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Veatch OJ, Butler MG, Elsea SH, Malow BA, Sutcliffe JS, Moore JH. An Automated Functional Annotation Pipeline That Rapidly Prioritizes Clinically Relevant Genes for Autism Spectrum Disorder. Int J Mol Sci 2020; 21:ijms21239029. [PMID: 33261099 PMCID: PMC7734579 DOI: 10.3390/ijms21239029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022] Open
Abstract
Human genetic studies have implicated more than a hundred genes in Autism Spectrum Disorder (ASD). Understanding how variation in implicated genes influence expression of co-occurring conditions and drug response can inform more effective, personalized approaches for treatment of individuals with ASD. Rapidly translating this information into the clinic requires efficient algorithms to sort through the myriad of genes implicated by rare gene-damaging single nucleotide and copy number variants, and common variation detected in genome-wide association studies (GWAS). To pinpoint genes that are more likely to have clinically relevant variants, we developed a functional annotation pipeline. We defined clinical relevance in this project as any ASD associated gene with evidence indicating a patient may have a complex, co-occurring condition that requires direct intervention (e.g., sleep and gastrointestinal disturbances, attention deficit hyperactivity, anxiety, seizures, depression), or is relevant to drug development and/or approaches to maximizing efficacy and minimizing adverse events (i.e., pharmacogenomics). Starting with a list of all candidate genes implicated in all manifestations of ASD (i.e., idiopathic and syndromic), this pipeline uses databases that represent multiple lines of evidence to identify genes: (1) expressed in the human brain, (2) involved in ASD-relevant biological processes and resulting in analogous phenotypes in mice, (3) whose products are targeted by approved pharmaceutical compounds or possessing pharmacogenetic variation and (4) whose products directly interact with those of genes with variants recommended to be tested for by the American College of Medical Genetics (ACMG). Compared with 1000 gene sets, each with a random selection of human protein coding genes, more genes in the ASD set were annotated for each category evaluated (p ≤ 1.99 × 10−2). Of the 956 ASD-implicated genes in the full set, 18 were flagged based on evidence in all categories. Fewer genes from randomly drawn sets were annotated in all categories (x = 8.02, sd = 2.56, p = 7.75 × 10−4). Notably, none of the prioritized genes are represented among the 59 genes compiled by the ACMG, and 78% had a pathogenic or likely pathogenic variant in ClinVar. Results from this work should rapidly prioritize potentially actionable results from genetic studies and, in turn, inform future work toward clinical decision support for personalized care based on genetic testing.
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Affiliation(s)
- Olivia J. Veatch
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, MO 66160, USA;
- Correspondence:
| | - Merlin G. Butler
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, MO 66160, USA;
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Beth A. Malow
- Sleep Disorders Division, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
| | - James S. Sutcliffe
- Vanderbilt Genetics Institute, Department of Molecular Physiology & Biophysics, Department of Psychiatry and Behavioral Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
| | - Jason H. Moore
- Department of Biostatistics, Epidemiology, & Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA;
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Karunakaran KB, Chaparala S, Ganapathiraju MK. Potentially repurposable drugs for schizophrenia identified from its interactome. Sci Rep 2019; 9:12682. [PMID: 31481665 PMCID: PMC6722087 DOI: 10.1038/s41598-019-48307-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 07/11/2019] [Indexed: 12/13/2022] Open
Abstract
We previously presented the protein-protein interaction network of schizophrenia associated genes, and from it, the drug-protein interactome which showed the drugs that target any of the proteins in the interactome. Here, we studied these drugs further to identify whether any of them may potentially be repurposable for schizophrenia. In schizophrenia, gene expression has been described as a measurable aspect of the disease reflecting the action of risk genes. We studied each of the drugs from the interactome using the BaseSpace Correlation Engine, and shortlisted those that had a negative correlation with differential gene expression of schizophrenia. This analysis resulted in 12 drugs whose differential gene expression (drug versus normal) had an anti-correlation with differential expression for schizophrenia (disorder versus normal). Some of these drugs were already being tested for their clinical activity in schizophrenia and other neuropsychiatric disorders. Several proteins in the protein interactome of the targets of several of these drugs were associated with various neuropsychiatric disorders. The network of genes with opposite drug-induced versus schizophrenia-associated expression profiles were significantly enriched in pathways relevant to schizophrenia etiology and GWAS genes associated with traits or diseases that had a pathophysiological overlap with schizophrenia. Drugs that targeted the same genes as the shortlisted drugs, have also demonstrated clinical activity in schizophrenia and other related disorders. This integrated computational analysis will help translate insights from the schizophrenia drug-protein interactome to clinical research - an important step, especially in the field of psychiatric drug development which faces a high failure rate.
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Affiliation(s)
- Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Indian Institute of Science, Bengaluru, India
| | | | - Madhavi K Ganapathiraju
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA.
- Intelligent Systems Program, University of Pittsburgh, Pittsburgh, USA.
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Luz-Escamilla L, Morales-González JA. Association between Interictal Epileptiform Discharges and Autistic Spectrum Disorder. Brain Sci 2019; 9:brainsci9080185. [PMID: 31366163 PMCID: PMC6721430 DOI: 10.3390/brainsci9080185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
It has been reported that bioelectric alterations in an electroencephalogram (EEG) may play an etiological role in neurodevelopmental disorders. The clinical impact of interictal epileptiform discharges (IEDs) in association with autistic spectrum disorder (ASD) is unknown. The Autism Diagnostic Interview-Revised (ADI-R) is one of the gold standards for the diagnosis of autistic spectrum disorder. Some studies have indicated high comorbidity of IED and ASD, while other studies have not supported an association between the central symptoms of autism and IED. This review examines the high comorbidity and clinical impact of IED; patients with epilepsy are excluded from the scope of this review. ASD can be disabling and is diagnosed at an average age of 5 years old, at which point the greatest neurological development has occurred. If an association between IED and ASD is identified, a clinical tool that entails an innocuous procedure could enable diagnosis in the first years of life. However, in the absence of reports that prove an association between IED and ASD, patients should not be subjected to expensive treatments, such as the administration of anticonvulsant therapies.
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Affiliation(s)
- Laura Luz-Escamilla
- Laboratorio de Medicina de Conservación y Maestría en Ciencias de la Salud, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo CP 11340, México.
- Departamento de Higiene Mental, Hospital General Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Distrito Federal CP 02990, México.
| | - José Antonio Morales-González
- Laboratorio de Medicina de Conservación y Maestría en Ciencias de la Salud, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo CP 11340, México.
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Kirino E. Efficacy and tolerability of pharmacotherapy options for the treatment of irritability in autistic children. CLINICAL MEDICINE INSIGHTS-PEDIATRICS 2014; 8:17-30. [PMID: 24932108 PMCID: PMC4051788 DOI: 10.4137/cmped.s8304] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 05/04/2014] [Accepted: 05/05/2014] [Indexed: 11/22/2022]
Abstract
Children with autism have a high rate of irritability and aggressive symptoms. Irritability or self-injurious behavior can result in significant harm to those affected, as well as to marked distress for their families. This paper provides a literature review regarding the efficacy and tolerability of pharmacotherapy for the treatment of irritability in autistic children. Although antipsychotics have not yet been approved for the treatment of autistic children by many countries, they are often used to reduce symptoms of behavioral problems, including irritability, aggression, hyperactivity, and panic. However, among antipsychotics, the Food and Drug Administration has approved only risperidone and aripiprazole to treat irritability in autism. Among atypical antipsychotics, olanzapine and quetiapine are limited in their use for autism spectrum disorders in children because of high incidences of weight gain and sedation. In comparison, aripiprazole and ziprasidone cause less weight gain and sedation. However, potential QTc interval prolongation with ziprasidone has been reported. Contrary to ziprasidone, no changes were evident in the QT interval in any of the trials for aripiprazole. However, head-to-head comparison studies are needed to support that aripiprazole may be a promising drug that can be used to treat irritability in autistic children. On the other hand, risperidone has the greatest amount of evidence supporting it, including randomized controlled trials; thus, its efficacy and tolerability has been established in comparison with other agents. Further studies with risperidone as a control drug are needed.
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Affiliation(s)
- Eiji Kirino
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan. ; Department of Psychiatry, Juntendo University Shizuoka Hospital, Shizuoka, Japan. ; Juntendo Institute of Mental Health, Saitama Japan
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Smith RM, Banks W, Hansen E, Sadee W, Herman GE. Family-based clinical associations and functional characterization of the serotonin 2A receptor gene (HTR2A) in autism spectrum disorder. Autism Res 2014; 7:459-67. [PMID: 24753316 DOI: 10.1002/aur.1383] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 03/24/2014] [Indexed: 01/03/2023]
Abstract
The serotonin 2A receptor gene (HTR2A) harbors two functional single nucleotide polymorphisms (SNPs) that are frequent in populations of African and European descent; rs6311, which affects mRNA expression, and rs6314, which changes the amino acid sequence of the encoded protein and affects the signaling properties of the receptor. Multiple clinical associations support a role for these SNPs in cognitive and neuropsychiatric phenotypes, although studies in autism spectrum disorder (ASD) remain equivocal. Here, we tested transmission disequilibrium of rs6311 and rs6314 in a cohort of 158 ASD trios (simplex and multiplex), observing significant under-transmission of the minor "A" allele of rs6311 to offspring with ASD (permuted P = 0.0004). Consistent with our previous findings in the dorsolateral prefrontal cortex of unaffected individuals, rs6311/A decreases expression of HTR2A mRNA with an extended 5' untranslated region (UTR) in the frontopolar cortex in brain samples from 54 ASD patients and controls. Interpreting the clinical results in the context of our mRNA expression analysis, we speculate that any risk associated with rs6311 is conferred by greater expression of the long 5'UTR mRNA isoform. The current study corroborates earlier associations between rs6311 and ASD in a family study, supporting the hypothesis that rs6311 plays a modulatory role in ASD risk.
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Affiliation(s)
- Ryan M Smith
- Department of Pharmacology, OSU College of Medicine Center for Pharmacogenomics, The Ohio State University, Columbus, Ohio
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McKinney C, Renk K. Atypical antipsychotic medications in the management of disruptive behaviors in children: Safety guidelines and recommendations. Clin Psychol Rev 2011; 31:465-71. [DOI: 10.1016/j.cpr.2010.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 11/04/2010] [Accepted: 11/10/2010] [Indexed: 11/30/2022]
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Abstract
Autism (ie, the autism spectrum disorders) is now recognized in 1 in 150 children. This article highlights the definition, neurobiology, screening, and diagnosis of autism. The genetics, immunology, imaging, and neurophysiology of autism are reviewed, with particular emphasis on areas that impact pediatricians. Early recognition of the social deficits that characterize autism is key to maximizing the potential of these children.
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Affiliation(s)
- Isabelle Rapin
- Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA.
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Abstract
Autism spectrum disorder is a spectrum of neurodevelopmental disorders that includes autistic disorder and pervasive developmental disorder-not otherwise specified. This article provides the reader with an overview of the major psychosocial issues related to adolescents with autism. This discussion is followed by an interjection of medications that may be useful in maximizing the functioning of adolescents with autism.
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Affiliation(s)
- Amit M Deokar
- Division of Adolescent Medicine, Department of Pediatrics, University of Kentucky, Lexington, KY 40536, USA
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