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Xu C, Bao S, Wang Y, Li W, Chen H, Shen Y, Jiang T, Zhang C. Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome Res 2024; 34:1052-1065. [PMID: 39060028 PMCID: PMC11368187 DOI: 10.1101/gr.279044.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods on various prediction tasks, including evolutionary sequence divergence on lineage-specific splicing and splicing-altering mutations in human populations and neurodevelopmental disorders, and demonstrated that DeltaSplice outperformed consistently. DeltaSplice predicted ∼15% of splicing quantitative trait loci (sQTLs) in the human brain as causal splicing-altering variants. It also predicted splicing-altering de novo mutations outside the splice sites in a subset of patients affected by autism and other neurodevelopmental disorders (NDDs), including 19 genes with recurrent splicing-altering mutations. Integration of splicing-altering mutations with other types of de novo mutation burdens allowed the prediction of eight novel NDD-risk genes. Our work expanded the capacity of in silico splicing models with potential applications in genetic diagnosis and the development of splicing-based precision medicine.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Suying Bao
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Ye Wang
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Wenxing Li
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Tao Jiang
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China;
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, New York 10032, USA;
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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2
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Denisova K. Neurobiology of cognitive abilities in early childhood autism. JCPP ADVANCES 2024; 4:e12214. [PMID: 38827984 PMCID: PMC11143961 DOI: 10.1002/jcv2.12214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/12/2023] [Indexed: 06/05/2024] Open
Abstract
This perspective considers complexities in the relationship between impaired cognitive abilities and autism from a maturational, developmental perspective, and aims to serve as a helpful guide for the complex and growing investigation of cognitive abilities and Autism Spectrum Disorder (ASD). Low Intelligence Quotient (IQ) and ASD are frequently co-occurring. About 37% of 8-year old children and 48% of 4-year old children diagnosed with ASD also have Intellectual Disability, with IQ below 70. And, low IQ in early infancy, including below 1 year of age, carries a 40% greater chance of receiving ASD diagnosis in early childhood. We consider the evidence that may explain this co-occurrence, including the possibility that high IQ may "rescue" the social communication issues, as well as the possible role of critical periods during growth and development. We consider how early low IQ may subsume a part of a subgroup of individuals with ASD, in particular, those diagnosed with autism in very early childhood, and we provide neurobiological evidence in support of this subtype. Moreover, we distinguish the concept of early low IQ from the delay in speech onset in preschool and school-aged children, based on (i) age and (ii) impairments in both verbal and non-verbal domains. The etiology of these early-diagnosed, early low IQ ASD cases is different from later-diagnosed, average or higher-IQ cases, and from children with speech delay onset. Given recent interest in formulating new subtypes of autism, rather than continuing to conceive of ASD as a spectrum, as well as new subtypes that vary in the degree of severity along the spectrum, we identify gaps in knowledge and directions for future work in this complex and growing area.
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Affiliation(s)
- Kristina Denisova
- Division of Math and Natural SciencesDepartment of PsychologyAutism Origins LabCity University of New YorkQueens College and Graduate CenterQueensNew YorkUSA
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3
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Menteşe Babayiğit T, Gümüş-Akay G, Uytun MÇ, Doğan Ö, Serdar MA, Efendi GY, Erman AG, Yürümez E, Öztop DB. Investigation of Liver X Receptor Gene Variants and Oxysterol Dysregulation in Autism Spectrum Disorder. CHILDREN (BASEL, SWITZERLAND) 2024; 11:551. [PMID: 38790546 PMCID: PMC11120122 DOI: 10.3390/children11050551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024]
Abstract
The NR1H2 gene produces the Liver X Receptor Beta (LXRB) protein, which is crucial for brain cholesterol metabolism and neuronal development. However, its involvement in autism spectrum disorder (ASD) remains largely unexplored, aside from animal studies. This study is the first to explore the potential link between autism and rs2695121/rs17373080 single nucleotide polymorphisms (SNPs) in the regulatory regions of NR1H2, known for their association with neuropsychiatric functions. Additionally, we assessed levels of oxysterols (24-Hydroxycholesterol, 25-Hydroxycholesterol, 27-Hydroxycholesterol), crucial ligands of LXR, and lipid profiles. Our cohort comprised 107 children with ASD and 103 healthy children aged 2-18 years. Clinical assessment tools included the Childhood Autism Rating Scale, Autistic Behavior Checklist, and Repetitive Behavior Scale-Revised. Genotyping for SNPs was conducted using PCR-RFLP. Lipid profiles were analyzed with Beckman Coulter kits, while oxysterol levels were determined through liquid chromatography-tandem mass spectrometry. Significantly higher total cholesterol (p = 0.003), LDL (p = 0.008), and triglyceride (p < 0.001) levels were observed in the ASD group. 27-Hydroxycholesterol levels were markedly lower in the ASD group (p ≤ 0.001). ROC analysis indicated the potential of 27-Hydroxycholesterol to discriminate ASD diagnosis. The SNP genotype and allele frequencies were similar in both groups (p > 0.05). Our findings suggest that disturbances in oxysterol metabolism, previously linked to neurodegeneration, may constitute a risk factor for ASD and contribute to its heterogeneous phenotype.
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Affiliation(s)
- Tuğba Menteşe Babayiğit
- Department of Child and Adolescent Psychiatry, Aksaray University School of Medicine Training and Research Hospital, Aksaray 68100, Turkey
| | - Güvem Gümüş-Akay
- Department of Physiology, Ankara University School of Medicine, Ankara 06100, Turkey;
- Brain Research Center (AUBAUM), Ankara University, Ankara 06340, Turkey
- Neuroscience and Neurotechnology Center of Excellence (NÖROM), Ankara University, Ankara 06560, Turkey
| | - Merve Çikili Uytun
- Department of Child and Adolescent Psychiatry, Ankara University School of Medicine, Ankara 06100, Turkey; (M.Ç.U.); (E.Y.); (D.B.Ö.)
| | - Özlem Doğan
- Department of Biochemistry, Ankara University School of Medicine, Ankara 06100, Turkey;
| | - Muhittin A. Serdar
- Department of Medical Biochemistry, Acıbadem University School of Medicine, Ankara 06460, Turkey;
| | - Gökçe Yağmur Efendi
- Department of Child and Adolescent Psychiatry, Kocaeli University School of Medicine, Kocaeli 41001, Turkey;
| | - Ayşe Gökçe Erman
- Department of Basic Biotechnology, Ankara University Institute of Biotechnology, Ankara 06135, Turkey;
| | - Esra Yürümez
- Department of Child and Adolescent Psychiatry, Ankara University School of Medicine, Ankara 06100, Turkey; (M.Ç.U.); (E.Y.); (D.B.Ö.)
| | - Didem Behice Öztop
- Department of Child and Adolescent Psychiatry, Ankara University School of Medicine, Ankara 06100, Turkey; (M.Ç.U.); (E.Y.); (D.B.Ö.)
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4
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Xu C, Bao S, Chen H, Jiang T, Zhang C. Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586363. [PMID: 38586002 PMCID: PMC10996483 DOI: 10.1101/2024.03.22.586363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods on various prediction tasks, including evolutionary sequence divergence on lineage-specific splicing and splicing-altering mutations in human populations and neurodevelopmental disorders, and demonstrated that DeltaSplice outperformed consistently. DeltaSplice predicted ~15% of splicing quantitative trait loci (sQTLs) in the human brain as causal splicing-altering variants. It also predicted splicing-altering de novo mutations outside the splice sites in a subset of patients affected by autism and other neurodevelopmental disorders, including 19 genes with recurrent splicing-altering mutations. Among the new candidate disease risk genes, MFN1 is involved in mitochondria fusion, which is frequently disrupted in autism patients. Our work expanded the capacity of in silico splicing models with potential applications in genetic diagnosis and the development of splicing-based precision medicine.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
- Present address: Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Suying Bao
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Present address: Regeneron Pharmaceuticals, Terrytown, NY 10591, USA
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
- Present address: Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tao Jiang
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
- Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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5
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Chen GT, Nair G, Osorio AJ, Holley SM, Ghassemzadeh K, Gonzalez J, Lu C, Sanjana NE, Cepeda C, Geschwind DH. Enhancer-targeted CRISPR-Activation Rescues Haploinsufficient Autism Susceptibility Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584921. [PMID: 38559217 PMCID: PMC10980046 DOI: 10.1101/2024.03.13.584921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Autism Spectrum Disorder (ASD) is a highly heritable condition with diverse clinical presentations. Approximately 20% of ASD's genetic susceptibility is imparted by de novo mutations of major effect, most of which cause haploinsufficiency. We mapped enhancers of two high confidence autism genes - CHD8 and SCN2A and used CRISPR-based gene activation (CRISPR-A) in hPSC-derived excitatory neurons and cerebral forebrain organoids to correct the effects of haploinsufficiency, taking advantage of the presence of a wildtype allele of each gene and endogenous gene regulation. We found that CRISPR-A induced a sustained increase in CHD8 and SCN2A expression in treated neurons and organoids, with rescue of gene expression levels and mutation-associated phenotypes, including gene expression and physiology. These data support gene activation via targeting enhancers of haploinsufficient genes, as a therapeutic intervention in ASD and other neurodevelopmental disorders.
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Wang X, Ling Z, Luo T, Zhou Q, Zhao G, Li B, Xia K, Li J. Severity of Autism Spectrum Disorder Symptoms Associated with de novo Variants and Pregnancy-Induced Hypertension. J Autism Dev Disord 2024; 54:749-764. [PMID: 36445517 DOI: 10.1007/s10803-022-05824-4] [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] [Accepted: 11/10/2022] [Indexed: 11/30/2022]
Abstract
Genetic factors, particularly, de novo variants (DNV), and an environment factor, exposure to pregnancy-induced hypertension (PIH), were reported to be associated with risk of autism spectrum disorder (ASD); however, how they jointly affect the severity of ASD symptom is unclear. We assessed the severity of core ASD symptoms affected by functional de novo variants or PIH. We selected phenotype data from Simon's Simplex Collection database, used genotypes from previous studies, and created linear regression models. We found that ASD patients carrying DNV with PIH exposure had increased adaptive and cognitive ability, decreased social problems, and enhanced repetitive behaviors; however, there was no difference in patients without DNV between those with or without PIH exposure. In addition, the DNV genes carried by patients exposed to PIH were enriched in ubiquitin-dependent proteolytic processes, highlighting how candidate genes in pathways and environments interact. The results indicate the joint contribution of DNV and PIH to ASD.
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Affiliation(s)
- Xiaomeng Wang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 41008, Hunan, China
- Centre for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 41008, Hunan, China
| | - Zhengbao Ling
- Centre for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 41008, Hunan, China
| | - Tengfei Luo
- Centre for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 41008, Hunan, China
| | - Qiao Zhou
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 41008, Hunan, China
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 41008, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Li
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 41008, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Centre for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 41008, Hunan, China.
- University of South China, Hengyang, Hunan, China.
| | - Jinchen Li
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 41008, Hunan, China.
- Centre for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 41008, Hunan, China.
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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7
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Lima MO, Saraiva LC, Ramos VR, Oliveira MC, Costa DLC, Fernandez TV, Crowley JJ, Storch EA, Shavitt RG, Miguel EC, Cappi C. Clinical characteristics of probands with obsessive-compulsive disorder from simplex and multiplex families. Psychiatry Res 2024; 331:115627. [PMID: 38113811 PMCID: PMC11129832 DOI: 10.1016/j.psychres.2023.115627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023]
Abstract
Genetic and non-genetic factors contribute to obsessive-compulsive disorder (OCD), with strong evidence of familial clustering. Genomic studies in psychiatry have used the concepts of families that are "simplex" (one affected) versus "multiplex" (multiple affected). Our study compares demographic and clinical data from OCD probands in simplex and multiplex families to uncover potential differences. We analyzed 994 OCD probands (501 multiplex, 493 simplex) from the Brazilian Research Consortium on Obsessive-Compulsive Spectrum Disorders (C-TOC). Clinicians administered the Structured Clinical Interview for DSM-IV (SCID-IV) to diagnose, Yale-Brown Obsessive-Compulsive Scale (Y-BOCS) to assess severity, and Dimensional Yale-Brown Obsessive-Compulsive Scale (DY-BOCS) to assess symptom dimensionality. Demographics, clinical history, and family data were collected. Compared to simplex probands, multiplex probands had earlier onset, higher sexual/religious and hoarding dimensions severity, increased comorbidity with other obsessive-compulsive-related disorders (OCRD), and higher family history of psychiatric disorders. These comparisons provide the first insights into demographic and clinical differences between Latin American simplex and multiplex families with OCD. Distinct clinical patterns may suggest diverse genetic and environmental influences. Further research is needed to clarify these differences, which have implications for symptom monitoring and management.
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Affiliation(s)
- Monicke O Lima
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil
| | - Leonardo C Saraiva
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil
| | - Vanessa R Ramos
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil
| | - Melaine C Oliveira
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil
| | - Daniel L C Costa
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil
| | - Thomas V Fernandez
- Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - James J Crowley
- Departments of Genetics and Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric A Storch
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Roseli G Shavitt
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil
| | - Euripedes C Miguel
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil
| | - Carolina Cappi
- Department & Institute of Psychiatry, Faculdade de Medicina, Hospital das Clinicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo (SP), Brazil; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy, New York, NY, USA.
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Cho CH, Deyneko IV, Cordova-Martinez D, Vazquez J, Maguire AS, Diaz JR, Carbonell AU, Tindi JO, Cui MH, Fleysher R, Molholm S, Lipton ML, Branch CA, Hodgson L, Jordan BA. ANKS1B encoded AIDA-1 regulates social behaviors by controlling oligodendrocyte function. Nat Commun 2023; 14:8499. [PMID: 38129387 PMCID: PMC10739966 DOI: 10.1038/s41467-023-43438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
Heterozygous deletions in the ANKS1B gene cause ANKS1B neurodevelopmental syndrome (ANDS), a rare genetic disease characterized by autism spectrum disorder (ASD), attention deficit/hyperactivity disorder, and speech and motor deficits. The ANKS1B gene encodes for AIDA-1, a protein that is enriched at neuronal synapses and regulates synaptic plasticity. Here we report an unexpected role for oligodendroglial deficits in ANDS pathophysiology. We show that Anks1b-deficient mouse models display deficits in oligodendrocyte maturation, myelination, and Rac1 function, and recapitulate white matter abnormalities observed in ANDS patients. Selective loss of Anks1b from the oligodendrocyte lineage, but not from neuronal populations, leads to deficits in social preference and sensory reactivity previously observed in a brain-wide Anks1b haploinsufficiency model. Furthermore, we find that clemastine, an antihistamine shown to increase oligodendrocyte precursor cell maturation and central nervous system myelination, rescues deficits in social preference in 7-month-old Anks1b-deficient mice. Our work shows that deficits in social behaviors present in ANDS may originate from abnormal Rac1 activity within oligodendrocytes.
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Affiliation(s)
- Chang Hoon Cho
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Human Pathobiology and OMNI Reverse Translation, Genentech, Inc., San Francisco, CA, USA
| | - Ilana Vasilisa Deyneko
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Dylann Cordova-Martinez
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Juan Vazquez
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anne S Maguire
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jenny R Diaz
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Abigail U Carbonell
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jaafar O Tindi
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Min-Hui Cui
- Department of Radiology, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Roman Fleysher
- Department of Radiology, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sophie Molholm
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michael L Lipton
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Radiology, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Craig A Branch
- Department of Radiology, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Louis Hodgson
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA.
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Rahim F, Toguzbaeva K, Qasim NH, Dzhusupov KO, Zhumagaliuly A, Khozhamkul R. Probiotics, prebiotics, and synbiotics for patients with autism spectrum disorder: a meta-analysis and umbrella review. Front Nutr 2023; 10:1294089. [PMID: 38148790 PMCID: PMC10750421 DOI: 10.3389/fnut.2023.1294089] [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: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023] Open
Abstract
Background and objective The potential impact of gut health on general physical and mental well-being, particularly in relation to brain function, has led to a growing interest in the potential health advantages of prebiotics, probiotics, and synbiotics for the management of ASD. A comprehensive meta-analysis and systematic review was conducted in order to evaluate the effectiveness and protection of many drugs targeted at manipulating the microbiota in the treatment of ASD. Methods The present study employed a comprehensive examination of various electronic databases yielded a total of 3,393 records that were deemed possibly pertinent to the study. RCTs encompassed a total of 720 individuals between the ages of 2 and 17, as well as 112 adults and participants ranging from 5 to 55 years old, all of whom had received a diagnosis of ASD. Results Overall, 10 studies reported Autism-Related Behavioral Symptoms (ARBS). Regarding the enhancement of autism-related behavioral symptoms, there wasn't a statistically significant difference between the intervention groups (combined standardized mean difference = -0.07, 95% confidence interval: -0.39 to 0.24, Z = 0.46, p = 0.65). We observed that in the patients with ASD treated with probiotic frontopolar's power decreased significantly from baseline to endpoints in beta band (Baseline: 13.09 ± 3.46, vs. endpoint: 10.75 ± 2.42, p = 0.043, respectively) and gamma band (Baseline: 5.80 ± 2.42, vs. endpoint: 4.63 ± 1.39, p = 0.033, respectively). Among all tested biochemical measures, a significant negative correlation was found between frontopolar coherence in the gamma band and TNF-α (r = -0.30, p = 0.04). Conclusion The existing body of research provides a comprehensive analysis of the developing evidence that indicates the potential of probiotics, prebiotics, and synbiotics as therapeutic therapies for ASD. Our findings revealed that those there was no significant effect of such therapy on autism-related behavioral symptoms, it has significant effect on the brain connectivity through frontopolar power in beta and gamma bands mediated by chemicals and cytokines, such as TNF-α. The psychobiotics showed no serious side-effects.
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Affiliation(s)
- Fakher Rahim
- College of Health Sciences, Cihan University Sulaimaniya, Sulaymaniyah, Iraq
| | - Karlygash Toguzbaeva
- School of Public Health, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Nameer Hashim Qasim
- Cihan University Sulaimaniya Research Center (CUSRC), Cihan University – Sulaimaniya, Kurdistan Region, Suleymania, Iraq
| | - Kenesh O. Dzhusupov
- Head of Public Health Department, International Higher School of Medicine, Bishkek, Kyrgyzstan
| | - Abzal Zhumagaliuly
- School of Public Health, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Rabiga Khozhamkul
- Department of Biostatistics and Basics of Research, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
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10
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Matrone C, Ferretti G. Semaphorin 3A influences neuronal processes that are altered in patients with autism spectrum disorder: Potential diagnostic and therapeutic implications. Neurosci Biobehav Rev 2023; 153:105338. [PMID: 37524141 DOI: 10.1016/j.neubiorev.2023.105338] [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: 02/16/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Autism spectrum disorder (ASD) is a pervasive disorder that most frequently manifests in early childhood and lasts for their entire lifespan. Several behavioural traits characterise the phenotype of patients with ASD, including difficulties in reciprocal social communication as well as compulsive/repetitive stereotyped verbal and non-verbal behaviours. Although multiple hypotheses have been proposed to explain the aetiology of ASD and many resources have been used to improve our understanding of ASD, several aspects remain largely unexplored. Class 3 semaphorins (SEMA3) are secreted proteins involved in the organisation of structural and functional connectivity in the brain that regulate synaptic and dendritic development. Alterations in brain connectivity and aberrant neuronal development have been described in some patients with ASD. Mutations and polymorphisms in SEMA3A and alterations in its receptors and signalling have been associated with some neurological disorders such as schizophrenia and epilepsy, which are comorbidities in ASD, but also with ASD itself. In addition, SEMA3A is a key regulator of the immune response and neuroinflammatory processes, which have been found to be dysregulated in mothers of children who develop ASD and in affected patients. In this review, we highlight neurodevelopmental-related processes in which SEMA3A is involved, which are altered in ASD, and provide a viewpoint emphasising the development of strategies targeting changes in the SEMA3A signal to identify patterns of anomalies distinctive of ASD or to predict the prognosis of affected patients.
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Affiliation(s)
- Carmela Matrone
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy.
| | - Gabriella Ferretti
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy
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11
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Watanabe R, Nakachi Y, Matsubara H, Ueda J, Ishii T, Ukai W, Hashimoto E, Kasai K, Simizu S, Kato T, Bundo M, Iwamoto K. Identification of epigenetically active L1 promoters in the human brain and their relationship with psychiatric disorders. Neurosci Res 2023; 195:37-51. [PMID: 37141946 DOI: 10.1016/j.neures.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/09/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
Long interspersed nuclear element-1 (LINE-1, L1) affects the transcriptome landscape in multiple ways. Promoter activity within its 5'UTR plays a critical role in regulating diverse L1 activities. However, the epigenetic status of L1 promoters in adult brain cells and their relationship with psychiatric disorders remain poorly understood. Here, we examined DNA methylation and hydroxymethylation of the full-length L1s in neurons and nonneurons and identified "epigenetically active" L1s. Notably, some of epigenetically active L1s were retrotransposition competent, which even had chimeric transcripts from the antisense promoters at their 5'UTRs. We also identified differentially methylated L1s in the prefrontal cortices of patients with psychiatric disorders. In nonneurons of bipolar disorder patients, one L1 was significantly hypomethylated and showed an inverse correlation with the expression level of the overlapping gene NREP. Finally, we observed that altered DNA methylation levels of L1 in patients with psychiatric disorders were not affected by the surrounding genomic regions but originated from the L1 sequences. These results suggested that altered epigenetic regulation of the L1 5'UTR in the brain was involved in the pathophysiology of psychiatric disorders.
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Affiliation(s)
- Risa Watanabe
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hikari Matsubara
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takao Ishii
- Department of Occupational Therapy, Sapporo Medical University School of Health Sciences, Sapporo, Japan
| | - Wataru Ukai
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Eri Hashimoto
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan; University of Tokyo Institute for Diversity and Adaptation of Human Mind (UTIDAHM), The University of Tokyo, Tokyo, Japan; UTokyo Center for Integrative Science of Human Behaviour (CiSHuB), The University of Tokyo, Tokyo, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
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12
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Cirnigliaro M, Chang TS, Arteaga SA, Pérez-Cano L, Ruzzo EK, Gordon A, Bicks LK, Jung JY, Lowe JK, Wall DP, Geschwind DH. The contributions of rare inherited and polygenic risk to ASD in multiplex families. Proc Natl Acad Sci U S A 2023; 120:e2215632120. [PMID: 37506195 PMCID: PMC10400943 DOI: 10.1073/pnas.2215632120] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
Autism spectrum disorder (ASD) has a complex genetic architecture involving contributions from both de novo and inherited variation. Few studies have been designed to address the role of rare inherited variation or its interaction with common polygenic risk in ASD. Here, we performed whole-genome sequencing of the largest cohort of multiplex families to date, consisting of 4,551 individuals in 1,004 families having two or more autistic children. Using this study design, we identify seven previously unrecognized ASD risk genes supported by a majority of rare inherited variants, finding support for a total of 74 genes in our cohort and a total of 152 genes after combined analysis with other studies. Autistic children from multiplex families demonstrate an increased burden of rare inherited protein-truncating variants in known ASD risk genes. We also find that ASD polygenic score (PGS) is overtransmitted from nonautistic parents to autistic children who also harbor rare inherited variants, consistent with combinatorial effects in the offspring, which may explain the reduced penetrance of these rare variants in parents. We also observe that in addition to social dysfunction, language delay is associated with ASD PGS overtransmission. These results are consistent with an additive complex genetic risk architecture of ASD involving rare and common variation and further suggest that language delay is a core biological feature of ASD.
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Affiliation(s)
- Matilde Cirnigliaro
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Timothy S. Chang
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Stephanie A. Arteaga
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Laura Pérez-Cano
- STALICLA Discovery and Data Science Unit, World Trade Center, Barcelona08039, Spain
| | - Elizabeth K. Ruzzo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Aaron Gordon
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Lucy K. Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Jae-Yoon Jung
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Jennifer K. Lowe
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Dennis P. Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Daniel H. Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
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13
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Noel JP, Angelaki DE. A theory of autism bridging across levels of description. Trends Cogn Sci 2023; 27:631-641. [PMID: 37183143 PMCID: PMC10330321 DOI: 10.1016/j.tics.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/16/2023]
Abstract
Autism impacts a wide range of behaviors and neural functions. As such, theories of autism spectrum disorder (ASD) are numerous and span different levels of description, from neurocognitive to molecular. We propose how existent behavioral, computational, algorithmic, and neural accounts of ASD may relate to one another. Specifically, we argue that ASD may be cast as a disorder of causal inference (computational level). This computation relies on marginalization, which is thought to be subserved by divisive normalization (algorithmic level). In turn, divisive normalization may be impaired by excitatory-to-inhibitory imbalances (neural implementation level). We also discuss ASD within similar frameworks, those of predictive coding and circular inference. Together, we hope to motivate work unifying the different accounts of ASD.
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Affiliation(s)
- Jean-Paul Noel
- Center for Neural Science, New York University, New York, NY, USA.
| | - Dora E Angelaki
- Center for Neural Science, New York University, New York, NY, USA; Tandon School of Engineering, New York University, New York, NY, USA
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14
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Gandhi T, Canepa CR, Adeyelu TT, Adeniyi PA, Lee CC. Neuroanatomical Alterations in the CNTNAP2 Mouse Model of Autism Spectrum Disorder. Brain Sci 2023; 13:891. [PMID: 37371370 DOI: 10.3390/brainsci13060891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Autism spectrum disorder (ASD) is associated with neurodevelopmental alterations, including atypical forebrain cellular organization. Mutations in several ASD-related genes often result in cerebral cortical anomalies, such as the abnormal developmental migration of excitatory pyramidal cells and the malformation of inhibitory neuronal circuitry. Notably here, mutations in the CNTNAP2 gene result in ectopic superficial cortical neurons stalled in lower cortical layers and alterations to the balance of cortical excitation and inhibition. However, the broader circuit-level implications of these findings have not been previously investigated. Therefore, we assessed whether ectopic cortical neurons in CNTNAP2 mutant mice form aberrant connections with higher-order thalamic nuclei, potentially accounting for some autistic behaviors, such as repetitive and hyperactive behaviors. Furthermore, we assessed whether the development of parvalbumin-positive (PV) cortical interneurons and their specialized matrix support structures, called perineuronal nets (PNNs), were altered in these mutant mice. We found alterations in both ectopic neuronal connectivity and in the development of PNNs, PV neurons and PNNs enwrapping PV neurons in various sensory cortical regions and at different postnatal ages in the CNTNAP2 mutant mice, which likely lead to some of the cortical excitation/inhibition (E/I) imbalance associated with ASD. These findings suggest neuroanatomical alterations in cortical regions that underlie the emergence of ASD-related behaviors in this mouse model of the disorder.
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Affiliation(s)
- Tanya Gandhi
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Cade R Canepa
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Tolulope T Adeyelu
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Philip A Adeniyi
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Charles C Lee
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70806, USA
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15
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Carbonell AU, Freire-Cobo C, Deyneko IV, Dobariya S, Erdjument-Bromage H, Clipperton-Allen AE, Page DT, Neubert TA, Jordan BA. Comparing synaptic proteomes across five mouse models for autism reveals converging molecular similarities including deficits in oxidative phosphorylation and Rho GTPase signaling. Front Aging Neurosci 2023; 15:1152562. [PMID: 37255534 PMCID: PMC10225639 DOI: 10.3389/fnagi.2023.1152562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
Specific and effective treatments for autism spectrum disorder (ASD) are lacking due to a poor understanding of disease mechanisms. Here we test the idea that similarities between diverse ASD mouse models are caused by deficits in common molecular pathways at neuronal synapses. To do this, we leverage the availability of multiple genetic models of ASD that exhibit shared synaptic and behavioral deficits and use quantitative mass spectrometry with isobaric tandem mass tagging (TMT) to compare their hippocampal synaptic proteomes. Comparative analyses of mouse models for Fragile X syndrome (Fmr1 knockout), cortical dysplasia focal epilepsy syndrome (Cntnap2 knockout), PTEN hamartoma tumor syndrome (Pten haploinsufficiency), ANKS1B syndrome (Anks1b haploinsufficiency), and idiopathic autism (BTBR+) revealed several common altered cellular and molecular pathways at the synapse, including changes in oxidative phosphorylation, and Rho family small GTPase signaling. Functional validation of one of these aberrant pathways, Rac1 signaling, confirms that the ANKS1B model displays altered Rac1 activity counter to that observed in other models, as predicted by the bioinformatic analyses. Overall similarity analyses reveal clusters of synaptic profiles, which may form the basis for molecular subtypes that explain genetic heterogeneity in ASD despite a common clinical diagnosis. Our results suggest that ASD-linked susceptibility genes ultimately converge on common signaling pathways regulating synaptic function and propose that these points of convergence are key to understanding the pathogenesis of this disorder.
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Affiliation(s)
- Abigail U. Carbonell
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carmen Freire-Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ilana V. Deyneko
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Saunil Dobariya
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Amy E. Clipperton-Allen
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Damon T. Page
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Thomas A. Neubert
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Bryen A. Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
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16
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Mourkani RS, Kohan S, Mohebbi-Dehnavi Z, Shaghaghi F, Najiabhary M, Gholami M. Comparative study of the relationship between pregnancy and childbirth factors and autism in healthy children and children with autism. JOURNAL OF EDUCATION AND HEALTH PROMOTION 2023; 12:135. [PMID: 37397101 PMCID: PMC10312421 DOI: 10.4103/jehp.jehp_36_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 07/26/2022] [Indexed: 07/04/2023]
Abstract
BACKGROUND Autism is a group of developmental disorders of the nervous system, the main manifestations of which are defects in social interactions and communication, as well as repetitive behaviors and limited interests. The etiology of autism is not limited to a single factor. Therefore, the aim of this study was to compare the relationship between pregnancy and childbirth factors and autism in healthy children and children with autism. MATERIALS AND METHODS The present study was a cross-sectional study that was performed on 200 children in Isfahan in 2021. The instrument in this study was a researcher-made questionnaire. The collected data were analyzed using the Statistical Package for the Social Sciences (SPSS) version 22 software. RESULTS The results of data analysis between the two groups with Mann-Whitney U test showed that there was a significant relationship between maternal age at delivery, father's age at delivery, gestational age at delivery, interval between pregnancies, and the length of hospital stay (P ≤ 0.05). Also, the results of data analysis with Chi-squared test showed that there is a significant relationship between the two groups in terms of economic status, place of residence, multiple pregnancies, neonatal sex, and disease in infancy (P ≤ 0.05). CONCLUSION The results of this study showed that economic status, place of residence, multiple pregnancies, sex of the baby, and disease in infancy can be effective factors for this disease. According to the results of the study, by considering the factors related to autism, many cases can be adjusted and corrected as much as possible before attempting to conceive.
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Affiliation(s)
- Razieh Shams Mourkani
- M.Sc. of Midwifery, Student Research Committee, School of Nursing and Midwifery, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shahnaz Kohan
- Department of Midwifery and Reproductive Health, School of Nursing and Midwifery, Nursing and Midwifery Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Mohebbi-Dehnavi
- PhD Candidate in Reproductive Health, Department of Midwifery and Reproductive Health, School of Nursing and Midwifery, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Shaghaghi
- Phd Candidate of Sexual and Reproductive Health, Department of Reproductive Health and Midwifery, School of Nursing and Midwifery, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Najiabhary
- MSc of Counseling in Midwifery, Department of Midwifery, School of Nursing and Midwifery, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobe Gholami
- Assistant Professor, Department of Midwifery, Neyshabur University of Medical Sciences, Neyshabur, Iran
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17
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He X, Liu W, Tang F, Chen X, Song G. Effects of Probiotics on Autism Spectrum Disorder in Children: A Systematic Review and Meta-Analysis of Clinical Trials. Nutrients 2023; 15:nu15061415. [PMID: 36986145 PMCID: PMC10054498 DOI: 10.3390/nu15061415] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
Many studies have explored the efficacy of probiotics on autism spectrum disorder (ASD) in children, but there is no consensus on the curative effect. This systematic review and meta-analysis aimed to comprehensively investigate whether probiotics could improve behavioral symptoms in children with ASD. A systematic database search was conducted and a total of seven studies were included in the meta-analysis. We found a nonsignificant overall effect size of probiotics on behavioral symptoms in children with ASD (SMD = −0.24, 95% CI: −0.60 to 0.11, p = 0.18). However, a significant overall effect size was found in the subgroup of the probiotic blend (SMD = −0.42, 95% CI: −0.83 to −0.02, p = 0.04). Additionally, these studies provided limited evidence for the efficacy of probiotics due to their small sample sizes, a shorter intervention duration, different probiotics used, different scales used, and poor research quality. Thus, randomized, double-blind, and placebo-controlled studies following strict trial guidelines are needed to precisely demonstrate the therapeutic effects of probiotics on ASD in children.
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Affiliation(s)
- Xiao He
- Department of Health Statistics, School of Public Health, Dalian Medical University, No. 9 South Road, Lvshun District, Dalian 116044, China; (X.H.); (W.L.); (F.T.)
| | - Wenxi Liu
- Department of Health Statistics, School of Public Health, Dalian Medical University, No. 9 South Road, Lvshun District, Dalian 116044, China; (X.H.); (W.L.); (F.T.)
| | - Fengrao Tang
- Department of Health Statistics, School of Public Health, Dalian Medical University, No. 9 South Road, Lvshun District, Dalian 116044, China; (X.H.); (W.L.); (F.T.)
| | - Xin Chen
- Department of Epidemiology, School of Public Health, Dalian Medical University, No. 9 South Road, Lvshun District, Dalian 116044, China;
| | - Guirong Song
- Department of Health Statistics, School of Public Health, Dalian Medical University, No. 9 South Road, Lvshun District, Dalian 116044, China; (X.H.); (W.L.); (F.T.)
- Correspondence:
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18
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Gandhi T, Liu CC, Adeyelu TT, Canepa CR, Lee CC. Behavioral regulation by perineuronal nets in the prefrontal cortex of the CNTNAP2 mouse model of autism spectrum disorder. Front Behav Neurosci 2023; 17:1114789. [PMID: 36998537 PMCID: PMC10043266 DOI: 10.3389/fnbeh.2023.1114789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Autism spectrum disorders (ASDs) arise from altered development of the central nervous system, and manifest behaviorally as social interaction deficits and restricted and repetitive behaviors. Alterations to parvalbumin (PV) expressing interneurons have been implicated in the neuropathological and behavioral deficits in autism. In addition, perineuronal nets (PNNs), specialized extracellular matrix structures that enwrap the PV-expressing neurons, also may be altered, which compromises neuronal function and susceptibility to oxidative stress. In particular, the prefrontal cortex (PFC), which regulates several core autistic traits, relies on the normal organization of PNNs and PV-expressing cells, as well as other neural circuit elements. Consequently, we investigated whether PNNs and PV-expressing cells were altered in the PFC of the CNTNAP2 knockout mouse model of ASD and whether these contributed to core autistic-like behaviors in this model system. We observed an overexpression of PNNs, PV-expressing cells, and PNNs enwrapping PV-expressing cells in adult CNTNAP2 mice. Transient digestion of PNNs from the prefrontal cortex (PFC) by injection of chondroitinase ABC in CNTNAP2 mutant mice rescued some of the social interaction deficits, but not the restricted and repetitive behaviors. These findings suggest that the neurobiological regulation of PNNs and PVs in the PFC contribute to social interaction behaviors in neurological disorders including autism.
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Affiliation(s)
- Tanya Gandhi
- Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Chin-Chi Liu
- Department of Veterinary Clinical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Tolulope T. Adeyelu
- Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Cade R. Canepa
- Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Charles C. Lee
- Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
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19
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Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment. J Autism Dev Disord 2023; 53:1091-1106. [PMID: 35759154 DOI: 10.1007/s10803-022-05636-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2022] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) have been implicated in autism spectrum disorder (ASD). However, our understanding of their roles is far from complete. Herein, we explored de novo TE insertions (dnTEIs) and de novo variants (DNVs) across the genomes of dizygotic twins with ASD and their parents. The neuronal regulatory elements had a tendency to harbor dnTEIs that were shared between twins, but ASD-risk genes had dnTEIs that were unique to each twin. The dnTEIs were 4.6-fold enriched in enhancers that are active in embryonic stem cell (ESC)-neurons (p < 0.001), but DNVs were 1.5-fold enriched in active enhancers of astrocytes (p = 0.0051). Our findings suggest that dnTEIs and DNVs play a role in ASD etiology by disrupting enhancers of neurons and astrocytes.
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20
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Wolstencroft J, Srinivasan R, Hall J, van den Bree MBM, Owen MJ, Raymond FL, Skuse D. Mental health impact of autism on families of children with intellectual and developmental disabilities of genetic origin. JCPP ADVANCES 2023; 3:e12128. [PMID: 37431317 PMCID: PMC10241472 DOI: 10.1002/jcv2.12128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/10/2022] [Indexed: 01/15/2023] Open
Abstract
Background Many children with an intellectual or developmental disability (IDD) have associated autism spectrum disorders (ASD), as well as an increased risk of mental health difficulties. In a cohort with IDD of genetic aetiology, we tested the hypothesis that excess risk attached to those with ASD + IDD, in terms of both children's mental health and parental psychological distress. Methods Participants with a copy number variant or single nucleotide variant (5-19 years) were recruited via UK National Health Service. 1904 caregivers competed an online assessment of child mental health and reported on their own psychological wellbeing. We used regression to examine the association between IDD with and without co-occurring ASD, and co-occurring mental health difficulties, as well as with parental psychological distress. We adjusted for children's sex, developmental level, physical health, and socio-economic deprivation. Results Of the 1904 participants with IDD, 701 (36.8%) had co-occurring ASD. Children with both IDD and ASD were at higher risk of associated disorders than those with IDD alone (ADHD: OR = 1.84, 95% confidence interval [CI] 1.46-2.32, p < 0.0001; emotional disorders: OR = 1.85, 95%CI 1.36-2.5, p < 0.0001; disruptive behaviour disorders: OR = 1.79, 95%CI 1.36-2.37, p < 0.0001). The severity of associated symptoms was also greater in those with ASD (hyperactivity: B = 0.25, 95%CI 0.07-0.34, p = 0.006; emotional difficulties: B = 0.91, 95%CI 0.67 to 1.14, p < 0.0001; conduct problems: B = 0.25, 95%CI 0.05 to 0.46, p = 0.013). Parents of children with IDD and ASD also reported greater psychological distress than those with IDD alone (β = 0.1, 95% CI 0.85 to 2.21, p < 0.0001). Specifically, in those with ASD, symptoms of hyperactivity (β = 0.13, 95% CI 0.29-0.63, p < 0.0001), emotional difficulties (β = 0.15, 95% CI 0.26-0.51, p < 0.0001) and conduct difficulties (β = 0.07, 95% CI 0.07-0.37, p < 0.004) all significantly contributed to parental psychological distress. Conclusions Among children with IDD of genetic aetiology, one third have co-occurring ASD. Not only do those with co-occurring ASD present with a wider range of associated mental health disorders and more severe mental health difficulties than those with IDD alone, but their parents also experience more psychological distress. Our findings suggest that the additional mental health and behavioural symptoms in those with ASD contributed to the degree of parental psychological distress.
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Affiliation(s)
- Jeanne Wolstencroft
- UCL NIHR BRC Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Ramya Srinivasan
- UCL NIHR BRC Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- UCL Division of PsychiatryUniversity College LondonLondonUK
| | - Jeremy Hall
- Medical Research Council Centre for Neuropsychiatric Genetics and GenomicsDivision of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUK
- Neuroscience and Mental Health Research InstituteCardiff UniversityCardiffUK
| | - Marianne B. M. van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and GenomicsDivision of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUK
- Neuroscience and Mental Health Research InstituteCardiff UniversityCardiffUK
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and GenomicsDivision of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUK
- Neuroscience and Mental Health Research InstituteCardiff UniversityCardiffUK
| | | | - F. Lucy Raymond
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
- Cambridge University Hospitals NHS Foundation TrustCambridge Biomedical CampusCambridgeUK
- NIHR BioresourceCambridge Biomedical CampusCambridgeUK
| | - David Skuse
- UCL NIHR BRC Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
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21
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Tabbaa M, Knoll A, Levitt P. Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency. Neuron 2023; 111:539-556.e5. [PMID: 36738737 PMCID: PMC9960295 DOI: 10.1016/j.neuron.2023.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Preclinical models of neurodevelopmental disorders typically use single inbred mouse strains, which fail to capture the genetic diversity and symptom heterogeneity that is common clinically. We tested whether modeling genetic background diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. We measured clinically relevant phenotypes in >1,000 mice from 33 strains, including brain and body weights and cognition, activity, anxiety, and social behaviors, using 5 behavioral assays: cued fear conditioning, open field tests in dark and bright light, direct social interaction, and social dominance. Trait disruptions mimicked those seen clinically, with robust strain and sex differences. Some strains exhibited large effect-size trait disruptions, sometimes in opposite directions, and-remarkably-others expressed resilience. Therefore, systematically introducing genetic diversity into models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies.
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Affiliation(s)
- Manal Tabbaa
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Allison Knoll
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Pat Levitt
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
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22
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Koesterich J, An JY, Inoue F, Sohota A, Ahituv N, Sanders SJ, Kreimer A. Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. Int J Mol Sci 2023; 24:3509. [PMID: 36834916 PMCID: PMC9959321 DOI: 10.3390/ijms24043509] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/13/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Autism spectrum disorder (ASD) is a common, complex, and highly heritable condition with contributions from both common and rare genetic variations. While disruptive, rare variants in protein-coding regions clearly contribute to symptoms, the role of rare non-coding remains unclear. Variants in these regions, including promoters, can alter downstream RNA and protein quantity; however, the functional impacts of specific variants observed in ASD cohorts remain largely uncharacterized. Here, we analyzed 3600 de novo mutations in promoter regions previously identified by whole-genome sequencing of autistic probands and neurotypical siblings to test the hypothesis that mutations in cases have a greater functional impact than those in controls. We leveraged massively parallel reporter assays (MPRAs) to detect transcriptional consequences of these variants in neural progenitor cells and identified 165 functionally high confidence de novo variants (HcDNVs). While these HcDNVs are enriched for markers of active transcription, disruption to transcription factor binding sites, and open chromatin, we did not identify differences in functional impact based on ASD diagnostic status.
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Affiliation(s)
- Justin Koesterich
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
- Department of Cell and Developmental Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Joon-Yong An
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neuroscience, University of California, San Francisco, CA 94143, USA
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul 02841, Republic of Korea
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94158, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Ajuni Sohota
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94158, USA
| | - Stephan J. Sanders
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neuroscience, University of California, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94158, USA
- Institute for Developmental and Regenerative Medicine, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, UK
| | - Anat Kreimer
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
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23
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Annunziata S, Bulgheroni S, D'Arrigo S, Esposito S, Taddei M, Saletti V, Alfei E, Sciacca FL, Rizzo A, Pantaleoni C, Riva D. CGH Findings in Children with Complex and Essential Autistic Spectrum Disorder. J Autism Dev Disord 2023; 53:615-623. [PMID: 33394245 DOI: 10.1007/s10803-020-04833-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 11/28/2022]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition with a strong genetic basis. We accurately assessed 209 ASD subjects, categorized in complex (47) and essential (162), and performed array comparative genomic hybridization to identify pathogenic and recurrent Copy Number Variants (CNVs). We found 117 CNVs in 75 patients, 11 classified as pathogenic. The complex ASD subjects have higher frequency of pathogenic CNVs with a diagnostic yield of 12.8%. Familiality, cognitive and verbal abilities, severity of autistic symptoms, neuroimaging and neurophysiological findings are not related to genetic data. This study identifies loci of interest for ASD and highlights the importance of a careful phenotypic characterization, as complex ASD is related to higher rate of pathogenic CNVs.
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Affiliation(s)
- Silvia Annunziata
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy.,Child Neurology and Psychiatry Unit, Brain and Behavioral Sciences Department, University of Pavia, 27100, Pavia, Italy
| | - Sara Bulgheroni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Stefano D'Arrigo
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Silvia Esposito
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy.
| | - Matilde Taddei
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Enrico Alfei
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy.,Pediatric Neurology Unit, "Vittore Buzzi" Children's Hospital ASST Fatebenefratelli-Sacco, 20100, Milan, Italy
| | - Francesca Luisa Sciacca
- Laboratory of Clinical Pathology and Medical Genetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Ambra Rizzo
- Laboratory of Clinical Pathology and Medical Genetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Daria Riva
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
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24
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Modeling Autism Spectrum Disorders with Induced Pluripotent Stem Cell-Derived Brain Organoids. Biomolecules 2023; 13:biom13020260. [PMID: 36830629 PMCID: PMC9953447 DOI: 10.3390/biom13020260] [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: 12/16/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
Autism spectrum disorders (ASD) are a group of complex neurodevelopmental disorders that affect communication and social interactions and present with restricted interests and repetitive behavior patterns. The susceptibility to ASD is strongly influenced by genetic/heritable factors; however, there is still a large gap in understanding the cellular and molecular mechanisms underlying the neurobiology of ASD. Significant progress has been made in identifying ASD risk genes and the possible convergent pathways regulated by these gene networks during development. The breakthrough of cellular reprogramming technology has allowed the generation of induced pluripotent stem cells (iPSCs) from individuals with syndromic and idiopathic ASD, providing patient-specific cell models for mechanistic studies. In the past decade, protocols for developing brain organoids from these cells have been established, leading to significant advances in the in vitro reproducibility of the early steps of human brain development. Here, we reviewed the most relevant literature regarding the application of brain organoids to the study of ASD, providing the current state of the art, and discussing the impact of such models on the field, limitations, and opportunities for future development.
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25
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Iannuzzo F, Genovese G, Lombardo C, Infortuna C, De Stefano R, Mento C, Muscatello MRA, Bruno A. Autistic Traits, Arousal, and Gender Features in a Nonclinical Sample of Italian Adolescents. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:693. [PMID: 36613013 PMCID: PMC9819561 DOI: 10.3390/ijerph20010693] [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: 10/30/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
(1) Background: Subthreshold autism is a sub-clinical pattern of autism spectrum disorder-like (ASD-like) traits, including poor social skills, cognitive rigidity, anxiety, and aloofness. These ASD-like traits are significantly more prevalent among parents and relatives of participants with autism; however, evidence suggests that subclinical autistic traits are not restricted to the family members of individuals with autism but rather are continuously distributed in the general population. Though the autistic subclinical form is perhaps prevalent among adults, little attention has been paid to the association between autistic traits and global functioning in adolescence. The aim of the present study is to investigate the subthreshold autism phenotype in adolescence and its relationship with arousal correlates, exploring gender differences emerging in the sample. (2) Methods: A sample of 725 students (293 males and 432 females; mean age 17.19) were recruited from three high schools in Southern Italy. They were assessed by the following instruments: Autism Spectrum Quotient, Adult Autism Subthreshold Spectrum, Ritvo Autism and Asperger Diagnostic Scale 14, and Hyperarousal Scale. (3) Results: In males, significant direct correlations between all dimensions of arousal and all variables related to autistic traits emerged except for the correlations between the H-Scale "Introspection score", the AQ questionnaire "Total score" (p = 0.094), and the AdAS-Spectrum questionnaire "Empathy factor" (p = 0.210); in females, significant positive correlations between all dimensions of arousal and all variables related to autistic traits emerged. (4) Conclusions: In the sample of adolescents with subclinical profiles of autistic traits, the Empathy factor of the AdAS Spectrum questionnaire was significantly higher in the male group than in the female group, underscoring lower empathic abilities in the former group. In the male group, the empathy factor did not have a statistically significant correlation with the H-scale introspection factor or with the autistic traits measured by AQ. We suppose that in male adolescents, another hypothetical factor seems to intervene in the relationship between autistic traits and arousal. Otherwise, empathy is a preponderant factor closely related to hyper-arousal responses in female adolescents with autistic traits.
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Affiliation(s)
- Fiammetta Iannuzzo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
| | - Giovanni Genovese
- Psychiatry Unit, Polyclinic Hospital University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
| | - Clara Lombardo
- Psychiatry Unit, Polyclinic Hospital University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
| | - Carmenrita Infortuna
- Psychiatry Unit, Polyclinic Hospital University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
| | - Rosa De Stefano
- Psychiatry Unit, Polyclinic Hospital University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
| | - Carmela Mento
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
| | - Maria Rosaria Anna Muscatello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
| | - Antonio Bruno
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, Contesse, 98125 Messina, Italy
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26
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Hamoudi W, Tripathi MK, Ojha SK, Amal H. A cross-talk between nitric oxide and the glutamatergic system in a Shank3 mouse model of autism. Free Radic Biol Med 2022; 188:83-91. [PMID: 35716826 DOI: 10.1016/j.freeradbiomed.2022.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022]
Abstract
Nitric oxide (NO) is a multifunctional signaling molecule that plays a crucial role in synaptic transmission and neuronal function. Pioneering studies show that nitric oxide (NO) and S-nitrosylation (SNO, the NO-mediated posttranslational modification) can engender nitrosative stress in the brain, contributing to neurodegenerative diseases. Little is known, however, about the aberrant NO signaling in neurodevelopmental disorders including autism spectrum disorder (ASD). We have recently shown that the Shank3 mutation in mice representing a model of ASD causes excessive NO levels and aberrant protein SNO. The glutamatergic system is involved in ASD, specifically in SHANK3 pathology. We used SNOTRAP technology to identify the SNO-proteome in the brain of the Shank3 mutant mice to understand the role of SNO in the glutamatergic system during the development of these mice. We conducted a systems biology analysis of the SNO-proteome to investigate the biological processes and signaling pathways in the brain of juvenile and adult Shank3 mutant and wild-type mice. The Shank3 mutation caused significant SNO-enrichment of a glutamate signaling pathway in the juvenile and adult mutant mice, although different protein subsets were S-nitrosylated in both ages. Cellular compartments analysis showed that "glutamatergic Synapse" is SNO-enriched significantly in the mutant mice of both ages. We also found eight S-nitrosylated proteins involved in glutamate transmission in both ages. 38 SNO-proteins found in the mutant mice are among the high-risk SFARI gene list. Biochemical examination shows a reduction in the levels of NMDA Receptor (NR1) in the cortex and striatum of the mutant mice of both ages. Neuronal NOS knockdown in SHSY-5Y rescued NR1 levels. In conclusion, this study reveals novel SNO of key glutamatergic proteins in Shank3 mutant mice and a cross-talk between nitric oxide and the glutamatergic system.
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Affiliation(s)
- Wajeha Hamoudi
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Manish Kumar Tripathi
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Shashank Kumar Ojha
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Haitham Amal
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
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27
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Yoneyama T, Utsumi A, Ishizaki A, Takahashi M, Yamaguchi S, Asami T, Hironaka S. Can dentists contribute to early screening for developmental disorders in five-year-old children during health checkups? PEDIATRIC DENTAL JOURNAL 2022. [DOI: 10.1016/j.pdj.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Deng J, Wang Y, Hu M, Lin J, Li Q, Liu C, Xu X. Deleterious Variation in BR Serine/Threonine Kinase 2 Classified a Subtype of Autism. Front Mol Neurosci 2022; 15:904935. [PMID: 35754711 PMCID: PMC9231588 DOI: 10.3389/fnmol.2022.904935] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, deleterious variants in the BR serine/threonine kinase 2 (BRSK2) gene have been reported in patients with autism spectrum disorder (ASD), suggesting that BRSK2 is a new high-confidence ASD risk gene, which presents an opportunity to understand the underlying neuropathological mechanisms of ASD. In this study, we performed clinical and neurobehavioral evaluations of a proband with a de novo non-sense variant in BRSK2 (p.R222X) with other reported BRSK2 mutant patients. To validate BRSK2 as an ASD risk gene, we generated a novel brsk2b-deficient zebrafish line through CRISPR/Cas9 and characterized its morphological and neurobehavioral features as well as performed molecular analysis of neurogenesis-related markers. The proband displayed typical ASD behaviors and language and motor delay, which were similar to other published BRSK2 mutant patients. Morphologically, brsk2b–/– larvae exhibited a higher embryonic mortality and rate of pericardium edema, severe developmental delay, and depigmentation as well as growth retardation in the early developmental stage. Behaviorally, brsk2b–/– zebrafish displayed significantly decreased activity in open field tests and enhanced anxiety levels in light/dark tests and thigmotaxis analysis. Specifically, brsk2b–/– zebrafish showed a prominent reduction of social interaction with peers and disrupted social cohesion among homogeneous groups. Molecularly, the mRNA expression levels of homer1b (a postsynaptic density scaffolding protein), and mbpa, mpz, and plp1b (molecular markers of oligodendrocytes and myelination) were increased in the brain tissues of adult brsk2b–/– zebrafish, while the expression level of isl1a, a marker of motor neurons, was decreased. Taken together, for the first time, we established a novel brsk2b-deficient zebrafish model that showed prominent ASD-like behaviors. In addition, the disturbed mRNA expression levels of neurogenesis-related markers implied that the processes of postsynaptic signaling as well as oligodendrocytes and myelination may be involved. This discovery may suggest a path for further research to identify the underlying neuropathological mechanisms between BRSK2 and ASD.
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Affiliation(s)
- Jingxin Deng
- Division of Child Health Care, National Children' Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yi Wang
- Division of Child Health Care, National Children' Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Meixin Hu
- Division of Child Health Care, National Children' Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jia Lin
- Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Translational Medical Center for Development and Disease, National Children's Medical Center, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
| | - Qiang Li
- Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Translational Medical Center for Development and Disease, National Children's Medical Center, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
| | - Chunxue Liu
- Division of Child Health Care, National Children' Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiu Xu
- Division of Child Health Care, National Children' Medical Center, Children's Hospital of Fudan University, Shanghai, China
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29
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Wigdor EM, Weiner DJ, Grove J, Fu JM, Thompson WK, Carey CE, Baya N, van der Merwe C, Walters RK, Satterstrom FK, Palmer DS, Rosengren A, Bybjerg-Grauholm J, Hougaard DM, Mortensen PB, Daly MJ, Talkowski ME, Sanders SJ, Bishop SL, Børglum AD, Robinson EB. The female protective effect against autism spectrum disorder. CELL GENOMICS 2022; 2:100134. [PMID: 36778135 PMCID: PMC9903803 DOI: 10.1016/j.xgen.2022.100134] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/26/2022] [Accepted: 04/27/2022] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is diagnosed three to four times more frequently in males than in females. Genetic studies of rare variants support a female protective effect (FPE) against ASD. However, sex differences in common inherited genetic risk for ASD are less studied, particularly within families. Leveraging the Danish iPSYCH resource, we found siblings of female ASD cases (n = 1,707) had higher rates of ASD than siblings of male ASD cases (n = 6,270; p < 1.0 × 10-10). In the Simons Simplex and SPARK collections, mothers of ASD cases (n = 7,436) carried more polygenic risk for ASD than fathers of ASD cases (n = 5,926; 0.08 polygenic risk score [PRS] SD; p = 7.0 × 10-7). Further, male unaffected siblings under-inherited polygenic risk (n = 1,519; p = 0.03). Using both epidemiologic and genetic approaches, our findings strongly support an FPE against ASD's common inherited influences.
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Affiliation(s)
- Emilie M. Wigdor
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Daniel J. Weiner
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jakob Grove
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, 8000 Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Jack M. Fu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Caitlin E. Carey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nikolas Baya
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Celia van der Merwe
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Raymond K. Walters
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - F. Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Duncan S. Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anders Rosengren
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, 4000 Roskilde, Denmark
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark
| | | | - David M. Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Preben Bo Mortensen
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, 8000 Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, 4000 Roskilde, Denmark
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus, Denmark
- Center for Integrated Register-based Research, Aarhus University, 8210 Aarhus, Denmark
| | - Mark J. Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Finnish Institute for Molecular Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Michael E. Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephan J. Sanders
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Somer L. Bishop
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anders D. Børglum
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, 8000 Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, 4000 Roskilde, Denmark
| | - Elise B. Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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30
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Pohl TT, Hörnberg H. Neuroligins in neurodevelopmental conditions: how mouse models of de novo mutations can help us link synaptic function to social behavior. Neuronal Signal 2022; 6:NS20210030. [PMID: 35601025 PMCID: PMC9093077 DOI: 10.1042/ns20210030] [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: 11/09/2021] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
Neurodevelopmental conditions (or neurodevelopmental disorders, NDDs) are highly heterogeneous with overlapping characteristics and shared genetic etiology. The large symptom variability and etiological heterogeneity have made it challenging to understand the biological mechanisms underpinning NDDs. To accommodate this individual variability, one approach is to move away from diagnostic criteria and focus on distinct dimensions with relevance to multiple NDDs. This domain approach is well suited to preclinical research, where genetically modified animal models can be used to link genetic variability to neurobiological mechanisms and behavioral traits. Genetic factors associated with NDDs can be grouped functionally into common biological pathways, with one prominent functional group being genes associated with the synapse. These include the neuroligins (Nlgns), a family of postsynaptic transmembrane proteins that are key modulators of synaptic function. Here, we review how research using Nlgn mouse models has provided insight into how synaptic proteins contribute to behavioral traits associated with NDDs. We focus on how mutations in different Nlgns affect social behaviors, as differences in social interaction and communication are a common feature of most NDDs. Importantly, mice carrying distinct mutations in Nlgns share some neurobiological and behavioral phenotypes with other synaptic gene mutations. Comparing the functional implications of mutations in multiple synaptic proteins is a first step towards identifying convergent neurobiological pathways in multiple brain regions and circuits.
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Affiliation(s)
- Tobias T. Pohl
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Hanna Hörnberg
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, Berlin 13125, Germany
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31
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Sandoval KC, Thackray SE, Wong A, Niewinski N, Chipak C, Rehal S, Dyck RH. Lack of Vesicular Zinc Does Not Affect the Behavioral Phenotype of Polyinosinic:Polycytidylic Acid-Induced Maternal Immune Activation Mice. Front Behav Neurosci 2022; 16:769322. [PMID: 35273483 PMCID: PMC8902171 DOI: 10.3389/fnbeh.2022.769322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Zinc is important in neural and synaptic development and neuronal transmission. Within the brain, zinc transporter 3 (ZnT3) is essential for zinc uptake into vesicles. Loss of vesicular zinc has been shown to produce neurodevelopmental disorder (NDD)-like behavior, such as decreased social interaction and increased anxiety- and repetitive-like behavior. Maternal immune activation (MIA) has been identified as an environmental factor for NDDs, such as autism spectrum disorders (ASDs) and schizophrenia (SZ), in offspring, which occurs during pregnancy when the mother’s immune system reacts to the exposure to viruses or infectious diseases. In this study, we investigated the interaction effect of a genetic factor [ZnT3 knockout (KO) mice] and an environmental factor (MIA). We induced MIA in pregnant female (dams) mice during mid-gestation, using polyinosinic:polycytidylic acid (polyI:C), which mimics a viral infection. Male and female ZnT3 KO and wild-type (WT) offspring were tested in five behavioral paradigms: Ultrasonic Vocalizations (USVs) at postnatal day 9 (P9), Open Field Test, Marble Burying Test, three-Chamber Social Test, and Pre-pulse Inhibition (PPI) in adulthood (P60–75). Our results indicate that loss of vesicular zinc does not result in enhanced ASD- and SZ-like phenotype compared to WT, nor does it show a more pronounced phenotype in male ZnT3 KO compared to female ZnT3 KO. Finally, MIA offspring demonstrated an ASD- and SZ-like phenotype only in specific behavioral tests: increased calls emitted in USVs and fewer marbles buried. Our results suggest that there is no interaction between the loss of vesicular zinc and MIA induction in the susceptibility to developing an ASD- and SZ-like phenotype.
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Affiliation(s)
- Katy Celina Sandoval
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
| | - Sarah E. Thackray
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
| | - Alison Wong
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
| | - Nicole Niewinski
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
| | - Colten Chipak
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
| | - Suhkjinder Rehal
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
| | - Richard H. Dyck
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
- *Correspondence: Richard H. Dyck,
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32
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Terashima H, Minatohara K, Maruoka H, Okabe S. Imaging neural circuit pathology of autism spectrum disorders: autism-associated genes, animal models and the application of in vivo two-photon imaging. Microscopy (Oxf) 2022; 71:i81-i99. [DOI: 10.1093/jmicro/dfab039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/11/2021] [Accepted: 11/08/2021] [Indexed: 11/12/2022] Open
Abstract
Abstract
Recent advances in human genetics identified genetic variants involved in causing autism spectrum disorders (ASDs). Mouse models that mimic mutations found in patients with ASD exhibit behavioral phenotypes consistent with ASD symptoms. These mouse models suggest critical biological factors of ASD etiology. Another important implication of ASD genetics is the enrichment of ASD risk genes in molecules involved in developing synapses and regulating neural circuit function. Sophisticated in vivo imaging technologies applied to ASD mouse models identify common synaptic impairments in the neocortex, with genetic-mutation-specific defects in local neural circuits. In this article, we review synapse- and circuit-level phenotypes identified by in vivo two-photon imaging in multiple mouse models of ASD and discuss the contributions of altered synapse properties and neural circuit activity to ASD pathogenesis.
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Affiliation(s)
- Hiroshi Terashima
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiichiro Minatohara
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hisato Maruoka
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Nadeem A, Ahmad SF, Al-Harbi NO, Al-Ayadhi LY, Alanazi MM, Alfardan AS, Attia SM, Algahtani M, Bakheet SA. Dysregulated Nrf2 signaling in response to di(2-ethylhexyl) phthalate in neutrophils of children with autism. Int Immunopharmacol 2022; 106:108619. [PMID: 35183033 DOI: 10.1016/j.intimp.2022.108619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by constellation of impaired behaviors that include deficits in social interaction/communication and the presence of restricted/repetitive behavioral patterns. Both genetic component and environmental factors are thought to play a key role in the initiation and progression of ASD. Several environmental factors such as heavy metals and plasticizers are known to affect the progression of ASD. One of the most common pollutants in the environment today is di-2-ethylhexyl phthalate (DEHP). DEHP is utilized as a plasticizer in several household and office materials which range from medical devices to plastic toys. Children usually get exposed to DEHP at an early age through use of plastic toys and other plastic materials. Nuclear factor erythroid 2 (NFE2)-relatedfactor-2 (Nrf2) is a master redox regulator as it controls transcription of several antioxidant genes. DEHP has been reported to cause dysregulation in Nrf2 signaling in vitro/in vivo and ASD subjects also exhibit oxidant-antioxidant imbalance.Therefore, this study attempted to delineate the effect of DEHP on Nrf2 signaling in neutrophils of ASD and typically developing healthy children (TDC) in vitro. Our data display that neutrophils of ASD subjects have dysregulated Nrf2 and hemeoxygenase-1 (HO-1) expression as compared to TDC subjects. DEHP treatment leads to elevation of oxidant stress in neutrophils of both ASD and TDC subjects, however TDC neutrophils have better antioxidant response to mitigate oxidative stress. This is depicted by enhancement of Nrf2/HO-1 signaling in TDC neutrophils in response to DEHP whereas ASD neutrophils fail to do so. These results suggest that plasticizer, DEHP may cause further dysregulation in Nrf2 signaling which may promote progression of ASD.
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Affiliation(s)
- Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Sheikh F Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Naif O Al-Harbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Laila Y Al-Ayadhi
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali S Alfardan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sabry M Attia
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Algahtani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh A Bakheet
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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Chen S, Xiong J, Chen B, Zhang C, Deng X, He F, Yang L, Chen C, Peng J, Yin F. Autism spectrum disorder and comorbid neurodevelopmental disorders (ASD-NDDs): Clinical and genetic profile of a pediatric cohort. Clin Chim Acta 2022; 524:179-186. [PMID: 34800434 DOI: 10.1016/j.cca.2021.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD), a neurodevelopmental disorder, is featured by impaired social communication and restricted and repetitive behaviors and interests. ASD and comorbid neurodevelopmental disorders (ASD-NDDs), especially epilepsy and intellectual disability (ID)/global developmental delay (GDD) are frequently presented in genetic disorders. The aim of this study was to explore the clinical and genetic profile of ASD in combination with epilepsy or ID/GDD. METHODS We retrospectively analyzed the clinical characteristics, and genetic spectrum of pediatric patients presenting ASD-NDDs with proven genetic etiology. The pathogenicity of variants was conducted by molecular geneticists and clinicians complied with the guidelines of the American College of Medical Genetics and Genomics (ACMG). RESULTS Among 154 patients with ASD-NDDs, 79 (51.3%) patients gained a genetic diagnosis. Most patients (78/79, 98.7%) had comorbid ID or GDD, and 49 (49/79, 62.0%) had comorbid epilepsy. The clinical characteristics of those 79 patients were varied. 87 genetic variants were found among the 79 pedigrees. Most of the involved genes have roles in gene expression regulation (GER) and neuronal communication (NC). Most genes have been proven to be ASD-related genes, and some of them were not reported to contribute to ASD previously. CONCLUSION We summarized the genetic and clinical profile of 79 ASD-NDDs patients with proven genetic etiology. The genetic spectrum of ASD was expanded, and we highlighted a novel possible ASD candidate gene PRTG.
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Affiliation(s)
- Shimeng Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Baiyu Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ciliu Zhang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China.
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35
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Fanjul-Fernández M, Brown NJ, Hickey P, Diakumis P, Rafehi H, Bozaoglu K, Green CC, Rattray A, Young S, Alhuzaimi D, Mountford HS, Gillies G, Lukic V, Vick T, Finlay K, Coe BP, Eichler EE, Delatycki MB, Wilson SJ, Bahlo M, Scheffer IE, Lockhart PJ. A family study implicates GBE1 in the etiology of autism spectrum disorder. Hum Mutat 2022; 43:16-29. [PMID: 34633740 PMCID: PMC8720068 DOI: 10.1002/humu.24289] [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: 02/13/2021] [Revised: 09/17/2021] [Accepted: 10/07/2021] [Indexed: 11/06/2022]
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental disorders with an estimated heritability of >60%. Family-based genetic studies of ASD have generally focused on multiple small kindreds, searching for de novo variants of major effect. We hypothesized that molecular genetic analysis of large multiplex families would enable the identification of variants of milder effects. We studied a large multigenerational family of European ancestry with multiple family members affected with ASD or the broader autism phenotype (BAP). We identified a rare heterozygous variant in the gene encoding 1,4-ɑ-glucan branching enzyme 1 (GBE1) that was present in seven of seven individuals with ASD, nine of ten individuals with the BAP, and none of four tested unaffected individuals. We genotyped a community-acquired cohort of 389 individuals with ASD and identified three additional probands. Cascade analysis demonstrated that the variant was present in 11 of 13 individuals with familial ASD/BAP and neither of the two tested unaffected individuals in these three families, also of European ancestry. The variant was not enriched in the combined UK10K ASD cohorts of European ancestry but heterozygous GBE1 deletion was overrepresented in large ASD cohorts, collectively suggesting an association between GBE1 and ASD.
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Affiliation(s)
- Miriam Fanjul-Fernández
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute Victoria, Parkville, Victoria, Australia
- Royal Children’s Hospital Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Barwon Health, Geelong, Victoria, Australia
| | - Peter Hickey
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Kiymet Bozaoglu
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cherie C Green
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Department of Psychology and Counselling, School of Psychology and Public Health, La Trobe University, Melbourne, Victoria, Australia
| | - Audrey Rattray
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Savannah Young
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dana Alhuzaimi
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hayley S Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Vesna Lukic
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Tanya Vick
- Barwon Health, Geelong, Victoria, Australia
| | | | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington, USA
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sarah J Wilson
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Paul J Lockhart
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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36
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Wang L, Zheng R, Xu Y, Zhou Z, Guan P, Wu Y, Zhou J, Cheng Z, Zhang L. Altered Metabolic Characteristics in Plasma of Young Boys with Autism Spectrum Disorder. J Autism Dev Disord 2021; 52:4897-4907. [PMID: 34800227 DOI: 10.1007/s10803-021-05364-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2021] [Indexed: 12/16/2022]
Abstract
Autism Spectrum Disorder (ASD) is a serious neurodevelopmental disorder with no clinical biomarker. This study used untargeted metabolomic analysis to identify metabolic characteristics in plasma that can distinguish ASD children. 29 boys with ASD (3.02 ± 0.67 years) and 30 typically developing (TD) boys (3.13 ± 0.46 years) were recruited. Developmental and behavioral assessments were conducted in ASD group. Samples of plasma were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The association between metabolite concentration and scale score was assessed by Spearman rank correlation. Altered metabolic characteristics were found in boys with ASD. In Receiver Operating Characteristic (ROC) analysis, ornithine had the highest AUC (Area under ROC) value. Furthermore, the concentration of choline and ornithine was negatively correlated with ABC-language score in ASD group.
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Affiliation(s)
- Lei Wang
- Department of Child Healthcare, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China
| | - Ruixuan Zheng
- Department of Child Healthcare, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China
| | - Ying Xu
- Department of Child Healthcare, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China
| | - Ziyun Zhou
- Department of Child Healthcare, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China
| | - Ping Guan
- Department of Child Healthcare, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China
| | - Yanling Wu
- Department of Child Healthcare, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China
| | - Jian Zhou
- Department of Pediatric Laboratory, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China
| | - Zaohuo Cheng
- Department of Clinical Psychology, Wuxi Mental Health Center, 156 Qianrong Road, Wuxi, 214000, China
| | - Lili Zhang
- Department of Child Healthcare, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, 214000, China.
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37
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Disruption of Alternative Splicing in the Amygdala of Pigs Exposed to Maternal Immune Activation. IMMUNO 2021. [DOI: 10.3390/immuno1040035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The inflammatory response of gestating females to infection or stress can disrupt gene expression in the offspring’s amygdala, resulting in lasting neurodevelopmental, physiological, and behavioral disorders. The effects of maternal immune activation (MIA) can be impacted by the offspring’s sex and exposure to additional stressors later in life. The objectives of this study were to investigate the disruption of alternative splicing patterns associated with MIA in the offspring’s amygdala and characterize this disruption in the context of the second stress of weaning and sex. Differential alternative splicing was tested on the RNA-seq profiles of a pig model of viral-induced MIA. Compared to controls, MIA was associated with the differential alternative splicing (FDR-adjusted p-value < 0.1) of 292 and 240 genes in weaned females and males, respectively, whereas 132 and 176 genes were differentially spliced in control nursed female and male, respectively. The majority of the differentially spliced (FDR-adjusted p-value < 0.001) genes (e.g., SHANK1, ZNF672, KCNA6) and many associated enriched pathways (e.g., Fc gamma R-mediated phagocytosis, non-alcoholic fatty liver disease, and cGMP-PKG signaling) have been reported in MIA-related disorders including autism and schizophrenia in humans. Differential alternative splicing associated with MIA was detected in the gene MAG across all sex-stress groups except for unstressed males and SLC2A11 across all groups except unstressed females. Precise understanding of the effect of MIA across second stressors and sexes necessitates the consideration of splicing isoform profiles.
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38
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Shu C, Green Snyder L, Shen Y, Chung WK. Imputing cognitive impairment in SPARK, a large autism cohort. Autism Res 2021; 15:156-170. [PMID: 34636158 DOI: 10.1002/aur.2622] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 11/10/2022]
Abstract
Diverse large cohorts are necessary for dissecting subtypes of autism, and intellectual disability is one of the most robust endophenotypes for analysis. However, current cognitive assessment methods are not feasible at scale. We developed five commonly used machine learning models to predict cognitive impairment (FSIQ<80 and FSIQ<70) and FSIQ scores among 521 children with autism using parent-reported online surveys in SPARK, and evaluated them in an independent set (n = 1346) with a missing data rate up to 70%. We assessed accuracy, sensitivity, and specificity by comparing predicted cognitive levels against clinical IQ data. The elastic-net model has good performance (AUC = 0.876, sensitivity = 0.772, specificity = 0.803) using 129 predictive features to impute cognitive impairment (FSIQ<80). Top-ranked predictive features included parent-reported language and cognitive levels, age at autism diagnosis, and history of services. Prediction of FSIQ<70 and FSIQ scores also showed good performance. We show cognitive levels can be imputed with high accuracy for children with autism, using commonly collected parent-reported data and standardized surveys. The current model offers a method for large-scale autism studies seeking estimates of cognitive ability when standardized psychometric testing is not feasible. LAY SUMMARY: Children with autism who have more severe learning challenges or cognitive impairment have different needs that are important to consider in research studies. When children in our study were missing standardized cognitive testing scores, we were able to use machine learning with other information to correctly "guess" when they have cognitive impairment about 80% of the time. We can use this information in research in the future to develop more appropriate treatments for children with autism and cognitive impairment.
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Affiliation(s)
- Chang Shu
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA.,Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - LeeAnne Green Snyder
- Simons Foundation Autism Research Initiative, Simons Foundation, New York, New York, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA.,Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA.,Simons Foundation Autism Research Initiative, Simons Foundation, New York, New York, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
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39
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Wu N, Wang Y, Jia JY, Pan YH, Yuan XB. Association of CDH11 with Autism Spectrum Disorder Revealed by Matched-gene Co-expression Analysis and Mouse Behavioral Studies. Neurosci Bull 2021; 38:29-46. [PMID: 34523068 PMCID: PMC8783018 DOI: 10.1007/s12264-021-00770-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022] Open
Abstract
A large number of putative risk genes for autism spectrum disorder (ASD) have been reported. The functions of most of these susceptibility genes in developing brains remain unknown, and causal relationships between their variation and autism traits have not been established. The aim of this study was to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high-confidence ASD risk genes (hcASDs). The results showed that three gene features - gene size, mRNA abundance, and guanine-cytosine content - affect the genome-wide co-expression profiles of hcASDs. To circumvent the interference of these features in gene co-expression analysis, we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes. This method is referred to as "matched-gene co-expression analysis" (MGCA). With MGCA, we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction. The results of analysis of two recently-reported ASD candidate genes, CDH11 and CDH9, suggested the involvement of CDH11, but not CDH9, in ASD. Consistent with this prediction, behavioral studies showed that Cdh11-null mice, but not Cdh9-null mice, have multiple autism-like behavioral alterations. This study highlights the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.
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Affiliation(s)
- Nan Wu
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yue Wang
- Hussman Institute for Autism, Baltimore, 21201, USA
| | - Jing-Yan Jia
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China.
| | - Xiao-Bing Yuan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China. .,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, 21201, USA.
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40
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Zhang Y, Lu Q, Ye Y, Huang K, Liu W, Wu Y, Zhong X, Li B, Yu Z, Travers BG, Werling DM, Li JJ, Zhao H. SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits. Genome Biol 2021; 22:262. [PMID: 34493297 PMCID: PMC8422619 DOI: 10.1186/s13059-021-02478-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 08/23/2021] [Indexed: 01/09/2023] Open
Abstract
Local genetic correlation quantifies the genetic similarity of complex traits in specific genomic regions. However, accurate estimation of local genetic correlation remains challenging, due to linkage disequilibrium in local genomic regions and sample overlap across studies. We introduce SUPERGNOVA, a statistical framework to estimate local genetic correlations using summary statistics from genome-wide association studies. We demonstrate that SUPERGNOVA outperforms existing methods through simulations and analyses of 30 complex traits. In particular, we show that the positive yet paradoxical genetic correlation between autism spectrum disorder and cognitive performance could be explained by two etiologically distinct genetic signatures with bidirectional local genetic correlations.
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Affiliation(s)
- Yiliang Zhang
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yixuan Ye
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA
| | - Kunling Huang
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Wei Liu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA
| | - Yuchang Wu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xiaoyuan Zhong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Zhaolong Yu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA
| | - Brittany G Travers
- Occupational Therapy Program in the Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Donna M Werling
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - James J Li
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Psychology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
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41
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Yoon S, Munoz A, Yamrom B, Lee YH, Andrews P, Marks S, Wang Z, Reeves C, Winterkorn L, Krieger AM, Buja A, Pradhan K, Ronemus M, Baldwin KK, Levy D, Wigler M, Iossifov I. Rates of contributory de novo mutation in high and low-risk autism families. Commun Biol 2021; 4:1026. [PMID: 34471188 PMCID: PMC8410909 DOI: 10.1038/s42003-021-02533-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Autism arises in high and low-risk families. De novo mutation contributes to autism incidence in low-risk families as there is a higher incidence in the affected of the simplex families than in their unaffected siblings. But the extent of contribution in low-risk families cannot be determined solely from simplex families as they are a mixture of low and high-risk. The rate of de novo mutation in nearly pure populations of high-risk families, the multiplex families, has not previously been rigorously determined. Moreover, rates of de novo mutation have been underestimated from studies based on low resolution microarrays and whole exome sequencing. Here we report on findings from whole genome sequence (WGS) of both simplex families from the Simons Simplex Collection (SSC) and multiplex families from the Autism Genetic Resource Exchange (AGRE). After removing the multiplex samples with excessive cell-line genetic drift, we find that the contribution of de novo mutation in multiplex is significantly smaller than the contribution in simplex. We use WGS to provide high resolution CNV profiles and to analyze more than coding regions, and revise upward the rate in simplex autism due to an excess of de novo events targeting introns. Based on this study, we now estimate that de novo events contribute to 52-67% of cases of autism arising from low risk families, and 30-39% of cases of all autism.
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Affiliation(s)
- Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Adriana Munoz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Yoon-Ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Steven Marks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | | | - Abba M Krieger
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Andreas Buja
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Kith Pradhan
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Kristin K Baldwin
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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42
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Trost B, Loureiro LO, Scherer SW. Discovery of genomic variation across a generation. Hum Mol Genet 2021; 30:R174-R186. [PMID: 34296264 PMCID: PMC8490016 DOI: 10.1093/hmg/ddab209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Over the past 30 years (the timespan of a generation), advances in genomics technologies have revealed tremendous and unexpected variation in the human genome and have provided increasingly accurate answers to long-standing questions of how much genetic variation exists in human populations and to what degree the DNA complement changes between parents and offspring. Tracking the characteristics of these inherited and spontaneous (or de novo) variations has been the basis of the study of human genetic disease. From genome-wide microarray and next-generation sequencing scans, we now know that each human genome contains over 3 million single nucleotide variants when compared with the ~ 3 billion base pairs in the human reference genome, along with roughly an order of magnitude more DNA—approximately 30 megabase pairs (Mb)—being ‘structurally variable’, mostly in the form of indels and copy number changes. Additional large-scale variations include balanced inversions (average of 18 Mb) and complex, difficult-to-resolve alterations. Collectively, ~1% of an individual’s genome will differ from the human reference sequence. When comparing across a generation, fewer than 100 new genetic variants are typically detected in the euchromatic portion of a child’s genome. Driven by increasingly higher-resolution and higher-throughput sequencing technologies, newer and more accurate databases of genetic variation (for instance, more comprehensive structural variation data and phasing of combinations of variants along chromosomes) of worldwide populations will emerge to underpin the next era of discovery in human molecular genetics.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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43
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Basu-Shrivastava M, Kozoriz A, Desagher S, Lassot I. To Ubiquitinate or Not to Ubiquitinate: TRIM17 in Cell Life and Death. Cells 2021; 10:1235. [PMID: 34069831 PMCID: PMC8157266 DOI: 10.3390/cells10051235] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022] Open
Abstract
TRIM17 is a member of the TRIM family, a large class of RING-containing E3 ubiquitin-ligases. It is expressed at low levels in adult tissues, except in testis and in some brain regions. However, it can be highly induced in stress conditions which makes it a putative stress sensor required for the triggering of key cellular responses. As most TRIM members, TRIM17 can act as an E3 ubiquitin-ligase and promote the degradation by the proteasome of substrates such as the antiapoptotic protein MCL1. Intriguingly, TRIM17 can also prevent the ubiquitination of other proteins and stabilize them, by binding to other TRIM proteins and inhibiting their E3 ubiquitin-ligase activity. This duality of action confers several pivotal roles to TRIM17 in crucial cellular processes such as apoptosis, autophagy or cell division, but also in pathological conditions as diverse as Parkinson's disease or cancer. Here, in addition to recent data that endorse this duality, we review what is currently known from public databases and the literature about TRIM17 gene regulation and expression, TRIM17 protein structure and interactions, as well as its involvement in cell physiology and human disorders.
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Affiliation(s)
| | - Alina Kozoriz
- Institut de Génétique Moléculaire de Montpellier, University Montpellier, CNRS, Montpellier, France
| | - Solange Desagher
- Institut de Génétique Moléculaire de Montpellier, University Montpellier, CNRS, Montpellier, France
| | - Iréna Lassot
- Institut de Génétique Moléculaire de Montpellier, University Montpellier, CNRS, Montpellier, France
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44
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Yu T, Lien YJ, Liang FW, Kuo PL. Parental Socioeconomic Status and Autism Spectrum Disorder in Offspring: A Population-Based Cohort Study in Taiwan. Am J Epidemiol 2021; 190:807-816. [PMID: 33128070 DOI: 10.1093/aje/kwaa241] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 10/11/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Studies from the United States have shown increasing incidence of autism spectrum disorder (ASD) with increasing socioeconomic status (SES), whereas in Scandinavian countries, no such relation was identified. We investigated how ASD risk in offspring varied according to parental SES in Taiwan, where there is universal health care. Through linking birth reporting data and data from Taiwan's national health insurance program, we studied 706,111 singleton births from 2004 to 2007 and followed them until 2015. Parental SES was determined by monthly salary at the time of childbirth, and child neuropsychiatric outcomes were defined using International Classification of Diseases codes. We identified 7,323 ASD cases and 7,438 intellectual disability (ID) cases; 17% of ASD cases had co-occurring ID. In multivariable Cox regression analysis, higher SES was independently associated with higher risk of ASD after we took into account urbanization levels, child sex, parental age, and other covariates. By contrast, higher SES was independently associated with lower risk of ID. Besides the SES disparity in ASD case ascertainment and in the access to health care, findings from Taiwan suggest that other social, environmental, biological, and immunological factors linked with parental SES levels may contribute to the positive relation of SES and ASD risk.
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45
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Chiang AH, Chang J, Wang J, Vitkup D. Exons as units of phenotypic impact for truncating mutations in autism. Mol Psychiatry 2021; 26:1685-1695. [PMID: 33110259 DOI: 10.1038/s41380-020-00876-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorders (ASD) are a group of related neurodevelopmental diseases displaying significant genetic and phenotypic heterogeneity. Despite recent progress in understanding ASD genetics, the nature of phenotypic heterogeneity across probands remains unclear. Notably, likely gene-disrupting (LGD) de novo mutations affecting the same gene often result in substantially different ASD phenotypes. Nevertheless, we find that truncating mutations affecting the same exon frequently lead to strikingly similar intellectual phenotypes in unrelated ASD probands. Analogous patterns are observed for two independent proband cohorts and several other important ASD-associated phenotypes. We find that exons biased toward prenatal and postnatal expression preferentially contribute to ASD cases with lower and higher IQ phenotypes, respectively. These results suggest that exons, rather than genes, often represent a unit of effective phenotypic impact for truncating mutations in autism. The observed phenotypic patterns are likely mediated by nonsense-mediated decay (NMD) of splicing isoforms, with autism phenotypes usually triggered by relatively mild (15-30%) decreases in overall gene dosage. We find that each ASD gene with recurrent mutations can be characterized by a parameter, phenotype dosage sensitivity (PDS), which quantifies the relationship between changes in a gene's dosage and changes in a given disease phenotype. We further demonstrate analogous relationships between exon LGDs and gene expression changes in multiple human tissues. Therefore, similar phenotypic patterns may be also observed in other human genetic disorders.
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Affiliation(s)
- Andrew H Chiang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Jonathan Chang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Jiayao Wang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Dennis Vitkup
- Department of Biomedical Informatics, Columbia University, New York, NY, USA. .,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA.
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46
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Cederquist GY, Tchieu J, Callahan SJ, Ramnarine K, Ryan S, Zhang C, Rittenhouse C, Zeltner N, Chung SY, Zhou T, Chen S, Betel D, White RM, Tomishima M, Studer L. A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes. Cell Stem Cell 2021; 27:35-49.e6. [PMID: 32619517 DOI: 10.1016/j.stem.2020.06.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 01/12/2023]
Abstract
Autism is a clinically heterogeneous neurodevelopmental disorder characterized by impaired social interactions, restricted interests, and repetitive behaviors. Despite significant advances in the genetics of autism, understanding how genetic changes perturb brain development and affect clinical symptoms remains elusive. Here, we present a multiplex human pluripotent stem cell (hPSC) platform, in which 30 isogenic disease lines are pooled in a single dish and differentiated into prefrontal cortex (PFC) lineages to efficiently test early-developmental hypotheses of autism. We define subgroups of autism mutations that perturb PFC neurogenesis and are correlated to abnormal WNT/βcatenin responses. Class 1 mutations (8 of 27) inhibit while class 2 mutations (5 of 27) enhance PFC neurogenesis. Remarkably, autism patient data reveal that individuals carrying subclass-specific mutations differ clinically in their corresponding language acquisition profiles. Our study provides a framework to disentangle genetic heterogeneity associated with autism and points toward converging molecular and developmental pathways of diverse autism-associated mutations.
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Affiliation(s)
- Gustav Y Cederquist
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Jason Tchieu
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Scott J Callahan
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Cancer Genetics and Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Gerstner Graduate School of Biomedical Sciences, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Kiran Ramnarine
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Sean Ryan
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chelsea Rittenhouse
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Nadja Zeltner
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Center for Molecular Medicine, Department of Cellular Biology, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sun Young Chung
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Ting Zhou
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Doron Betel
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Richard M White
- Cancer Genetics and Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Mark Tomishima
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA.
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47
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Haltigan JD, Del Giudice M, Khorsand S. Growing points in attachment disorganization: looking back to advance forward. Attach Hum Dev 2021; 23:438-454. [PMID: 33890555 DOI: 10.1080/14616734.2021.1918454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this special issue paper we reflect on the next generation of attachment research with a focus on disorganization, a central but still poorly understood topic in this area. We suggest that progress will be facilitated by a return to attachment theory's evolutionary roots, and to the emphasis on biological function that inspired Bowlby's original thinking. Increased interdisciplinary cross-fertilization and collaborations would enable novel and generative research on some of the long-standing questions surrounding attachment disorganization. Accordingly, we present an agenda for future research that encompasses contributions of modern ethology and neurobiology, novel hypotheses based on the concept of adaptive decanalization, connections with neurodevelopmental vulnerability and risk for mental disorders such as schizophrenia, and the possibility of sex differences in the behavioral manifestations of attachment disorganization. We believe that these avenues of theory and research offer exciting potential for innovative work in attachment disorganization in the years ahead.
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Affiliation(s)
- John D Haltigan
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Marco Del Giudice
- Department of Psychology, University of New Mexico, Albuquerque, NM, USA
| | - Soha Khorsand
- Faculty of Science, Western University, London, Canada
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48
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Upadhyay J, Patra J, Tiwari N, Salankar N, Ansari MN, Ahmad W. Dysregulation of Multiple Signaling Neurodevelopmental Pathways during Embryogenesis: A Possible Cause of Autism Spectrum Disorder. Cells 2021; 10:958. [PMID: 33924211 PMCID: PMC8074600 DOI: 10.3390/cells10040958] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
Understanding the autistic brain and the involvement of genetic, non-genetic, and numerous signaling pathways in the etiology and pathophysiology of autism spectrum disorder (ASD) is complex, as is evident from various studies. Apart from multiple developmental disorders of the brain, autistic subjects show a few characteristics like impairment in social communications related to repetitive, restricted, or stereotypical behavior, which suggests alterations in neuronal circuits caused by defects in various signaling pathways during embryogenesis. Most of the research studies on ASD subjects and genetic models revealed the involvement of mutated genes with alterations of numerous signaling pathways like Wnt, hedgehog, and Retinoic Acid (RA). Despite significant improvement in understanding the pathogenesis and etiology of ASD, there is an increasing awareness related to it as well as a need for more in-depth research because no effective therapy has been developed to address ASD symptoms. Therefore, identifying better therapeutic interventions like "novel drugs for ASD" and biomarkers for early detection and disease condition determination are required. This review article investigated various etiological factors as well as the signaling mechanisms and their alterations to understand ASD pathophysiology. It summarizes the mechanism of signaling pathways, their significance, and implications for ASD.
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Affiliation(s)
- Jyoti Upadhyay
- Department of Pharmaceutical Sciences, School of Health Sciences, University of Petroleum and Energy Studies, Energy Acre Campus Bidholi, Dehradun 248007, Uttarakhand, India; (J.U.); (J.P.)
| | - Jeevan Patra
- Department of Pharmaceutical Sciences, School of Health Sciences, University of Petroleum and Energy Studies, Energy Acre Campus Bidholi, Dehradun 248007, Uttarakhand, India; (J.U.); (J.P.)
| | - Nidhi Tiwari
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organisation, Delhi 110054, India;
| | - Nilima Salankar
- School of Computer Sciences, University of Petroleum and Energy Studies, Energy Acre Campus Bidholi, Dehradun 248007, Uttarakhand, India;
| | - Mohd Nazam Ansari
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Wasim Ahmad
- Department of Pharmacy, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia;
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Wang H, Avillach P. Diagnostic Classification and Prognostic Prediction Using Common Genetic Variants in Autism Spectrum Disorder: Genotype-Based Deep Learning. JMIR Med Inform 2021; 9:e24754. [PMID: 33714937 PMCID: PMC8060867 DOI: 10.2196/24754] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 02/18/2021] [Accepted: 03/14/2021] [Indexed: 02/07/2023] Open
Abstract
Background In the United States, about 3 million people have autism spectrum disorder (ASD), and around 1 out of 59 children are diagnosed with ASD. People with ASD have characteristic social communication deficits and repetitive behaviors. The causes of this disorder remain unknown; however, in up to 25% of cases, a genetic cause can be identified. Detecting ASD as early as possible is desirable because early detection of ASD enables timely interventions in children with ASD. Identification of ASD based on objective pathogenic mutation screening is the major first step toward early intervention and effective treatment of affected children. Objective Recent investigation interrogated genomics data for detecting and treating autism disorders, in addition to the conventional clinical interview as a diagnostic test. Since deep neural networks perform better than shallow machine learning models on complex and high-dimensional data, in this study, we sought to apply deep learning to genetic data obtained across thousands of simplex families at risk for ASD to identify contributory mutations and to create an advanced diagnostic classifier for autism screening. Methods After preprocessing the genomics data from the Simons Simplex Collection, we extracted top ranking common variants that may be protective or pathogenic for autism based on a chi-square test. A convolutional neural network–based diagnostic classifier was then designed using the identified significant common variants to predict autism. The performance was then compared with shallow machine learning–based classifiers and randomly selected common variants. Results The selected contributory common variants were significantly enriched in chromosome X while chromosome Y was also discriminatory in determining the identification of autistic individuals from nonautistic individuals. The ARSD, MAGEB16, and MXRA5 genes had the largest effect in the contributory variants. Thus, screening algorithms were adapted to include these common variants. The deep learning model yielded an area under the receiver operating characteristic curve of 0.955 and an accuracy of 88% for identifying autistic individuals from nonautistic individuals. Our classifier demonstrated a considerable improvement of ~13% in terms of classification accuracy compared to standard autism screening tools. Conclusions Common variants are informative for autism identification. Our findings also suggest that the deep learning process is a reliable method for distinguishing the diseased group from the control group based on the common variants of autism.
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Affiliation(s)
- Haishuai Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Department of Computer Science and Engineering, Fairfield University, Fairfield, CT, United States
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
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50
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Castroflorio E, den Hoed J, Svistunova D, Finelli MJ, Cebrian-Serrano A, Corrochano S, Bassett AR, Davies B, Oliver PL. The Ncoa7 locus regulates V-ATPase formation and function, neurodevelopment and behaviour. Cell Mol Life Sci 2021; 78:3503-3524. [PMID: 33340069 PMCID: PMC8038996 DOI: 10.1007/s00018-020-03721-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/08/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
Members of the Tre2/Bub2/Cdc16 (TBC), lysin motif (LysM), domain catalytic (TLDc) protein family are associated with multiple neurodevelopmental disorders, although their exact roles in disease remain unclear. For example, nuclear receptor coactivator 7 (NCOA7) has been associated with autism, although almost nothing is known regarding the mode-of-action of this TLDc protein in the nervous system. Here we investigated the molecular function of NCOA7 in neurons and generated a novel mouse model to determine the consequences of deleting this locus in vivo. We show that NCOA7 interacts with the cytoplasmic domain of the vacuolar (V)-ATPase in the brain and demonstrate that this protein is required for normal assembly and activity of this critical proton pump. Neurons lacking Ncoa7 exhibit altered development alongside defective lysosomal formation and function; accordingly, Ncoa7 deletion animals exhibited abnormal neuronal patterning defects and a reduced expression of lysosomal markers. Furthermore, behavioural assessment revealed anxiety and social defects in mice lacking Ncoa7. In summary, we demonstrate that NCOA7 is an important V-ATPase regulatory protein in the brain, modulating lysosomal function, neuronal connectivity and behaviour; thus our study reveals a molecular mechanism controlling endolysosomal homeostasis that is essential for neurodevelopment.
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Affiliation(s)
| | - Joery den Hoed
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Daria Svistunova
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Mattéa J Finelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | | | - Silvia Corrochano
- MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK
- Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos, Calle del Prof Martín Lagos s/n, 28040, Madrid, Spain
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Peter L Oliver
- MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.
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