentially expressed genes in CHD8+/− human-induced pluripotent cell-derived neurons and cerebral organoids from independent studies. Conclusions DNAm signatures can provide clinical utility complementary to next-generation sequencing in the interpretation of variants of unknown significance. Our study constitutes a novel approach for ASD risk-associated molecular classification that elucidates the vital cross-talk between genetics and epigenetics in the etiology of ASD. Electronic supplementary material The online version of this article (10.1186/s13148-019-0684-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - D T Butcher
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - A L Turinsky
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C Cytrynbaum
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, Ontario, M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - D J Stavropoulos
- Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - S Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - O Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - M Carter
- Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Y Lou
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - R Nicolson
- Department of Psychiatry, University of Western Ontario, London, Ontario, Canada
| | - S Georgiades
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, Ontario, Canada
| | - P Szatmari
- Child and Youth Mental Health Collaborative, Centre for Addiction and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - E Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - S W Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - M Brudno
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - R Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, Ontario, M5G 1X8, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. .,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, Ontario, Canada.
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21
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Prata J, Machado AS, von Doellinger O, Almeida MI, Barbosa MA, Coelho R, Santos SG. The Contribution of Inflammation to Autism Spectrum Disorders: Recent Clinical Evidence. Methods Mol Biol 2019; 2011:493-510. [PMID: 31273718 DOI: 10.1007/978-1-4939-9554-7_29] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Autism comprises a complex and heterogeneous spectrum of neurodevelopmental disorders, usually termed autism spectrum disorders (ASD). It is more prevalent in males than females, and genetic and environmental factors are believed to account in similar percentages to the development of ASD. In recent years, the contribution of inflammation and inflammatory mediators to disease aetiology and perpetuation has been the object of intense research. In this chapter, inflammatory aspects that contribute to ASD are discussed, including abnormal microglia activation and polarization phenotypes, increased systemic levels of pro-inflammatory mediators, and altered patterns of immune cell response to activation stimuli. Also, inflammation in the context of gut microbiome and the impact of inflammation on gender prevalence of ASD are considered. Finally, treatment impact on inflammatory parameters and the potential for use of anti-inflammatory drugs, alone or in combination with antipsychotics, to manage ASD are examined.
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Affiliation(s)
- J Prata
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
- Department of Psychiatry and Mental Health, Centro Hospitalar Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
| | - A S Machado
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
- Department of Clinical Neurosciences and Mental Health, Centro Hospitalar UniversitÃrio São João, Porto, Portugal
| | - O von Doellinger
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
- Department of Psychiatry and Mental Health, Centro Hospitalar do Tâmega e Sousa, Penafiel, Portugal
| | - M I Almeida
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- INEB-Instituto de Engenharia Biomédica, University of Porto, Porto, Portugal
| | - M A Barbosa
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- INEB-Instituto de Engenharia Biomédica, University of Porto, Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - R Coelho
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
- Department of Clinical Neurosciences and Mental Health, Centro Hospitalar UniversitÃrio São João, Porto, Portugal
| | - S G Santos
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
- INEB-Instituto de Engenharia Biomédica, University of Porto, Porto, Portugal.
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal.
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22
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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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23
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Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology. PLoS One 2018; 13:e0208626. [PMID: 30532199 PMCID: PMC6287949 DOI: 10.1371/journal.pone.0208626] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
Identifying disease genes from a vast amount of genetic data is one of the most challenging tasks in the post-genomic era. Also, complex diseases present highly heterogeneous genotype, which difficult biological marker identification. Machine learning methods are widely used to identify these markers, but their performance is highly dependent upon the size and quality of available data. In this study, we demonstrated that machine learning classifiers trained on gene functional similarities, using Gene Ontology (GO), can improve the identification of genes involved in complex diseases. For this purpose, we developed a supervised machine learning methodology to predict complex disease genes. The proposed pipeline was assessed using Autism Spectrum Disorder (ASD) candidate genes. A quantitative measure of gene functional similarities was obtained by employing different semantic similarity measures. To infer the hidden functional similarities between ASD genes, various types of machine learning classifiers were built on quantitative semantic similarity matrices of ASD and non-ASD genes. The classifiers trained and tested on ASD and non-ASD gene functional similarities outperformed previously reported ASD classifiers. For example, a Random Forest (RF) classifier achieved an AUC of 0. 80 for predicting new ASD genes, which was higher than the reported classifier (0.73). Additionally, this classifier was able to predict 73 novel ASD candidate genes that were enriched for core ASD phenotypes, such as autism and obsessive-compulsive behavior. In addition, predicted genes were also enriched for ASD co-occurring conditions, including Attention Deficit Hyperactivity Disorder (ADHD). We also developed a KNIME workflow with the proposed methodology which allows users to configure and execute it without requiring machine learning and programming skills. Machine learning is an effective and reliable technique to decipher ASD mechanism by identifying novel disease genes, but this study further demonstrated that their performance can be improved by incorporating a quantitative measure of gene functional similarities. Source code and the workflow of the proposed methodology are available at https://github.com/Muh-Asif/ASD-genes-prediction.
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24
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Kalkman HO, Feuerbach D. Microglia M2A Polarization as Potential Link between Food Allergy and Autism Spectrum Disorders. Pharmaceuticals (Basel) 2017; 10:ph10040095. [PMID: 29232822 PMCID: PMC5748650 DOI: 10.3390/ph10040095] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
Atopic diseases are frequently co-morbid with autism spectrum disorders (ASD). Allergic responses are associated with an activation of mast cells, innate lymphoid cells, and Th2 cells. These cells produce type-2 cytokines (IL4 and IL13), which stimulate microglia and macrophages to adopt a phenotype referred to as ‘alternative activation’ or ‘M2A’. M2A-polarized macrophages and microglia play a physiological role in tissue repair by secreting growth factors such as brain-derived neurotrophic factor (BDNF) and insulin-like growth factor-1. In ASD there is evidence for increased type-2 cytokines, microglia activation, M2A polarization, and increased levels of growth factors. In neurons, these growth factors drive a signal transduction pathway that leads to activation of the enzyme mammalian Target of Rapamycin (mTOR), and thereby to the inhibition of autophagy. Activation of mTOR is an effect that is also common to several of the genetic forms of autism. In the central nervous system, redundant synapses are removed via an autophagic process. Activation of mTOR would diminish the pruning of redundant synapses, which in the context of ASD is likely to be undesired. Based on this line of reasoning, atopic diseases like food allergy, eczema or asthma would represent risk factors for autism spectrum disorders.
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25
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Morris G, Puri BK, Frye RE. The putative role of environmental aluminium in the development of chronic neuropathology in adults and children. How strong is the evidence and what could be the mechanisms involved? Metab Brain Dis 2017; 32:1335-1355. [PMID: 28752219 PMCID: PMC5596046 DOI: 10.1007/s11011-017-0077-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/19/2017] [Indexed: 02/06/2023]
Abstract
The conceptualisation of autistic spectrum disorder and Alzheimer's disease has undergone something of a paradigm shift in recent years and rather than being viewed as single illnesses with a unitary pathogenesis and pathophysiology they are increasingly considered to be heterogeneous syndromes with a complex multifactorial aetiopathogenesis, involving a highly complex and diverse combination of genetic, epigenetic and environmental factors. One such environmental factor implicated as a potential cause in both syndromes is aluminium, as an element or as part of a salt, received, for example, in oral form or as an adjuvant. Such administration has the potential to induce pathology via several routes such as provoking dysfunction and/or activation of glial cells which play an indispensable role in the regulation of central nervous system homeostasis and neurodevelopment. Other routes include the generation of oxidative stress, depletion of reduced glutathione, direct and indirect reductions in mitochondrial performance and integrity, and increasing the production of proinflammatory cytokines in both the brain and peripherally. The mechanisms whereby environmental aluminium could contribute to the development of the highly specific pattern of neuropathology seen in Alzheimer's disease are described. Also detailed are several mechanisms whereby significant quantities of aluminium introduced via immunisation could produce chronic neuropathology in genetically susceptible children. Accordingly, it is recommended that the use of aluminium salts in immunisations should be discontinued and that adults should take steps to minimise their exposure to environmental aluminium.
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Affiliation(s)
- Gerwyn Morris
- Tir Na Nog, Bryn Road seaside 87, Llanelli, Wales, SA15 2LW, UK
| | - Basant K Puri
- Department of Medicine, Imperial College London, Hammersmith Hospital, London, England, W12 0HS, UK.
| | - Richard E Frye
- College of Medicine, Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital Research Institute, Little Rock, AR, 72202, USA
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26
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Cirnigliaro M, Barbagallo C, Gulisano M, Domini CN, Barone R, Barbagallo D, Ragusa M, Di Pietro C, Rizzo R, Purrello M. Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder. Front Mol Neurosci 2017; 10:250. [PMID: 28848387 PMCID: PMC5554380 DOI: 10.3389/fnmol.2017.00250] [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: 04/21/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022] Open
Abstract
Given its prevalence and social impact, Autism Spectrum Disorder (ASD) is drawing much interest. Molecular basis of ASD is heterogeneous and only partially known. Many factors, including disorders comorbid with ASD, like TS (Tourette Syndrome), complicate ASD behavior-based diagnosis and make it vulnerable to bias. To further investigate ASD etiology and to identify potential biomarkers to support its precise diagnosis, we used TaqMan Low Density Array technology to profile serum miRNAs from ASD, TS, and TS+ASD patients, and unaffected controls (NCs). Through validation assays in 30 ASD, 24 TS, and 25 TS+ASD patients and 25 NCs, we demonstrated that miR-140-3p is upregulated in ASD vs.: NC, TS, and TS+ASD (Tukey's test, p-values = 0.03, = 0.01, < 0.0001, respectively). ΔCt values for miR-140-3p and YGTSS (Yale Global Tic Severity Scale) scores are positively correlated (Spearman r = 0.33; Benjamini-Hochberg p = 0.008) and show a linear relationship (p = 0.002). Network functional analysis showed that nodes controlled by miR-140-3p, especially CD38 and NRIP1 which are its validated targets, are involved in processes convergingly dysregulated in ASD, such as synaptic plasticity, immune response, and chromatin binding. Biomarker analysis proved that serum miR-140-3p can discriminate among: (1) ASD and NC (Area under the ROC curve, AUC: 0.70; sensitivity: 63.33%; specificity: 68%); (2) ASD and TS (AUC: 0.72; sensitivity: 66.66%; specificity: 70.83%); (3) ASD and TS+ASD (AUC: 0.78; sensitivity: 73.33%; specificity: 76%). Characterization of miR-140-3p network would contribute to further clarify ASD etiology. Serum miR-140-3p could represent a potential non-invasive biomarker for ASD, easy to test through liquid biopsy.
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Affiliation(s)
- Matilde Cirnigliaro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Cristina Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Mariangela Gulisano
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Carla N Domini
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Rita Barone
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy.,Associazione Oasi Maria SS. Onlus (IRCCS), Institute for Research on Mental Retardation and Brain AgingTroina, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Renata Rizzo
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Michele Purrello
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
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27
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Gudenas BL, Srivastava AK, Wang L. Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism. PLoS One 2017; 12:e0178532. [PMID: 28562671 PMCID: PMC5451068 DOI: 10.1371/journal.pone.0178532] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/15/2017] [Indexed: 12/20/2022] Open
Abstract
Genetic studies have identified many risk loci for autism spectrum disorder (ASD) although causal factors in the majority of cases are still unknown. Currently, known ASD risk genes are all protein-coding genes; however, the vast majority of transcripts in humans are non-coding RNAs (ncRNAs) which do not encode proteins. Recently, long non-coding RNAs (lncRNAs) were shown to be highly expressed in the human brain and crucial for normal brain development. We have constructed a computational pipeline for the integration of various genomic datasets to identify lncRNAs associated with ASD. This pipeline utilizes differential gene expression patterns in affected tissues in conjunction with gene co-expression networks in tissue-matched non-affected samples. We analyzed RNA-seq data from the cortical brain tissues from ASD cases and controls to identify lncRNAs differentially expressed in ASD. We derived a gene co-expression network from an independent human brain developmental transcriptome and detected a convergence of the differentially expressed lncRNAs and known ASD risk genes into specific co-expression modules. Co-expression network analysis facilitates the discovery of associations between previously uncharacterized lncRNAs with known ASD risk genes, affected molecular pathways and at-risk developmental time points. In addition, we show that some of these lncRNAs have a high degree of overlap with major CNVs detected in ASD genetic studies. By utilizing this integrative approach comprised of differential expression analysis in affected tissues and connectivity metrics from a developmental co-expression network, we have prioritized a set of candidate ASD-associated lncRNAs. The identification of lncRNAs as novel ASD susceptibility genes could help explain the genetic pathogenesis of ASD.
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Affiliation(s)
- Brian L. Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Anand K. Srivastava
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina, United States of America
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
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28
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Zhao D, Mokhtari R, Pedrosa E, Birnbaum R, Zheng D, Lachman HM. Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress. Mol Autism 2017; 8:17. [PMID: 28367307 PMCID: PMC5372344 DOI: 10.1186/s13229-017-0134-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/17/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a severe, neurodevelopmental disorder primarily affecting girls, characterized by progressive loss of cognitive, social, and motor skills after a relatively brief period of typical development. It is usually due to de novo loss of function mutations in the X-linked gene, MeCP2, which codes for the gene expression and chromatin regulator, methyl-CpG binding protein 2. Although the behavioral phenotype appears to be primarily due to neuronal Mecp2 deficiency in mice, other cell types, including astrocytes and oligodendrocytes, also appear to contribute to some aspects of the RTT phenotype. In addition, microglia may also play a role. However, the effect of Mecp2 deficiency in microglia on RTT pathogenesis is controversial. METHODS In the current study, we applied whole transcriptome analysis using RNA-seq to gain insight into molecular pathways in microglia that might be dysregulated during the transition, in female mice heterozygous for an Mecp2-null allele (Mecp2+/-; Het), from the pre-phenotypic (5 weeks) to the phenotypic phases (24 weeks). RESULTS We found a significant overlap in differentially expressed genes (DEGs) with genes involved in regulating the extracellular matrix, and those that are activated or inhibited when macrophages and microglia are stimulated towards the M1 and M2 activation states. However, the M1- and M2-associated genes were different in the 5- and 24-week samples. In addition, a substantial decrease in the expression of nine members of the heat shock protein (HSP) family was found in the 5-week samples, but not at 24 weeks. CONCLUSIONS These findings suggest that microglia from pre-phenotypic and phenotypic female mice are activated in a manner different from controls and that pre-phenotypic female mice may have alterations in their capacity to response to heat stress and other stressors that function through the HSP pathway.
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Affiliation(s)
- Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Ryan Mokhtari
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Rayna Birnbaum
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
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29
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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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Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 224:159-187. [PMID: 28551756 DOI: 10.1007/978-3-319-52498-6_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology.
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The emerging roles of MicroRNAs in autism spectrum disorders. Neurosci Biobehav Rev 2016; 71:729-738. [DOI: 10.1016/j.neubiorev.2016.10.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/27/2016] [Accepted: 10/22/2016] [Indexed: 12/21/2022]
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Nazeen S, Palmer NP, Berger B, Kohane IS. Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. Genome Biol 2016; 17:228. [PMID: 27842596 PMCID: PMC5108086 DOI: 10.1186/s13059-016-1084-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a common neurodevelopmental disorder that tends to co-occur with other diseases, including asthma, inflammatory bowel disease, infections, cerebral palsy, dilated cardiomyopathy, muscular dystrophy, and schizophrenia. However, the molecular basis of this co-occurrence, and whether it is due to a shared component that influences both pathophysiology and environmental triggering of illness, has not been elucidated. To address this, we deploy a three-tiered transcriptomic meta-analysis that functions at the gene, pathway, and disease levels across ASD and its co-morbidities. RESULTS Our analysis reveals a novel shared innate immune component between ASD and all but three of its co-morbidities that were examined. In particular, we find that the Toll-like receptor signaling and the chemokine signaling pathways, which are key pathways in the innate immune response, have the highest shared statistical significance. Moreover, the disease genes that overlap these two innate immunity pathways can be used to classify the cases of ASD and its co-morbidities vs. controls with at least 70 % accuracy. CONCLUSIONS This finding suggests that a neuropsychiatric condition and the majority of its non-brain-related co-morbidities share a dysregulated signal that serves as not only a common genetic basis for the diseases but also as a link to environmental triggers. It also raises the possibility that treatment and/or prophylaxis used for disorders of innate immunity may be successfully used for ASD patients with immune-related phenotypes.
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Affiliation(s)
- Sumaiya Nazeen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA USA
| | - Nathan P. Palmer
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston, 02115 MA USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA USA
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA USA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston, 02115 MA USA
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Leboyer M, Berk M, Yolken RH, Tamouza R, Kupfer D, Groc L. Immuno-psychiatry: an agenda for clinical practice and innovative research. BMC Med 2016; 14:173. [PMID: 27788673 PMCID: PMC5084344 DOI: 10.1186/s12916-016-0712-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 10/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The diagnostic scheme for psychiatric disorders is currently based purely on descriptive nomenclature given that biomarkers subtypes and clearly defined causal mechanisms are lacking for the vast majority of disorders. The emerging field of "immuno-psychiatry" has the potential to widen the exploration of a mechanism-based nosology, possibly leading to the discovery of more effective personalised treatment strategies. DISCUSSION Disturbances in immuno-inflammatory and related systems have been implicated in the aetiology, pathophysiology, phenomenology and comorbidity of several psychiatric disorders, including major mood disorders and schizophrenia. A fundamental challenge in their clinical management is to identify bio-signatures that might indicate risk, state, trait, prognosis or theragnosis. Here, we provide the rationale for a clinical and research agenda to refine future clinical practice and conceptual views, and to delineate pathways toward innovative treatment discovery. CONCLUSION The development of bio-signatures will allow clinicians to tailor interventions to the abovementioned biomarker subtypes - a major translational goal for research in this field.
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Affiliation(s)
- Marion Leboyer
- Psychiatry Department, University Paris-Est-Créteil, Mondor hospital, AP-HP, DHU PePSY, Translational Psychiatry laboratory, INSERM U955, Paris, France. .,Fondation FondaMental, Creteil, France. .,University of Bordeaux, UMR 5297, 33000, Bordeaux, France.
| | - Michael Berk
- Deakin University, IMPACT Strategic Research Centre (Barwon Health), School of Medicine, Geelong, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, Orygen, National Centre of Excellence for Youth Mental Health, Parkville, VIC, Australia.,Department of Psychiatry, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Robert H Yolken
- Stanley Division of Developmental Neurovirology, The Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ryad Tamouza
- Fondation FondaMental, Creteil, France.,INSERM, U1160, Hôpital Saint Louis, Paris, F75010, France.,Laboratoire Jean Dausset, LabexTransplantex, Hôpital Saint Louis, Paris, F75010, France
| | - David Kupfer
- Departments of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Laurent Groc
- Fondation FondaMental, Creteil, France. .,University of Bordeaux, UMR 5297, 33000, Bordeaux, France. .,Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, 33077, Bordeaux, France.
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Carter C. The barrier, airway particle clearance, placental and detoxification functions of autism susceptibility genes. Neurochem Int 2016; 99:42-51. [DOI: 10.1016/j.neuint.2016.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/11/2016] [Accepted: 06/07/2016] [Indexed: 02/08/2023]
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Estes ML, McAllister AK. Maternal immune activation: Implications for neuropsychiatric disorders. Science 2016; 353:772-7. [PMID: 27540164 DOI: 10.1126/science.aag3194] [Citation(s) in RCA: 732] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Epidemiological evidence implicates maternal infection as a risk factor for autism spectrum disorder and schizophrenia. Animal models corroborate this link and demonstrate that maternal immune activation (MIA) alone is sufficient to impart lifelong neuropathology and altered behaviors in offspring. This Review describes common principles revealed by these models, highlighting recent findings that strengthen their relevance for schizophrenia and autism and are starting to reveal the molecular mechanisms underlying the effects of MIA on offspring. The role of MIA as a primer for a much wider range of psychiatric and neurologic disorders is also discussed. Finally, the need for more research in this nascent field and the implications for identifying and developing new treatments for individuals at heightened risk for neuroimmune disorders are considered.
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Affiliation(s)
- Myka L Estes
- Center for Neuroscience, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
| | - A Kimberley McAllister
- Center for Neuroscience, University of California Davis, One Shields Avenue, Davis, CA 95618, USA.
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Solso S, Xu R, Proudfoot J, Hagler DJ, Campbell K, Venkatraman V, Barnes CC, Ahrens-Barbeau C, Pierce K, Dale A, Eyler L, Courchesne E. Diffusion Tensor Imaging Provides Evidence of Possible Axonal Overconnectivity in Frontal Lobes in Autism Spectrum Disorder Toddlers. Biol Psychiatry 2016; 79:676-84. [PMID: 26300272 PMCID: PMC4699869 DOI: 10.1016/j.biopsych.2015.06.029] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Theories of brain abnormality in autism spectrum disorder (ASD) have focused on underconnectivity as an explanation for social, language, and behavioral deficits but are based mainly on studies of older autistic children and adults. METHODS In 94 ASD and typical toddlers ages 1 to 4 years, we examined the microstructure (indexed by fractional anisotropy) and volume of axon pathways using in vivo diffusion tensor imaging of fronto-frontal, fronto-temporal, fronto-striatal, and fronto-amygdala axon pathways, as well as posterior contrast tracts. Differences between ASD and typical toddlers in the nature of the relationship of age to these measures were tested. RESULTS Frontal tracts in ASD toddlers displayed abnormal age-related changes with greater fractional anisotropy and volume than normal at younger ages but an overall slower than typical apparent rate of continued development across the span of years. Posterior cortical contrast tracts had few significant abnormalities. CONCLUSIONS Frontal fiber tracts displayed deviant early development and age-related changes that could underlie impaired brain functioning and impact social and communication behaviors in ASD.
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Affiliation(s)
- Stephanie Solso
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Ronghui Xu
- CTRI, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - James Proudfoot
- CTRI, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Donald J. Hagler
- Department of Radiology, Multimodal Imaging Laboratory, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kathleen Campbell
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Vijay Venkatraman
- Department of Radiology, Multimodal Imaging Laboratory, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Cynthia Carter Barnes
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Clelia Ahrens-Barbeau
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Karen Pierce
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Anders Dale
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093,Department of Radiology, Multimodal Imaging Laboratory, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Lisa Eyler
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093,Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093,Desert-Pacific Mental Illness Research, Education and Clinical Center, VA San Diego Healthcare System, San Diego, CA 92161
| | - Eric Courchesne
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla.
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Young AMH, Chakrabarti B, Roberts D, Lai MC, Suckling J, Baron-Cohen S. From molecules to neural morphology: understanding neuroinflammation in autism spectrum condition. Mol Autism 2016; 7:9. [PMID: 26793298 PMCID: PMC4719563 DOI: 10.1186/s13229-016-0068-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/04/2016] [Indexed: 12/31/2022] Open
Abstract
Growing evidence points toward a critical role for early (prenatal) atypical neurodevelopmental processes in the aetiology of autism spectrum condition (ASC). One such process that could impact early neural development is inflammation. We review the evidence for atypical expression of molecular markers in the amniotic fluid, serum, cerebrospinal fluid (CSF), and the brain parenchyma that suggest a role for inflammation in the emergence of ASC. This is complemented with a number of neuroimaging and neuropathological studies describing microglial activation. Implications for treatment are discussed.
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Affiliation(s)
- Adam M H Young
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, UK ; School of Clinical Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Bhismadev Chakrabarti
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, UK ; Centre for Integrative Neuroscience and Neurodynamics, School of Psychology and Clinical Language Science, University of Reading, Reading, UK
| | - David Roberts
- School of Clinical Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Meng-Chuan Lai
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, UK ; Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, Canada ; Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - John Suckling
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK ; Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, UK ; CLASS Clinic, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
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Nguyen LS, Lepleux M, Makhlouf M, Martin C, Fregeac J, Siquier-Pernet K, Philippe A, Feron F, Gepner B, Rougeulle C, Humeau Y, Colleaux L. Profiling olfactory stem cells from living patients identifies miRNAs relevant for autism pathophysiology. Mol Autism 2016; 7:1. [PMID: 26753090 PMCID: PMC4705753 DOI: 10.1186/s13229-015-0064-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/21/2015] [Indexed: 01/09/2023] Open
Abstract
Background Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders caused by the interaction between genetic vulnerability and environmental factors. MicroRNAs (miRNAs) are key posttranscriptional regulators involved in multiple aspects of brain development and function. Previous studies have investigated miRNAs expression in ASD using non-neural cells like lymphoblastoid cell lines (LCL) or postmortem tissues. However, the relevance of LCLs is questionable in the context of a neurodevelopmental disorder, and the impact of the cause of death and/or post-death handling of tissue likely contributes to the variations observed between studies on brain samples. Methods miRNA profiling using TLDA high-throughput real-time qPCR was performed on miRNAs extracted from olfactory mucosal stem cells (OMSCs) biopsied from eight patients and six controls. This tissue is considered as a closer tissue to neural stem cells that could be sampled in living patients and was never investigated for such a purpose before. Real-time PCR was used to validate a set of differentially expressed miRNAs, and bioinformatics analysis determined common pathways and gene targets. Luciferase assays and real-time PCR analysis were used to evaluate the effect of miRNAs misregulation on the expression and translation of several autism-related transcripts. Viral vector-mediated expression was used to evaluate the impact of miRNAs deregulation on neuronal or glial cells functions. Results We identified a signature of four miRNAs (miR-146a, miR-221, miR-654-5p, and miR-656) commonly deregulated in ASD. This signature is conserved in primary skin fibroblasts and may allow discriminating between ASD and intellectual disability samples. Putative target genes of the differentially expressed miRNAs were enriched for pathways previously associated to ASD, and altered levels of neuronal transcripts targeted by miR-146a, miR-221, and miR-656 were observed in patients’ cells. In the mouse brain, miR-146a, and miR-221 display strong neuronal expression in regions important for high cognitive functions, and we demonstrated that reproducing abnormal miR-146a expression in mouse primary cell cultures leads to impaired neuronal dendritic arborization and increased astrocyte glutamate uptake capacities. Conclusions While independent replication experiments are needed to clarify whether these four miRNAS could serve as early biomarkers of ASD, these findings may have important diagnostic implications. They also provide mechanistic connection between miRNA dysregulation and ASD pathophysiology and may open up new opportunities for therapeutic. Electronic supplementary material The online version of this article (doi:10.1186/s13229-015-0064-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lam Son Nguyen
- INSERM UMR 1163, Laboratory of Molecular and pathophysiological bases of cognitive disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, 24 boulevard du Montparnasse, 75015 Paris, France
| | - Marylin Lepleux
- Synapse in Cognition Laboratory, Institut Interdisciplinaire de NeuroSciences, Centre de génomique fonctionnelle, UMR 5297 CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33077 Bordeaux, France
| | - Mélanie Makhlouf
- Epigénétique et Destin Cellulaire, Université Paris Diderot, UMR 7216, 75205 Paris, France
| | - Christelle Martin
- Synapse in Cognition Laboratory, Institut Interdisciplinaire de NeuroSciences, Centre de génomique fonctionnelle, UMR 5297 CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33077 Bordeaux, France
| | - Julien Fregeac
- INSERM UMR 1163, Laboratory of Molecular and pathophysiological bases of cognitive disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, 24 boulevard du Montparnasse, 75015 Paris, France
| | - Karine Siquier-Pernet
- INSERM UMR 1163, Laboratory of Molecular and pathophysiological bases of cognitive disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, 24 boulevard du Montparnasse, 75015 Paris, France
| | - Anne Philippe
- INSERM UMR 1163, Laboratory of Molecular and pathophysiological bases of cognitive disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, 24 boulevard du Montparnasse, 75015 Paris, France
| | - François Feron
- Aix Marseille Université, NICN, CNRS UMR 7259, 13344 Marseille, France
| | - Bruno Gepner
- Aix Marseille Université, NICN, CNRS UMR 7259, 13344 Marseille, France
| | - Claire Rougeulle
- Epigénétique et Destin Cellulaire, Université Paris Diderot, UMR 7216, 75205 Paris, France
| | - Yann Humeau
- Synapse in Cognition Laboratory, Institut Interdisciplinaire de NeuroSciences, Centre de génomique fonctionnelle, UMR 5297 CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33077 Bordeaux, France
| | - Laurence Colleaux
- INSERM UMR 1163, Laboratory of Molecular and pathophysiological bases of cognitive disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, 24 boulevard du Montparnasse, 75015 Paris, France
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Businaro R, Corsi M, Azzara G, Di Raimo T, Laviola G, Romano E, Ricci L, Maccarrone M, Aronica E, Fuso A, Ricci S. Interleukin-18 modulation in autism spectrum disorders. J Neuroinflammation 2016; 13:2. [PMID: 26728085 PMCID: PMC4700739 DOI: 10.1186/s12974-015-0466-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 12/23/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental disease which affects 1 in 88 children. Its etiology remains basically unknown, but it is apparent that neuroinflammation is involved in disease development. Great attention has been focused on pro-inflammatory cytokines, and several studies have reported their dysfunction unbalance in serum as well as in the brain. The present work aimed at evaluating putative dysregulation of interleukin-18 (IL-18), a pro-inflammatory cytokine of the IL-1 family in the sera of patients with ASD of different grades, compared to healthy controls, as well as in postmortem brain samples obtained from patients with tuberous sclerosis as well as acute inflammatory diseases. Moreover, quantitative analysis of IL-18 was performed in the sera and brain obtained from Reeler mice, an experimental model of autism. METHODS Serum IL-18 levels were measured by ELISA. IL-18 was localized by immunohistochemical analysis in brain sections obtained from tuberous sclerosis and encephalitis patients, as well as from gender- and age-matched controls, and in the brain sections of both Reeler and wild-type mice. IL-18 was also quantified by Western blots in homogenates of Reeler and wild-type mice brains. IL-18 binding protein (IL-18BP) was evaluated in Reeler and wild-type mice plasma as well as in their brains (sections and homogenates). RESULTS IL-18 content decreased in the sera of patients with autism compared to healthy subjects and in Reeler sera compared to wild-type controls. IL-18 was detected within glial cells and neurons in the brain of subjects affected by tuberous sclerosis and encephalitis whereas in healthy subjects, only a weak IL-18 positivity was detected at the level of glial cells. Western blot identified higher amounts of IL-18 in Reeler brain homogenates compared to wild-type littermates. IL-18BP was expressed in higher amounts in Reeler brain compared to the brain of wild-type mice, whereas no significant difference was detected comparing IL-18BP plasma levels. CONCLUSIONS IL-18 is dysregulated in ASD patients. Further studies seemed necessary to clarify the molecular details behind IL-18 increase in the brain and IL-18 decrease in the sera of patients. An increase in the size of the patient cohort seems necessary to ascertain whether decreased IL-18 content in the sera can become a predictive biomarker of ASD and whether its measure, in combination with other markers (e.g., increased levels of brain-derived neurotrophic factor (BDNF)), may be included in a diagnostic panel.
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Affiliation(s)
- Rita Businaro
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Corso della Repubblica 79, 04100, Latina, Italy.
| | - Mariangela Corsi
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Corso della Repubblica 79, 04100, Latina, Italy.
| | - Gabriella Azzara
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Corso della Repubblica 79, 04100, Latina, Italy.
| | - Tania Di Raimo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Corso della Repubblica 79, 04100, Latina, Italy.
| | - Giovanni Laviola
- Section of Department of Cell Biology & Neuroscience, Section Behavioural Neuroscience, Istituto Superiore di Sanità, Roma, Italy.
| | - Emilia Romano
- Section of Department of Cell Biology & Neuroscience, Section Behavioural Neuroscience, Istituto Superiore di Sanità, Roma, Italy.
| | - Lidia Ricci
- Department of Anatomical, Histological, Legal Medicine and Orthopedics Sciences, Sapienza University of Rome, Rome, Italy.
| | - Mauro Maccarrone
- European Center for Brain Research (CERC)/IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano 64-65, 00143, Rome, Italy. .,School of Medicine and Center of Integrated Research, Campus Bio-Medico University of Rome, via Alvaro del Portillo 21, 00128, Rome, Italy.
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medical Center and Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands.
| | - Andrea Fuso
- European Center for Brain Research (CERC)/IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano 64-65, 00143, Rome, Italy. .,Department of Psychology, Sapienza University of Rome, Rome, Italy.
| | - Serafino Ricci
- Department of Anatomical, Histological, Legal Medicine and Orthopedics Sciences, Sapienza University of Rome, Rome, Italy.
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Grayson DR, Guidotti A. Merging data from genetic and epigenetic approaches to better understand autistic spectrum disorder. Epigenomics 2015; 8:85-104. [PMID: 26551091 PMCID: PMC4864049 DOI: 10.2217/epi.15.92] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that is characterized by a wide range of cognitive and behavioral abnormalities. Genetic research has identified large numbers of genes that contribute to ASD phenotypes. There is compelling evidence that environmental factors contribute to ASD through influences that differentially impact the brain through epigenetic mechanisms. Both genetic mutations and epigenetic influences alter gene expression in different cell types of the brain. Mutations impact the expression of large numbers of genes and also have downstream consequences depending on specific pathways associated with the mutation. Environmental factors impact the expression of sets of genes by altering methylation/hydroxymethylation patterns, local histone modification patterns and chromatin remodeling. Herein, we discuss recent developments in the research of ASD with a focus on epigenetic pathways as a complement to current genetic screening.
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Affiliation(s)
- Dennis R Grayson
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60607, USA
| | - Alessandro Guidotti
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60607, USA
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Targeted Gene Resequencing (Astrochip) to Explore the Tripartite Synapse in Autism-Epilepsy Phenotype with Macrocephaly. Neuromolecular Med 2015; 18:69-80. [PMID: 26537360 DOI: 10.1007/s12017-015-8378-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 12/26/2022]
Abstract
The frequent co-occurrence of autism spectrum disorders (ASD) and epilepsy, or paroxysmal EEG abnormalities, defines a condition termed autism-epilepsy phenotype (AEP). This condition results, in some cases , from dysfunctions of glial inwardly rectifying potassium channels (Kir), which are mainly expressed in astrocytes where they mediate neuron-glia communication. Macrocephaly is also often comorbid with autism-epilepsy (autism-epilepsy phenotype with macrocephaly, MAEP), and it is tempting to hypothesize that shared pathogenic mechanisms might explain concurrence of these conditions. In the present study, we assessed whether protein pathways involved, along with Kir channels, in astrocyte-neuron interaction at the tripartite synapse play a role in the etiopathogenesis of MAEP. Using a targeted resequencing methodology, we investigated the coding regions of 35 genes in 61 patients and correlated genetic results with clinical features. Variants were subdivided into 12 classes and clustered into four groups. We detected rare or previously unknown predicted deleterious missense changes in GJA1, SLC12A2, SNTA1, EFNA3, CNTNAP2, EPHA4, and STXBP1 in seven patients and two high-frequency variants in DLG1 in six individuals. We also found that a group of variants (predicted deleterious and non-coding), segregating with the comorbid MAEP/AEP subgroups, belong to proteins specifically involved in glutamate transport and metabolism (namely, SLC17A6, GRM8, and GLUL), as well as in potassium conductance (KCNN3). This "endophenotype-oriented" study, performed using a targeted strategy, helped to further delineate part of the complex genetic background of ASD, particularly in the presence of coexisting macrocephaly and/or epilepsy/paroxysmal EEG, and suggests that use of stringent clinical clustering might be an approach worth adopting in order to unravel the complex genomic data in neurodevelopmental disorders.
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Ander BP, Barger N, Stamova B, Sharp FR, Schumann CM. Atypical miRNA expression in temporal cortex associated with dysregulation of immune, cell cycle, and other pathways in autism spectrum disorders. Mol Autism 2015; 6:37. [PMID: 26146533 PMCID: PMC4491207 DOI: 10.1186/s13229-015-0029-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/27/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASDs) likely involve dysregulation of multiple genes related to brain function and development. Abnormalities in individual regulatory small non-coding RNA (sncRNA), including microRNA (miRNA), could have profound effects upon multiple functional pathways. We assessed whether a brain region associated with core social impairments in ASD, the superior temporal sulcus (STS), would evidence greater transcriptional dysregulation of sncRNA than adjacent, yet functionally distinct, primary auditory cortex (PAC). METHODS We measured sncRNA expression levels in 34 samples of postmortem brain from STS and PAC to find differentially expressed sncRNA in ASD compared with control cases. For differentially expressed miRNA, we further analyzed their predicted mRNA targets and carried out functional over-representation analysis of KEGG pathways to examine their functional significance and to compare our findings to reported alterations in ASD gene expression. RESULTS Two mature miRNAs (miR-4753-5p and miR-1) were differentially expressed in ASD relative to control in STS and four (miR-664-3p, miR-4709-3p, miR-4742-3p, and miR-297) in PAC. In both regions, miRNA were functionally related to various nervous system, cell cycle, and canonical signaling pathways, including PI3K-Akt signaling, previously implicated in ASD. Immune pathways were only disrupted in STS. snoRNA and pre-miRNA were also differentially expressed in ASD brain. CONCLUSIONS Alterations in sncRNA may underlie dysregulation of molecular pathways implicated in autism. sncRNA transcriptional abnormalities in ASD were apparent in STS and in PAC, a brain region not directly associated with core behavioral impairments. Disruption of miRNA in immune pathways, frequently implicated in ASD, was unique to STS.
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Affiliation(s)
- Bradley P Ander
- Department of Neurology, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Nicole Barger
- Department of Psychiatry & Behavioral Sciences, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Boryana Stamova
- Department of Neurology, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Frank R Sharp
- Department of Neurology, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
| | - Cynthia M Schumann
- Department of Psychiatry & Behavioral Sciences, MIND Institute, University of California at Davis Medical Center, 2805 50th Street, Sacramento, CA 95817 USA
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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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Kohane IS. An autism case history to review the systematic analysis of large-scale data to refine the diagnosis and treatment of neuropsychiatric disorders. Biol Psychiatry 2015; 77:59-65. [PMID: 25034947 PMCID: PMC4260993 DOI: 10.1016/j.biopsych.2014.05.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/05/2014] [Accepted: 05/22/2014] [Indexed: 01/18/2023]
Abstract
Analysis of large-scale systems of biomedical data provides a perspective on neuropsychiatric disease that may be otherwise elusive. Described here is an analysis of three large-scale systems of data from autism spectrum disorder (ASD) and of ASD research as an exemplar of what might be achieved from study of such data. First is the biomedical literature that highlights the fact that there are two very successful but quite separate research communities and findings pertaining to genetics and the molecular biology of ASD. There are those studies positing ASD causes that are related to immunological dysregulation and those related to disorders of synaptic function and neuronal connectivity. Second is the emerging use of electronic health record systems and other large clinical databases that allow the data acquired during the course of care to be used to identify distinct subpopulations, clinical trajectories, and pathophysiological substructures of ASD. These systems reveal subsets of patients with distinct clinical trajectories, some of which are immunologically related and others which follow pathologies conventionally thought of as neurological. The third is genome-wide genomic and transcriptomic analyses which show molecular pathways that overlap neurological and immunological mechanisms. The convergence of these three large-scale data perspectives illustrates the scientific leverage that large-scale data analyses can provide in guiding researchers in an approach to the diagnosis of neuropsychiatric disease that is inclusive and comprehensive.
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Affiliation(s)
- Isaac S Kohane
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts.
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Eapen V, Clarke RA. Autism spectrum disorders: from genotypes to phenotypes. Front Hum Neurosci 2014; 8:914. [PMID: 25429265 PMCID: PMC4228832 DOI: 10.3389/fnhum.2014.00914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 10/26/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Valsamma Eapen
- School of Psychiatry, University of New South Wales and Academic Unit of Child Psychiatry, Ingham Institute, South West Sydney (AUCS), Liverpool Hospital , Sydney, NSW , Australia
| | - Raymond A Clarke
- Ingham Institute, School of Medicine, University of Western Sydney , Sydney, NSW , Australia
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Duan Y, Wang SH, Song J, Mironova Y, Ming GL, Kolodkin AL, Giger RJ. Semaphorin 5A inhibits synaptogenesis in early postnatal- and adult-born hippocampal dentate granule cells. eLife 2014; 3. [PMID: 25313870 PMCID: PMC4236683 DOI: 10.7554/elife.04390] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/13/2014] [Indexed: 12/20/2022] Open
Abstract
Human SEMAPHORIN 5A (SEMA5A) is an autism susceptibility gene; however, its function in brain development is unknown. In this study, we show that mouse Sema5A negatively regulates synaptogenesis in early, developmentally born, hippocampal dentate granule cells (GCs). Sema5A is strongly expressed by GCs and regulates dendritic spine density in a cell-autonomous manner. In the adult mouse brain, newly born Sema5A-/- GCs show an increase in dendritic spine density and increased AMPA-type synaptic responses. Sema5A signals through PlexinA2 co-expressed by GCs, and the PlexinA2-RasGAP activity is necessary to suppress spinogenesis. Like Sema5A-/- mutants, PlexinA2-/- mice show an increase in GC glutamatergic synapses, and we show that Sema5A and PlexinA2 genetically interact with respect to GC spine phenotypes. Sema5A-/- mice display deficits in social interaction, a hallmark of autism-spectrum-disorders. These experiments identify novel intra-dendritic Sema5A/PlexinA2 interactions that inhibit excitatory synapse formation in developmentally born and adult-born GCs, and they provide support for SEMA5A contributions to autism-spectrum-disorders.
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Affiliation(s)
- Yuntao Duan
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, United States
| | - Shih-Hsiu Wang
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juan Song
- Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Yevgeniya Mironova
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, United States
| | - Guo-li Ming
- Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Alex L Kolodkin
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Roman J Giger
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, United States
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Abekhoukh S, Bardoni B. CYFIP family proteins between autism and intellectual disability: links with Fragile X syndrome. Front Cell Neurosci 2014; 8:81. [PMID: 24733999 PMCID: PMC3973919 DOI: 10.3389/fncel.2014.00081] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 02/27/2014] [Indexed: 12/14/2022] Open
Abstract
Intellectual disability (ID) and autism spectrum disorders (ASDs) have in common alterations in some brain circuits and brain abnormalities, such as synaptic transmission and dendritic spines morphology. Recent studies have indicated a differential expression for specific categories of genes as a cause for both types of disease, while an increasing number of genes is recognized to produce both disorders. An example is the Fragile X mental retardation gene 1 (FMR1), whose silencing causes the Fragile X syndrome, the most common form of ID and autism, also characterized by physical hallmarks. Fragile X mental retardation protein (FMRP), the protein encoded by FMR1, is an RNA-binding protein with an important role in translational control. Among the interactors of FMRP, CYFIP1/2 (cytoplasmic FMRP interacting protein) proteins are good candidates for ID and autism, on the bases of their genetic implication and functional properties, even if the precise functional significance of the CYFIP/FMRP interaction is not understood yet. CYFIP1 and CYFIP2 represent a link between Rac1, the WAVE (WAS protein family member) complex and FMRP, favoring the cross talk between actin polymerization and translational control.
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Affiliation(s)
- Sabiha Abekhoukh
- CNRS, Institute of Molecular and Cellular Pharmacology, UMR 7275 Valbonne, France ; University of Nice Sophia-Antipolis Nice, France ; CNRS, International Associated Laboratories-NEOGENEX Valbonne, France
| | - Barbara Bardoni
- CNRS, Institute of Molecular and Cellular Pharmacology, UMR 7275 Valbonne, France ; University of Nice Sophia-Antipolis Nice, France ; CNRS, International Associated Laboratories-NEOGENEX Valbonne, France
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