1
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Gao AYL, Lourdin-De Filippis E, Orlowski J, McKinney RA. Roles of Endomembrane Alkali Cation/Proton Exchangers in Synaptic Function and Neurodevelopmental Disorders. Front Physiol 2022; 13:892196. [PMID: 35547574 PMCID: PMC9081726 DOI: 10.3389/fphys.2022.892196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 12/25/2022] Open
Abstract
Endomembrane alkali cation (Na+, K+)/proton (H+) exchangers (eNHEs) are increasingly associated with neurological disorders. These eNHEs play integral roles in regulating the luminal pH, processing, and trafficking of cargo along the secretory (Golgi and post-Golgi vesicles) and endocytic (early, recycling, and late endosomes) pathways, essential regulatory processes vital for neuronal development and plasticity. Given the complex morphology and compartmentalization of multipolar neurons, the contribution of eNHEs in maintaining optimal pH homeostasis and cargo trafficking is especially significant during periods of structural and functional development and remodeling. While the importance of eNHEs has been demonstrated in a variety of non-neuronal cell types, their involvement in neuronal function is less well understood. In this review, we will discuss their emerging roles in excitatory synaptic function, particularly as it pertains to cellular learning and remodeling. We will also explore their connections to neurodevelopmental conditions, including intellectual disability, autism, and attention deficit hyperactivity disorders.
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Affiliation(s)
- Andy Y L Gao
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.,Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | | | - John Orlowski
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - R Anne McKinney
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
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2
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Passos-Bueno MR, Costa CIS, Zatz M. Dystrophin genetic variants and autism. DISCOVER MENTAL HEALTH 2022; 2:4. [PMID: 37861890 PMCID: PMC10501027 DOI: 10.1007/s44192-022-00008-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/07/2022] [Indexed: 10/21/2023]
Abstract
Loss-of-function variants in the dystrophin gene, a well-known cause of muscular dystrophies, have emerged as a mutational risk mechanism for autism spectrum disorder (ASD), which in turn is a highly prevalent (~ 1%) genetically heterogeneous neurodevelopmental disorder. Although the association of intellectual disability with the dystrophinopathies Duchenne (DMD) and Becker muscular dystrophy (BMD) has been long established, their association with ASD is more recent, and the dystrophin genotype-ASD phenotype correlation is unclear. We therefore present a review of the literature focused on the ASD prevalence among dystrophinopathies, the relevance of the dystrophin isoforms, and most particularly the relevance of the genetic background to the etiology of ASD in these patients. Four families with ASD-DMD/BMD patients are also reported here for the first time. These include a single ASD individual, ASD-discordant and ASD-concordant monozygotic twins, and non-identical ASD triplets. Notably, two unrelated individuals, which were first ascertained because of the ASD phenotype at ages 15 and 5 years respectively, present rare dystrophin variants still poorly characterized, suggesting that some dystrophin variants may compromise the brain more prominently. Whole exome sequencing in these ASD-DMD/BMD individuals together with the literature suggest, although based on preliminary data, a complex and heterogeneous genetic architecture underlying ASD in dystrophinopathies, that include rare variants of large and medium effect. The need for the establishment of a consortia for genomic investigation of ASD-DMD/BMD patients, which may shed light on the genetic architecture of ASD, is discussed.
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Affiliation(s)
- Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Claudia Ismania Samogy Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mayana Zatz
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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3
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Sun MW, Moretti S, Paskov KM, Stockham NT, Varma M, Chrisman BS, Washington PY, Jung JY, Wall DP. Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value. BMC Bioinformatics 2020; 21:356. [PMID: 32787845 PMCID: PMC7430867 DOI: 10.1186/s12859-020-03693-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/21/2020] [Indexed: 11/13/2022] Open
Abstract
Background Complex human health conditions with etiological heterogeneity like Autism Spectrum Disorder (ASD) often pose a challenge for traditional genome-wide association study approaches in defining a clear genotype to phenotype model. Coalitional game theory (CGT) is an exciting method that can consider the combinatorial effect of groups of variants working in concert to produce a phenotype. CGT has been applied to associate likely-gene-disrupting variants encoded from whole genome sequence data to ASD; however, this previous approach cannot take into account for prior biological knowledge. Here we extend CGT to incorporate a priori knowledge from biological networks through a game theoretic centrality measure based on Shapley value to rank genes by their relevance–the individual gene’s synergistic influence in a gene-to-gene interaction network. Game theoretic centrality extends the notion of Shapley value to the evaluation of a gene’s contribution to the overall connectivity of its corresponding node in a biological network. Results We implemented and applied game theoretic centrality to rank genes on whole genomes from 756 multiplex autism families. Top ranking genes with the highest game theoretic centrality in both the weighted and unweighted approaches were enriched for pathways previously associated with autism, including pathways of the immune system. Four of the selected genes HLA-A, HLA-B, HLA-G, and HLA-DRB1–have also been implicated in ASD and further support the link between ASD and the human leukocyte antigen complex. Conclusions Game theoretic centrality can prioritize influential, disease-associated genes within biological networks, and assist in the decoding of polygenic associations to complex disorders like autism.
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Affiliation(s)
- Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, USA.,Department of Pediatrics, Stanford University, Stanford, USA
| | - Stefano Moretti
- LAMSADE, CNRS, Université Paris-Dauphine, Université PSL, Paris, France
| | - Kelley M Paskov
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Nate T Stockham
- Department of Neuroscience, Stanford University, Stanford, USA
| | - Maya Varma
- Department of Computer Science, Stanford University, Stanford, USA
| | | | | | - Jae-Yoon Jung
- Department of Biomedical Data Science, Stanford University, Stanford, USA.,Department of Pediatrics, Stanford University, Stanford, USA
| | - Dennis P Wall
- Department of Biomedical Data Science, Stanford University, Stanford, USA. .,Department of Pediatrics, Stanford University, Stanford, USA. .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, United States.
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4
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Patak J, Faraone SV, Zhang-James Y. Sodium hydrogen exchanger 9 NHE9 (SLC9A9) and its emerging roles in neuropsychiatric comorbidity. Am J Med Genet B Neuropsychiatr Genet 2020; 183:289-305. [PMID: 32400953 DOI: 10.1002/ajmg.b.32787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 12/09/2019] [Accepted: 02/22/2020] [Indexed: 12/16/2022]
Abstract
Variations in SLC9A9 gene expression and protein function are associated with multiple human diseases, which range from Attention-deficit/hyperactivity disorder (ADHD) to glioblastoma multiforme. In an effort to determine the full spectrum of human disease associations with SLC9A9, we performed a systematic review of the literature. We also review SLC9A9's biochemistry, protein structure, and function, as well as its interacting partners with the goal of identifying mechanisms of disease and druggable targets. We report gaps in the literature regarding the genes function along with consistent trends in disease associations that can be used to further research into treating the respective diseases. We report that SLC9A9 has strong associations with neuropsychiatric diseases and various cancers. Interestingly, we find strong overlap in SLC9A9 disease associations and propose a novel role for SLC9A9 in neuropsychiatric comorbidity. In conclusion, SLC9A9 is a multifunctional protein that, through both its endosome regulatory function and its protein-protein interaction network, has the ability to modulate signaling axes, such as the PI3K pathway, among others.
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Affiliation(s)
- Jameson Patak
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York, USA.,College of Medicine, MD Program, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Stephen V Faraone
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York, USA.,Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Yanli Zhang-James
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
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5
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Lobzhanidze G, Japaridze N, Lordkipanidze T, Rzayev F, MacFabe D, Zhvania M. Behavioural and brain ultrastructural changes following the systemic administration of propionic acid in adolescent male rats. Further development of a rodent model of autism. Int J Dev Neurosci 2020; 80:139-156. [PMID: 31997401 DOI: 10.1002/jdn.10011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/08/2020] [Accepted: 01/19/2020] [Indexed: 12/18/2022] Open
Abstract
Short chain fatty acids, produced as gut microbiome metabolites but also present in the diet, exert broad effects in host physiology. Propionic acid (PPA), along with butyrate and acetate, plays a growing role in health, but also in neurological conditions. Increased PPA exposure in humans, animal models and cell lines elicit diverse behavioural and biochemical changes consistent with organic acidurias, mitochondrial disorders and autism spectrum disorders (ASD). ASD is considered a disorder of synaptic dysfunction and cell signalling, but also neuroinflammatory and neurometabolic components. We examined behaviour (Morris water and radial arm mazes) and the ultrastructure of the hippocampus and medial prefrontal cortex (electron microscopy) following a single intraperitoneal (i.p.) injection of PPA (175 mg/kg) in male adolescent rats. PPA treatment showed altered social and locomotor behaviour without changes in learning and memory. Both transient and enduring ultrastructural alterations in synapses, astro- and microglia were detected in the CA1 hippocampal area. Electron microscopic analysis showed the PPA treatment significantly decreased the total number of synaptic vesicles, presynaptic mitochondria and synapses with a symmetric active zone. Thus, brief systemic administration of this dietary and enteric short chain fatty acid produced behavioural and dynamic brain ultrastructural changes, providing further validation of the PPA model of ASD.
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Affiliation(s)
- Giorgi Lobzhanidze
- School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia.,Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia
| | - Nadezhda Japaridze
- Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia.,Medical School, New Vision University, Tbilisi, Georgia
| | - Tamar Lordkipanidze
- School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia.,Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia
| | - Fuad Rzayev
- Laboratory of Electron Microscopy, Research Center of Azerbaijan Medical University, Baku, Azerbaijan
| | - Derrick MacFabe
- The Kilee Patchell-Evans Autism Research Group, London, ON, Canada.,Faculty of Medicine, Department of Microbiology, Center for Healthy Eating and Food Innovation, Maastricht University, Maastricht, the Netherlands
| | - Mzia Zhvania
- School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia.,Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia
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6
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Gromova KV, Muhia M, Rothammer N, Gee CE, Thies E, Schaefer I, Kress S, Kilimann MW, Shevchuk O, Oertner TG, Kneussel M. Neurobeachin and the Kinesin KIF21B Are Critical for Endocytic Recycling of NMDA Receptors and Regulate Social Behavior. Cell Rep 2019; 23:2705-2717. [PMID: 29847800 DOI: 10.1016/j.celrep.2018.04.112] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 02/20/2018] [Accepted: 04/25/2018] [Indexed: 11/24/2022] Open
Abstract
Autism spectrum disorders (ASDs) are associated with mutations affecting synaptic components, including GluN2B-NMDA receptors (NMDARs) and neurobeachin (NBEA). NBEA participates in biosynthetic pathways to regulate synapse receptor targeting, synaptic function, cognition, and social behavior. However, the role of NBEA-mediated transport in specific trafficking routes is unclear. Here, we highlight an additional function for NBEA in the local delivery and surface re-insertion of synaptic receptors in mouse neurons. NBEA dynamically interacts with Rab4-positive recycling endosomes, transiently enters spines in an activity-dependent manner, and regulates GluN2B-NMDAR recycling. Furthermore, we show that the microtubule growth inhibitor kinesin KIF21B constrains NBEA dynamics and is present in the NBEA-recycling endosome-NMDAR complex. Notably, Kif21b knockout decreases NMDAR surface expression and alters social behavior in mice, consistent with reported social deficits in Nbea mutants. The influence of NBEA-KIF21B interactions on GluN2B-NMDAR local recycling may be relevant to mechanisms underlying ASD etiology.
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Affiliation(s)
- Kira V Gromova
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mary Muhia
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Rothammer
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christine E Gee
- Department of Synaptic Physiology, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Edda Thies
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irina Schaefer
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabrina Kress
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred W Kilimann
- Department of Molecular Neurobiology, Max-Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Olga Shevchuk
- Cellular Proteomics Research Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany; Leibniz Institute for Analytical Sciences, ISAS, Dortmund, Germany
| | - Thomas G Oertner
- Department of Synaptic Physiology, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Kneussel
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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7
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Faraone SV, Larsson H. Genetics of attention deficit hyperactivity disorder. Mol Psychiatry 2019; 24:562-575. [PMID: 29892054 PMCID: PMC6477889 DOI: 10.1038/s41380-018-0070-0] [Citation(s) in RCA: 467] [Impact Index Per Article: 93.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/31/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
Abstract
Decades of research show that genes play an vital role in the etiology of attention deficit hyperactivity disorder (ADHD) and its comorbidity with other disorders. Family, twin, and adoption studies show that ADHD runs in families. ADHD's high heritability of 74% motivated the search for ADHD susceptibility genes. Genetic linkage studies show that the effects of DNA risk variants on ADHD must, individually, be very small. Genome-wide association studies (GWAS) have implicated several genetic loci at the genome-wide level of statistical significance. These studies also show that about a third of ADHD's heritability is due to a polygenic component comprising many common variants each having small effects. From studies of copy number variants we have also learned that the rare insertions or deletions account for part of ADHD's heritability. These findings have implicated new biological pathways that may eventually have implications for treatment development.
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Affiliation(s)
- Stephen V Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Henrik Larsson
- School of Medical Sciences, Örebro University, Örebro, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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8
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Zhang-James Y, Vaudel M, Mjaavatten O, Berven FS, Haavik J, Faraone SV. Effect of disease-associated SLC9A9 mutations on protein-protein interaction networks: implications for molecular mechanisms for ADHD and autism. ACTA ACUST UNITED AC 2019; 11:91-105. [PMID: 30927234 DOI: 10.1007/s12402-018-0281-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022]
Abstract
Na+/H+ Exchanger 9 (NHE9) is an endosomal membrane protein encoded by the Solute Carrier 9A, member 9 gene (SLC9A9). SLC9A9 has been implicated in attention deficit hyperactivity disorder (ADHD), autism spectrum disorders (ASDs), epilepsy, multiple sclerosis and cancers. To better understand the function of NHE9 and the effects of disease-associated variants on protein-protein interactions, we conducted a quantitative analysis of the NHE9 interactome using co-immunoprecipitation and isobaric labeling-based quantitative mass spectrometry. We identified 100 proteins that interact with NHE9. These proteins were enriched in known functional pathways for NHE9: the endocytosis, protein ubiquitination and phagosome pathways, as well as some novel pathways including oxidative stress, mitochondrial dysfunction, mTOR signaling, cell death and RNA processing pathways. An ADHD-associated mutation (A409P) significantly altered NHE9's interactions with a subset of proteins involved in caveolae-mediated endocytosis and MAP2K2-mediated downstream signaling. An ASD nonsense mutation in SLC9A9, R423X, produced no-detectable amount of NHE9, suggesting the overall loss of NHE9 functional networks. In addition, seven of the NHE9 interactors are products of known autism candidate genes (Simons Foundation Autism Research Initiative, SFARI Gene) and 90% of the NHE9 interactome overlap with SFARI protein interaction network PIN (p < 0.0001), supporting the role of NHE9 interactome in ASDs molecular mechanisms. Our results provide a detailed understanding of the functions of protein NHE9 and its disrupted interactions, possibly underlying ADHD and ASDs. Furthermore, our methodological framework proved useful for functional characterization of disease-associated genetic variants and suggestion of druggable targets.
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Affiliation(s)
- Yanli Zhang-James
- Departments of Psychiatry, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Olav Mjaavatten
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway.,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Stephen V Faraone
- Departments of Psychiatry, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA. .,Neuroscience and Physiology, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA.
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9
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Di Gregorio E, Riberi E, Belligni EF, Biamino E, Spielmann M, Ala U, Calcia A, Bagnasco I, Carli D, Gai G, Giordano M, Guala A, Keller R, Mandrile G, Arduino C, Maffè A, Naretto VG, Sirchia F, Sorasio L, Ungari S, Zonta A, Zacchetti G, Talarico F, Pappi P, Cavalieri S, Giorgio E, Mancini C, Ferrero M, Brussino A, Savin E, Gandione M, Pelle A, Giachino DF, De Marchi M, Restagno G, Provero P, Cirillo Silengo M, Grosso E, Buxbaum JD, Pasini B, De Rubeis S, Brusco A, Ferrero GB. Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes. Clin Genet 2017; 92:415-422. [PMID: 28295210 DOI: 10.1111/cge.13009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). AIMS Identification of genomic disorders in DD/ID. MATERIALS AND METHODS We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. RESULTS We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape. DISCUSSION AND CONCLUSION We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects.
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Affiliation(s)
- E Di Gregorio
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - E Riberi
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E F Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Biamino
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - M Spielmann
- Research Group Mundlos, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - U Ala
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - A Calcia
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - I Bagnasco
- Neuropsichiatria Infantile, Martini Hospital, ASL TO1, Turin, Italy
| | - D Carli
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - G Gai
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Giordano
- Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - A Guala
- SOC Pediatria, Castelli Hospital, Verbania, Italy
| | - R Keller
- Mental Health Department, ASL TO2, Adult Autism Center, Turin, Italy
| | - G Mandrile
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - C Arduino
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - A Maffè
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - V G Naretto
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - F Sirchia
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - L Sorasio
- Pediatrics, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S Ungari
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - A Zonta
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G Zacchetti
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - F Talarico
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Pappi
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - S Cavalieri
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Giorgio
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - C Mancini
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - M Ferrero
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - A Brussino
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Savin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Gandione
- Department of Neuropsychiatry, University of Torino, Turin, Italy
| | - A Pelle
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - D F Giachino
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - M De Marchi
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - G Restagno
- Laboratory of Molecular Genetics, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Provero
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - M Cirillo Silengo
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Grosso
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - J D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - B Pasini
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - A Brusco
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G B Ferrero
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
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Patak J, Hess JL, Zhang-James Y, Glatt SJ, Faraone SV. SLC9A9 Co-expression modules in autism-associated brain regions. Autism Res 2016; 10:414-429. [PMID: 27439572 DOI: 10.1002/aur.1670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/27/2016] [Accepted: 06/13/2016] [Indexed: 12/16/2022]
Abstract
SLC9A9 is a sodium hydrogen exchanger present in the recycling endosome and highly expressed in the brain. It is implicated in neuropsychiatric disorders, including autism spectrum disorders (ASDs). Little research concerning its gene expression patterns and biological pathways has been conducted. We sought to investigate its possible biological roles in autism-associated brain regions throughout development. We conducted a weighted gene co-expression network analysis on RNA-seq data downloaded from Brainspan. We compared prenatal and postnatal gene expression networks for three ASD-associated brain regions known to have high SLC9A9 gene expression. We also performed an ASD-associated single nucleotide polymorphism enrichment analysis and a cell signature enrichment analysis. The modules showed differences in gene constituents (membership), gene number, and connectivity throughout time. SLC9A9 was highly associated with immune system functions, metabolism, apoptosis, endocytosis, and signaling cascades. Gene list comparison with co-immunoprecipitation data was significant for multiple modules. We found a disproportionately high autism risk signal among genes constituting the prenatal hippocampal module. The modules were enriched with astrocyte and oligodendrocyte markers. SLC9A9 is potentially involved in the pathophysiology of ASDs. Our investigation confirmed proposed functions for SLC9A9, such as endocytosis and immune regulation, while also revealing potential roles in mTOR signaling and cell survival.. By providing a concise molecular map and interactions, evidence of cell type and implicated brain regions we hope this will guide future research on SLC9A9. Autism Res 2017, 10: 414-429. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.
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Affiliation(s)
- Jameson Patak
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York
| | - Jonathan L Hess
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York
| | - Yanli Zhang-James
- Department of Psychiatry, Upstate Medical University, Syracuse, New York
| | - Stephen J Glatt
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York.,Department of Psychiatry, Upstate Medical University, Syracuse, New York
| | - Stephen V Faraone
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York.,Department of Psychiatry, Upstate Medical University, Syracuse, New York.,Department of Biomedicine, K.G. Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
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