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Ma K, Wang S, Ma Y, Zeng L, Xu K, Mu N, Lai Y, Shi Y, Yang C, Chen B, Quan Y, Li L, Lu Y, Yang Y, Liu Y, Hu R, Wang X, Chen Y, Bian X, Feng H, Li F, Chen T. Increased oxygen stimulation promotes chemoresistance and phenotype shifting through PLCB1 in gliomas. Drug Resist Updat 2024; 76:101113. [PMID: 39053384 DOI: 10.1016/j.drup.2024.101113] [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: 01/22/2024] [Revised: 04/24/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
Gliomas, the most common CNS (central nerve system) tumors, face poor survival due to severe chemoresistance exacerbated by hypoxia. However, studies on whether altered hypoxic conditions benefit for chemo-sensitivity and how gliomas react to increased oxygen stimulation are limited. In this study, we demonstrated that increased oxygen stimulation promotes glioma growth and chemoresistance. Mechanically, increased oxygen stimulation upregulates miR-1290 levels. miR-1290, in turn, downregulates PLCB1, while PLCB1 facilitates the proteasomal degradation of β-catenin and active-β-catenin by increasing the proportion of ubiquitinated β-catenin in a destruction complex-independent mechanism. This process inhibits PLCB1 expression, leads to the accumulation of active-β-catenin, boosting Wnt signaling through an independent mechanism and ultimately promoting chemoresistance in glioma cells. Pharmacological inhibition of Wnt by WNT974 could partially inhibit glioma volume growth and prolong the shortened survival caused by increased oxygen stimulation in a glioma-bearing mouse model. Moreover, PLCB1, a key molecule regulated by increased oxygen stimulation, shows promising predictive power in survival analysis and has great potential to be a biomarker for grading and prognosis in glioma patients. These results provide preliminary insights into clinical scenarios associated with altered hypoxic conditions in gliomas, and introduce a novel perspective on the role of the hypoxic microenvironment in glioma progression. Furthermore, the outcomes reveal the potential risks of utilizing hyperbaric oxygen treatment (HBOT) in glioma patients, particularly when considering HBOT as a standalone option to ameliorate neuro-dysfunctions or when combining HBOT with a single chemotherapy agent without radiotherapy.
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Affiliation(s)
- Kang Ma
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Shi Wang
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yingjie Ma
- Medical Data Science Academy, Chongqing Medical University, Chongqing, China
| | - Lan Zeng
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China; Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Kai Xu
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ning Mu
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ying Lai
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yaning Shi
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Chuanyan Yang
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Beike Chen
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yulian Quan
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Lan Li
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yongling Lu
- Medical Research Center, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yang Yang
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yan Liu
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Rong Hu
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiaoming Wang
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Yujie Chen
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiuwu Bian
- Institute of Pathology and Southwest Cancer Center, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Hua Feng
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Fei Li
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Tunan Chen
- Glioma Medical Research Center and Department of Neurosurgery, The First Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
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Abedini SS, Akhavantabasi S, Liang Y, Heng JIT, Alizadehsani R, Dehzangi I, Bauer DC, Alinejad-Rokny H. A critical review of the impact of candidate copy number variants on autism spectrum disorder. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108509. [PMID: 38977176 DOI: 10.1016/j.mrrev.2024.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder (NDD) influenced by genetic, epigenetic, and environmental factors. Recent advancements in genomic analysis have shed light on numerous genes associated with ASD, highlighting the significant role of both common and rare genetic mutations, as well as copy number variations (CNVs), single nucleotide polymorphisms (SNPs) and unique de novo variants. These genetic variations disrupt neurodevelopmental pathways, contributing to the disorder's complexity. Notably, CNVs are present in 10 %-20 % of individuals with autism, with 3 %-7 % detectable through cytogenetic methods. While the role of submicroscopic CNVs in ASD has been recently studied, their association with genomic loci and genes has not been thoroughly explored. In this review, we focus on 47 CNV regions linked to ASD, encompassing 1632 genes, including protein-coding genes and long non-coding RNAs (lncRNAs), of which 659 show significant brain expression. Using a list of ASD-associated genes from SFARI, we detect 17 regions harboring at least one known ASD-related protein-coding gene. Of the remaining 30 regions, we identify 24 regions containing at least one protein-coding gene with brain-enriched expression and a nervous system phenotype in mouse mutants, and one lncRNA with both brain-enriched expression and upregulation in iPSC to neuron differentiation. This review not only expands our understanding of the genetic diversity associated with ASD but also underscores the potential of lncRNAs in contributing to its etiology. Additionally, the discovered CNVs will be a valuable resource for future diagnostic, therapeutic, and research endeavors aimed at prioritizing genetic variations in ASD.
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Affiliation(s)
- Seyedeh Sedigheh Abedini
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology & Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shiva Akhavantabasi
- Department of Molecular Biology and Genetics, Yeni Yuzyil University, Istanbul, Turkey; Ghiaseddin Jamshid Kashani University, Andisheh University Town, Danesh Blvd, 3441356611, Abyek, Qazvin, Iran
| | - Yuheng Liang
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julian Ik-Tsen Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley 6845, Australia
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW 2052, Australia.
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Alhazmi S, Alharthi M, Alzahrani M, Alrofaidi A, Basingab F, Almuhammadi A, Alkhatabi H, Ashi A, Chaudhary A, Elaimi A. Copy number variations in autistic children. Biomed Rep 2024; 21:107. [PMID: 38868529 PMCID: PMC11168027 DOI: 10.3892/br.2024.1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/30/2024] [Indexed: 06/14/2024] Open
Abstract
Autism spectrum disorder (ASD) manifests as a neurodevelopmental condition marked by challenges in social communication, interaction and the performing of repetitive behaviors. The prevalence of autism increases markedly on an annual basis; however, the etiology remains incompletely understood. Cytogenetically visible chromosomal abnormalities, including copy number variations (CNVs), have been shown to contribute to the pathogenesis of ASD. More than 1% of ASD conditions can be explained based on a known genetic locus, whereas CNVs account for 5-10% of cases. However, there are no studies on the Saudi Arabian population for the detection of CNVs linked to ASD, to the best of our knowledge. Therefore, the aim of the present study was to explore the prevalence of CNVs in autistic Saudi Arabian children. Genomic DNA was extracted from the peripheral blood of 14 autistic children along with four healthy control children and then array-based comparative genomic hybridization (aCGH) was used to detect CNVs. Bioinformatics analysis of the aCGH results showed the presence of recurrent and non-recurrent deletion/duplication CNVs in several regions of the genome of autistic children. The most frequent CNVs were 1q21.2, 3p26.3, 4q13.2, 6p25.3, 6q24.2, 7p21.1, 7q34, 7q11.1, 8p23.2, 13q32.3, 14q11.1-q11.2 and 15q11.1-q11.2. In the present study, CNVs in autistic Saudi Arabian children were identified to improve the understanding of the etiology of autism and facilitate its diagnosis. Additionally, the present study identified certain possible pathogenic genes in the CNV region associated with several developmental and neurogenetic diseases.
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Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Neuroscience and Geroscience Research Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Central Laboratory of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maram Alharthi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Aisha Alrofaidi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Heba Alkhatabi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Hematology Research Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Abrar Ashi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Adeel Chaudhary
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Aisha Elaimi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
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Xu S, Wang N, Zuccaro MV, Gerhardt J, Iyyappan R, Scatolin GN, Jiang Z, Baslan T, Koren A, Egli D. DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility. Nat Commun 2024; 15:5247. [PMID: 38898078 PMCID: PMC11187207 DOI: 10.1038/s41467-024-49565-7] [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: 09/15/2023] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
DNA replication in differentiated cells follows a defined program, but when and how it is established during mammalian development is not known. Here we show using single-cell sequencing, that late replicating regions are established in association with the B compartment and the nuclear lamina from the first cell cycle after fertilization on both maternal and paternal genomes. Late replicating regions contain a relative paucity of active origins and few but long genes and low G/C content. In both bovine and mouse embryos, replication timing patterns are established prior to embryonic genome activation. Chromosome breaks, which form spontaneously in bovine embryos at sites concordant with human embryos, preferentially locate to late replicating regions. In mice, late replicating regions show enhanced fragility due to a sparsity of dormant origins that can be activated under conditions of replication stress. This pattern predisposes regions with long neuronal genes to fragility and genetic change prior to separation of soma and germ cell lineages. Our studies show that the segregation of early and late replicating regions is among the first layers of genome organization established after fertilization.
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Affiliation(s)
- Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
| | - Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
| | - Michael V Zuccaro
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
- Graduate Program, Department of Cellular Physiology and Biophysics, Columbia University, New York, NY, USA
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical School, New York, NY, USA
| | - Rajan Iyyappan
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | | | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Timour Baslan
- Department of Biomedical Sciences, School of Veterinary Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Amnon Koren
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA.
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Nóbrega IDS, Teles e Silva AL, Yokota-Moreno BY, Sertié AL. The Importance of Large-Scale Genomic Studies to Unravel Genetic Risk Factors for Autism. Int J Mol Sci 2024; 25:5816. [PMID: 38892002 PMCID: PMC11172008 DOI: 10.3390/ijms25115816] [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: 04/17/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Autism spectrum disorder (ASD) is a common and highly heritable neurodevelopmental disorder. During the last 15 years, advances in genomic technologies and the availability of increasingly large patient cohorts have greatly expanded our knowledge of the genetic architecture of ASD and its neurobiological mechanisms. Over two hundred risk regions and genes carrying rare de novo and transmitted high-impact variants have been identified. Additionally, common variants with small individual effect size are also important, and a number of loci are now being uncovered. At the same time, these new insights have highlighted ongoing challenges. In this perspective article, we summarize developments in ASD genetic research and address the enormous impact of large-scale genomic initiatives on ASD gene discovery.
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Affiliation(s)
| | | | | | - Andréa Laurato Sertié
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, Rua Comendador Elias Jafet, 755. Morumbi, São Paulo 05653-000, Brazil; (I.d.S.N.); (A.L.T.e.S.); (B.Y.Y.-M.)
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Cooper JN, Mittal J, Sangadi A, Klassen DL, King AM, Zalta M, Mittal R, Eshraghi AA. Landscape of NRXN1 Gene Variants in Phenotypic Manifestations of Autism Spectrum Disorder: A Systematic Review. J Clin Med 2024; 13:2067. [PMID: 38610832 PMCID: PMC11012327 DOI: 10.3390/jcm13072067] [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: 02/22/2024] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by social communication challenges and repetitive behaviors. Recent research has increasingly focused on the genetic underpinnings of ASD, with the Neurexin 1 (NRXN1) gene emerging as a key player. This comprehensive systematic review elucidates the contribution of NRXN1 gene variants in the pathophysiology of ASD. Methods: The protocol for this systematic review was designed a priori and was registered in the PROSPERO database (CRD42023450418). A risk of bias analysis was conducted using the Joanna Briggs Institute (JBI) critical appraisal tool. We examined various studies that link NRXN1 gene disruptions with ASD, discussing both the genotypic variability and the resulting phenotypic expressions. Results: Within this review, there was marked heterogeneity observed in ASD genotypic and phenotypic manifestations among individuals with NRXN1 mutations. The presence of NRXN1 mutations in this population emphasizes the gene's role in synaptic function and neural connectivity. Conclusion: This review not only highlights the role of NRXN1 in the pathophysiology of ASD but also highlights the need for further research to unravel the complex genetic underpinnings of the disorder. A better knowledge about the multifaceted role of NRXN1 in ASD can provide crucial insights into the neurobiological foundations of autism and pave the way for novel therapeutic strategies.
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Affiliation(s)
- Jaimee N. Cooper
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
- School of Medicine, New York Medical College, Valhalla, NY 10595, USA
| | - Jeenu Mittal
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
| | - Akhila Sangadi
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
| | - Delany L. Klassen
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
| | - Ava M. King
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
| | - Max Zalta
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
| | - Rahul Mittal
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
| | - Adrien A. Eshraghi
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (J.N.C.); (J.M.); (A.S.); (D.L.K.); (A.M.K.); (M.Z.); (R.M.)
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL 33146, USA
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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Engal E, Zhang Z, Geminder O, Jaffe-Herman S, Kay G, Ben-Hur A, Salton M. The spectrum of pre-mRNA splicing in autism. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1838. [PMID: 38509732 DOI: 10.1002/wrna.1838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre-mRNA splicing. Abnormal splicing patterns have been identified in the brains of individuals with ASD, and mutations in splicing factors have been found to contribute to neurodevelopmental delays associated with ASD. Here we review studies that shed light on the importance of splicing observed in ASD and that explored the intricate relationship between splicing factors and ASD, revealing how disruptions in pre-mRNA splicing may underlie ASD pathogenesis. We provide an overview of the research regarding all splicing factors associated with ASD and place a special emphasis on five specific splicing factors-HNRNPH2, NOVA2, WBP4, SRRM2, and RBFOX1-known to impact the splicing of ASD-related genes. In the discussion of the molecular mechanisms influenced by these splicing factors, we lay the groundwork for a deeper understanding of ASD's complex etiology. Finally, we discuss the potential benefit of unraveling the connection between splicing and ASD for the development of more precise diagnostic tools and targeted therapeutic interventions. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zhenwei Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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8
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Li LD, Zhou Y, Shi SF. Identification and characterization of biomarkers associated with endoplasmic reticulum protein processing in cerebral ischemia-reperfusion injury. PeerJ 2024; 12:e16707. [PMID: 38188159 PMCID: PMC10768662 DOI: 10.7717/peerj.16707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Background Cerebral ischemia (CI), ranking as the second leading global cause of death, is frequently treated by reestablishing blood flow and oxygenation. Paradoxically, this reperfusion can intensify tissue damage, leading to CI-reperfusion injury. This research sought to uncover biomarkers pertaining to protein processing in the endoplasmic reticulum (PER) during CI-reperfusion injury. Methods We utilized the Gene Expression Omnibus (GEO) dataset GSE163614 to discern differentially expressed genes (DEGs) and single out PER-related DEGs. The functions and pathways of these PER-related DEGs were identified via Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Core genes were pinpointed through protein-protein interaction (PPI) networks. Subsequent to this, genes with diagnostic relevance were distinguished using external validation datasets. A single-sample gene-set enrichment analysis (ssGSEA) was undertaken to pinpoint genes with strong associations to hypoxia and apoptosis, suggesting their potential roles as primary inducers of apoptosis in hypoxic conditions during ischemia-reperfusion injuries. Results Our study demonstrated that PER-related genes, specifically ADCY5, CAMK2A, PLCB1, NTRK2, and DLG4, were markedly down-regulated in models, exhibiting a robust association with hypoxia and apoptosis. Conclusion The data indicates that ADCY5, CAMK2A, PLCB1, NTRK2, and DLG4 could be pivotal genes responsible for triggering apoptosis in hypoxic environments during CI-reperfusion injury.
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Affiliation(s)
- Liang-da Li
- Department of Neurology, The People’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
| | - Yue Zhou
- Department of Neurology, The People’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
| | - Shan-fen Shi
- Department of Rheumatology, The People’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
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Singh M, Pradhan D, Kkani P, Prasad Rao G, Dhagudu NK, Kumar L, Ramasubramanian C, Kumar SG, Sonttineni S, Mohan KN. Genome-scale copy number variant analysis in schizophrenia patients and controls from South India. Front Mol Neurosci 2023; 16:1268827. [PMID: 38178910 PMCID: PMC10764592 DOI: 10.3389/fnmol.2023.1268827] [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: 07/28/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Copy number variants (CNVs) are among the main genetic factors identified in schizophrenia (SZ) through genome-scale studies conducted mostly in Caucasian populations. However, to date, there have been no genome-scale CNV reports on patients from India. To address this shortcoming, we generated, for the first time, genome-scale CNV data for 168 SZ patients and 168 controls from South India. In total, 63 different CNVs were identified in 56 patients and 46 controls with a significantly higher proportion of medium-sized deletions (100 kb-1 Mb) after multiple testing (FDR = 2.7E-4) in patients. Of these, 13 CNVs were previously reported; however, when searched against GWAS, transcriptome, exome, and DNA methylation studies, another 17 CNVs with candidate genes were identified. Of the total 30 CNVs, 28 were present in 38 patients and 12 in 27 controls, indicating a significantly higher representation in the former (p = 1.87E-5). Only 4q35.1-q35.2 duplications were significant (p = 0.020) and observed in 11 controls and 2 patients. Among the others that are not significant, a few examples of patient-specific and previously reported CNVs include deletions of 11q14.1 (DLG2), 22q11.21, and 14q21.1 (LRFN5). 16p13.3 deletion (RBFOX1), 3p14.2 duplication (CADPS), and 7p11.2 duplication (CCT6A) were some of the novel CNVs containing candidate genes. However, these observations need to be replicated in a larger sample size. In conclusion, this report constitutes an important foundation for future CNV studies in a relatively unexplored population. In addition, the data indicate that there are advantages in using an integrated approach for better identification of candidate CNVs for SZ and other mental health disorders.
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Affiliation(s)
- Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani – Hyderabad Campus, Hyderabad, India
| | - Dibyabhabha Pradhan
- Centralized Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Poornima Kkani
- Department of Zoology, Thiagarajar College, Madurai, India
| | | | | | - Lov Kumar
- Department of Computer Engineering, National Institute of Technology, Kurukshetra, India
| | | | | | | | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani – Hyderabad Campus, Hyderabad, India
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani – Hyderabad Campus, Hyderabad, India
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10
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Wright DC, Baluyot ML, Carmichael J, Darmanian A, Jose N, Ngo C, Heaps LS, Yendle A, Holman K, Ziso S, Khan F, Masi A, Silove N, Eapen V. Saliva DNA: An alternative biospecimen for single nucleotide polymorphism chromosomal microarray analysis in autism. Am J Med Genet A 2023; 191:2913-2920. [PMID: 37715344 DOI: 10.1002/ajmg.a.63400] [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: 07/16/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023]
Abstract
Chromosomal microarray analysis (CMA) is typically performed for investigation of autism using blood DNA. However, blood collection poses significant challenges for autistic children with repetitive behaviors and sensory and communication issues, often necessitating physical restraint or sedation. Noninvasive saliva collection offers an alternative, however, no published studies to date have evaluated saliva DNA for CMA in autism. Furthermore, previous reports suggest that saliva is suboptimal for detecting copy number variation. We therefore aimed to evaluate saliva DNA for single nucleotide polymorphism (SNP) CMA in autistic children. Saliva DNA from 48 probands and parents (n = 133) was obtained with a mean concentration of 141.7 ng/μL. SNP CMA was successful in 131/133 (98.5%) patients from which we correlated the size and accuracy of a copy number variant(s) called between a proband and carrier parent, and for a subgroup (n = 17 probands) who had a previous CMA using blood sample. There were no discordant copy number variant results between the proband and carrier parent, or the subgroup, however, there was an acceptable mean size difference of 0.009 and 0.07 Mb, respectively. Our findings demonstrate that saliva DNA can be an alternative for SNP CMA in autism, which avoids blood collection with significant implications for clinical practice guidelines.
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Affiliation(s)
- Dale Cameron Wright
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Maria Lourdes Baluyot
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Johanna Carmichael
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Artur Darmanian
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Ngaire Jose
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Con Ngo
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Luke St Heaps
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Amber Yendle
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Katherine Holman
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Sylvia Ziso
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Feroza Khan
- Academic Unit of Infant Child & Adolescent Psychiatry Services (AUCS), South Western Sydney Local Health District, Ingham Institute, Liverpool, Australia
- Discipline of Psychiatry & Mental Health, School of Clinical Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Anne Masi
- Academic Unit of Infant Child & Adolescent Psychiatry Services (AUCS), South Western Sydney Local Health District, Ingham Institute, Liverpool, Australia
| | - Natalie Silove
- Child Development Unit, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Valsa Eapen
- Academic Unit of Infant Child & Adolescent Psychiatry Services (AUCS), South Western Sydney Local Health District, Ingham Institute, Liverpool, Australia
- Discipline of Psychiatry & Mental Health, School of Clinical Medicine, University of New South Wales, Randwick, New South Wales, Australia
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11
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St George-Hyslop F, Haneklaus M, Kivisild T, Livesey FJ. Loss of CNTNAP2 Alters Human Cortical Excitatory Neuron Differentiation and Neural Network Development. Biol Psychiatry 2023; 94:780-791. [PMID: 37001843 DOI: 10.1016/j.biopsych.2023.03.014] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 05/14/2023]
Abstract
BACKGROUND Loss-of-function mutations in the contactin-associated protein-like 2 (CNTNAP2) gene are causal for neurodevelopmental disorders, including autism, schizophrenia, epilepsy, and intellectual disability. CNTNAP2 encodes CASPR2, a single-pass transmembrane protein that belongs to the neurexin family of cell adhesion molecules. These proteins have a variety of functions in developing neurons, including connecting presynaptic and postsynaptic neurons, and mediating signaling across the synapse. METHODS To study the effect of loss of CNTNAP2 function on human cerebral cortex development, and how this contributes to the pathogenesis of neurodevelopmental disorders, we generated human induced pluripotent stem cells from one neurotypical control donor null for full-length CNTNAP2, modeling cortical development from neurogenesis through to neural network formation in vitro. RESULTS CNTNAP2 is particularly highly expressed in the first two populations of early-born excitatory cortical neurons, and loss of CNTNAP2 shifted the relative proportions of these two neuronal types. Live imaging of excitatory neuronal growth showed that loss of CNTNAP2 reduced neurite branching and overall neuronal complexity. At the network level, developing cortical excitatory networks null for CNTNAP2 had complex changes in activity compared with isogenic controls: an initial period of relatively reduced activity compared with isogenic controls, followed by a lengthy period of hyperexcitability, and then a further switch to reduced activity. CONCLUSIONS Complete loss of CNTNAP2 contributes to the pathogenesis of neurodevelopmental disorders through complex changes in several aspects of human cerebral cortex excitatory neuron development that culminate in aberrant neural network formation and function.
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Affiliation(s)
- Frances St George-Hyslop
- University College London Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, University College London, London, United Kingdom
| | - Moritz Haneklaus
- University College London Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, University College London, London, United Kingdom
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Frederick J Livesey
- University College London Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, University College London, London, United Kingdom.
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12
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Shi Y, Shen H. DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma. Front Genet 2023; 14:1231415. [PMID: 37867602 PMCID: PMC10587545 DOI: 10.3389/fgene.2023.1231415] [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: 05/30/2023] [Accepted: 09/05/2023] [Indexed: 10/24/2023] Open
Abstract
Stomach Adenocarcinoma (STAD) is a leading cause of death worldwide. Somatic Copy Number Alterations (SCNAs), which result in Homologous recombination (HR) deficiency in double-strand break repair, are associated with the progression of STAD. However, the landscape of frequent breakpoints of SCNAs (hotspots) and their functional impacts remain poorly understood. In this study, we aimed to explore the frequency and impact of these hotspots in 332 STAD patients and 1,043 cancer cells using data from the Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE). We studied the rates of DSB (Double-Strand Breaks) loci in STAD patients by employing the Non-Homogeneous Poisson Distribution (λ), based on which we identified 145 DSB-hotspots with genes affected. We further verified DNA cytosine deamination as a critical process underlying the burden of DSB in STAD. Finally, we illustrated the clinical impact of the significant biological processes. Our findings highlighted the relationship between DNA cytosine deamination and SCNA in cancer was associated with recurrent Somatic Copy Number Alterations in STAD.
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Affiliation(s)
- Yilin Shi
- The College of Letters & Science, University of Wisconsin–Madison, Madison, WI, United States
| | - Huangxuan Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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13
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Shao W, Zheng H, Zhu J, Li W, Li Y, Hu W, Zhang J, Jing L, Wang K, Jiang X. Deletions of Cacna2d3 in parvalbumin-expressing neurons leads to autistic-like phenotypes in mice. Neurochem Int 2023; 169:105569. [PMID: 37419212 DOI: 10.1016/j.neuint.2023.105569] [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: 03/30/2023] [Revised: 06/23/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Autism spectrum disorder (ASD) is a series of highly inherited neurodevelopmental disorders. Loss-of-function (LOF) mutations in the CACNA2D3 gene are associated with ASD. However, the underlying mechanism is unknown. Dysfunction of cortical interneurons (INs) is strongly implicated in ASD. Parvalbumin-expressing (PV) INs and somatostatin-expressing (SOM) INs are the two most subtypes. Here, we characterized a mouse knockout of the Cacna2d3 gene in PV-expressing neurons (PVCre;Cacna2d3f/f mice) or in SOM-expressing neurons (SOMCre;Cacna2d3f/f mice), respectively. PVCre;Cacna2d3f/f mice showed deficits in the core ASD behavioral domains (including impaired sociability and increased repetitive behavior), as well as anxiety-like behavior and improved spatial memory. Furthermore, loss of Cacna2d3 from a subset of PV neurons results in a reduction of GAD67 and PV expression in the medial prefrontal cortex (mPFC). These may underlie the increased neuronal excitability in the mPFC, which contribute to the abnormal social behavior in PVCre;Cacna2d3f/f mice. Whereas, SOMCre;Cacna2d3f/f mice showed no obvious deficits in social, cognitive, or emotional phenotypes. Our findings provide the first evidence suggesting the causal role of Cacna2d3 insufficiency in PV neurons in autism.
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Affiliation(s)
- Wei Shao
- The School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China
| | - Hang Zheng
- The School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China
| | - Jingwen Zhu
- The School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China
| | - Wenhao Li
- The School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China
| | - Yifan Li
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wenjie Hu
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Juanjuan Zhang
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Liang Jing
- The School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China; Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China.
| | - Kai Wang
- The School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China; Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China; Collaborative Innovation Center for Neuropsychiatric Disorders and Mental Health, Hefei, China; Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China.
| | - Xiao Jiang
- The School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China; Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China.
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14
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Antinucci M, Comas D, Calafell F. Population history modulates the fitness effects of Copy Number Variation in the Roma. Hum Genet 2023; 142:1327-1343. [PMID: 37311904 PMCID: PMC10449987 DOI: 10.1007/s00439-023-02579-5] [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: 04/17/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
We provide the first whole genome Copy Number Variant (CNV) study addressing Roma, along with reference populations from South Asia, the Middle East and Europe. Using CNV calling software for short-read sequence data, we identified 3171 deletions and 489 duplications. Taking into account the known population history of the Roma, as inferred from whole genome nucleotide variation, we could discern how this history has shaped CNV variation. As expected, patterns of deletion variation, but not duplication, in the Roma followed those obtained from single nucleotide polymorphisms (SNPs). Reduced effective population size resulting in slightly relaxed natural selection may explain our observation of an increase in intronic (but not exonic) deletions within Loss of Function (LoF)-intolerant genes. Over-representation analysis for LoF-intolerant gene sets hosting intronic deletions highlights a substantial accumulation of shared biological processes in Roma, intriguingly related to signaling, nervous system and development features, which may be related to the known profile of private disease in the population. Finally, we show the link between deletions and known trait-related SNPs reported in the genome-wide association study (GWAS) catalog, which exhibited even frequency distributions among the studied populations. This suggests that, in general human populations, the strong association between deletions and SNPs associated to biomedical conditions and traits could be widespread across continental populations, reflecting a common background of potentially disease/trait-related CNVs.
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Affiliation(s)
- Marco Antinucci
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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15
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Vaz R, Edwards S, Dueñas-Rey A, Hofmeister W, Lindstrand A. Loss of ctnnd2b affects neuronal differentiation and behavior in zebrafish. Front Neurosci 2023; 17:1205653. [PMID: 37465584 PMCID: PMC10351287 DOI: 10.3389/fnins.2023.1205653] [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: 04/17/2023] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Delta-catenin (CTNND2) is an adhesive junction associated protein belonging to the family of p120 catenins. The human gene is located on the short arm of chromosome 5, the region deleted in Cri-du-chat syndrome (OMIM #123450). Heterozygous loss of CTNND2 has been linked to a wide spectrum of neurodevelopmental disorders such as autism, schizophrenia, and intellectual disability. Here we studied how heterozygous loss of ctnnd2b affects zebrafish embryonic development, and larvae and adult behavior. First, we observed a disorganization of neuronal subtypes in the developing forebrain, namely the presence of ectopic isl1-expressing cells and a local reduction of GABA-positive neurons in the optic recess region. Next, using time-lapse analysis, we found that the disorganized distribution of is1l-expressing forebrain neurons resulted from an increased specification of Isl1:GFP neurons. Finally, we studied the swimming patterns of both larval and adult heterozygous zebrafish and observed an increased activity compared to wildtype animals. Overall, this data suggests a role for ctnnd2b in the differentiation cascade of neuronal subtypes in specific regions of the vertebrate brain, with repercussions in the animal's behavior.
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Affiliation(s)
- Raquel Vaz
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Steven Edwards
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alfredo Dueñas-Rey
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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16
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Wadle SL, Schmitt TTX, Engel J, Kurt S, Hirtz JJ. Altered population activity and local tuning heterogeneity in auditory cortex of Cacna2d3-deficient mice. Biol Chem 2023; 404:607-617. [PMID: 36342370 DOI: 10.1515/hsz-2022-0269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
The α2δ3 auxiliary subunit of voltage-activated calcium channels is required for normal synaptic transmission and precise temporal processing of sounds in the auditory brainstem. In mice its loss additionally leads to an inability to distinguish amplitude-modulated tones. Furthermore, loss of function of α2δ3 has been associated with autism spectrum disorder in humans. To investigate possible alterations of network activity in the higher-order auditory system in α2δ3 knockout mice, we analyzed neuronal activity patterns and topography of frequency tuning within networks of the auditory cortex (AC) using two-photon Ca2+ imaging. Compared to wild-type mice we found distinct subfield-specific alterations in the primary auditory cortex, expressed in overall lower correlations between the network activity patterns in response to different sounds as well as lower reliability of these patterns upon repetitions of the same sound. Higher AC subfields did not display these alterations but showed a higher amount of well-tuned neurons along with lower local heterogeneity of the neurons' frequency tuning. Our results provide new insight into AC network activity alterations in an autism spectrum disorder-associated mouse model.
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Affiliation(s)
- Simon L Wadle
- Physiology of Neuronal Networks, Department of Biology, University of Kaiserslautern, Erwin-Schrödinger-Straße 13, D-67663 Kaiserslautern, Germany
| | - Tatjana T X Schmitt
- Physiology of Neuronal Networks, Department of Biology, University of Kaiserslautern, Erwin-Schrödinger-Straße 13, D-67663 Kaiserslautern, Germany
| | - Jutta Engel
- Department of Biophysics, Saarland University, School of Medicine, Center for Integrative Physiology and Molecular Medicine (CIPMM), D-66421 Homburg, Germany
| | - Simone Kurt
- Department of Biophysics, Saarland University, School of Medicine, Center for Integrative Physiology and Molecular Medicine (CIPMM), D-66421 Homburg, Germany
| | - Jan J Hirtz
- Physiology of Neuronal Networks, Department of Biology, University of Kaiserslautern, Erwin-Schrödinger-Straße 13, D-67663 Kaiserslautern, Germany
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17
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Chiu SL, Chen CM, Huganir RL. ICA69 regulates activity-dependent synaptic strengthening and learning and memory. Front Mol Neurosci 2023; 16:1171432. [PMID: 37251649 PMCID: PMC10213502 DOI: 10.3389/fnmol.2023.1171432] [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: 02/22/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Long-term potentiation (LTP) is one of the major cellular mechanisms for learning and memory. Activity-dependent increases in surface AMPA receptors (AMPARs) are important for enhanced synaptic efficacy during LTP. Here, we report a novel function of a secretory trafficking protein, ICA69, in AMPAR trafficking, synaptic plasticity, and animal cognition. ICA69 is first identified as a diabetes-associated protein well characterized for its function in the biogenesis of secretory vesicles and trafficking of insulin from ER, Golgi to post-Golgi in pancreatic beta cells. In the brain, ICA69 is found in the AMPAR protein complex through its interaction with PICK1, which binds directly to GluA2 or GluA3 AMPAR subunits. Here, we showed that ICA69 regulates PICK1's distribution in neurons and stability in the mouse hippocampus, which in turn can impact AMPAR function in the brain. Biochemical analysis of postsynaptic density (PSD) proteins from hippocampi of mice lacking ICA69 (Ica1 knockout) and their wild-type littermates revealed comparable AMPAR protein levels. Electrophysiological recording and morphological analysis of CA1 pyramidal neurons from Ica1 knockout also showed normal AMPAR-mediated currents and dendrite architecture, indicating that ICA69 does not regulate synaptic AMPAR function and neuron morphology at the basal state. However, genetic deletion of ICA69 in mice selectively impairs NMDA receptor (NMDAR)-dependent LTP but not LTD at Schaffer collateral to CA1 synapses, which correlates with behavioral deficits in tests of spatial and associative learning and memory. Together, we identified a critical and selective role of ICA69 in LTP, linking ICA69-mediated synaptic strengthening to hippocampus-dependent learning and memory.
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Affiliation(s)
- Shu-Ling Chiu
- Institute of Cellular and Organismic Biology and Neuroscience Program of Academia Sinica (NPAS), Academia Sinica, Taipei, Taiwan
- Solomon H. Snyder Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Chih-Ming Chen
- Solomon H. Snyder Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Richard L. Huganir
- Solomon H. Snyder Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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18
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Verbitsky M, Krishnamurthy S, Krithivasan P, Hughes D, Khan A, Marasà M, Vena N, Khosla P, Zhang J, Lim TY, Glessner JT, Weng C, Shang N, Shen Y, Hripcsak G, Hakonarson H, Ionita-Laza I, Levy B, Kenny EE, Loos RJ, Kiryluk K, Sanna-Cherchi S, Crosslin DR, Furth S, Warady BA, Igo RP, Iyengar SK, Wong CS, Parsa A, Feldman HI, Gharavi AG. Genomic Disorders in CKD across the Lifespan. J Am Soc Nephrol 2023; 34:607-618. [PMID: 36302597 PMCID: PMC10103259 DOI: 10.1681/asn.2022060725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
SIGNIFICANCE STATEMENT Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis. BACKGROUND Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility. METHODS We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II ( n =248), Chronic Renal Insufficiency Cohort (CRIC) study ( n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort. RESULTS We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk. CONCLUSION Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Pavan Khosla
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Joseph T. Glessner
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology and Columbia Genome Center, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David R. Crosslin
- Division of Biomedical Informatics and Genomics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Susan Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Barone R, Cirnigliaro L, Saccuzzo L, Valdese S, Pettinato F, Prato A, Bernardini L, Fichera M, Rizzo R. PARK2 microdeletion in a multiplex family with autism spectrum disorder. Int J Dev Neurosci 2023; 83:121-131. [PMID: 36478299 DOI: 10.1002/jdn.10246] [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: 07/15/2022] [Revised: 11/13/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND PARK2 (PRKN; MIM*602544) encodes Parkin protein, an ubiquitin-protein ligase required for proteasomal degradation and operating in the synaptic compartments. Copy number variations (CNVs) involving PARK2 have been associated with autism spectrum disorder (ASD). We report on a family with ASD (multiplex family) harbouring a microdeletion at chr. 6q26 causing PARK2 disruption. METHODS CNV analyses were performed using CGH/SNP-array platforms, and the detected microdeletion was confirmed by real-time quantitative PCR. Standardized psychometric evaluation was used for neurobehavioral characterization. RESULTS We found an intragenic ~157 kb microdeletion of the chromosomal region 6q26 causing PARK2 disruption in two male sibs with ASD and syndromic phenotype. They both had dysmorphic facial features with coarse faces, deeply set eyes with long horizontal palpebral fissures, long eyelashes and thick eyebrows, fleshy lips and mild skeletal problems. We found an intrafamilial clinical heterogeneity owing to different severity of the autism symptoms between the affected sibs: the younger one had minimally verbal autism and severe intellectual disability, whereas his older brother presented high-functioning autism and preserved speech. Parental analysis and real-time PCR using a PRKN fragment mapping within the deletion demonstrated that the deletion was inherited from their father having subthreshold features of ASD consisting with broad autism phenotype. CONCLUSIONS The study corroborates the hypothesis that PARK2 aberrations may be associated with ASD and highlights correlations between CNV affecting PARK2 and ASD in a multiplex family. We show remarkable intrafamilial variability in the severity of inherited ASD associated with PARK2 microdeletion.
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Affiliation(s)
- Rita Barone
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.,Reseach Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Lara Cirnigliaro
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Lucia Saccuzzo
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Silvia Valdese
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Fabio Pettinato
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Adriana Prato
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.,Department of Cognitive Sciences, Psychology, Education and Cultural Studies, University of Messina, Messina, Italy
| | - Laura Bernardini
- Cytogenetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, FG, Italy
| | - Marco Fichera
- Reseach Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy.,Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Renata Rizzo
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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20
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PTCHD1 Binds Cholesterol but Not Sonic Hedgehog, Suggesting a Distinct Cellular Function. Int J Mol Sci 2023; 24:ijms24032682. [PMID: 36769003 PMCID: PMC9917202 DOI: 10.3390/ijms24032682] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/09/2023] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Deleterious mutations in the X-linked Patched domain-containing 1 (PTCHD1) gene may account for up to 1% of autism cases. Despite this, the PTCHD1 protein remains poorly understood. Structural similarities to Patched family proteins point to a role in sterol transport, but this hypothesis has not been verified experimentally. Additionally, PTCHD1 has been suggested to be involved in Hedgehog signalling, but thus far, the experimental results have been conflicting. To enable a variety of biochemical and structural experiments, we developed a method for expressing PTCHD1 in Spodoptera frugiperda cells, solubilising it in glycol-diosgenin, and purifying it to homogeneity. In vitro and in silico experiments show that PTCHD1 function is not interchangeable with Patched 1 (PTCH1) in canonical Hedgehog signalling, since it does not repress Smoothened in Ptch1-/- mouse embryonic fibroblasts and does not bind Sonic Hedgehog. However, we found that PTCHD1 binds cholesterol similarly to PTCH1. Furthermore, we identified 13 PTCHD1-specific protein interactors through co-immunoprecipitation and demonstrated a link to cell stress responses and RNA stress granule formation. Thus, our results support the notion that despite structural similarities to other Patched family proteins, PTCHD1 may have a distinct cellular function.
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21
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Lansdon LA, Dickinson A, Arlis S, Liu H, Hlas A, Hahn A, Bonde G, Long A, Standley J, Tyryshkina A, Wehby G, Lee NR, Daack-Hirsch S, Mohlke K, Girirajan S, Darbro BW, Cornell RA, Houston DW, Murray JC, Manak JR. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes. Am J Hum Genet 2023; 110:71-91. [PMID: 36493769 PMCID: PMC9892779 DOI: 10.1016/j.ajhg.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology, University of Missouri - Kansas City School of Medicine, Kansas City, MO 64108, USA
| | | | - Sydney Arlis
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Huan Liu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Arman Hlas
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Alyssa Hahn
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Greg Bonde
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Abby Long
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | | | - George Wehby
- College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Nanette R Lee
- Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | | | - Karen Mohlke
- University of North Carolina, Chapel Hill, NC 27514, USA
| | | | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Robert A Cornell
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Douglas W Houston
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - J Robert Manak
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA.
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22
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Akter H, Rahman MM, Sarker S, Basiruzzaman M, Islam MM, Rahaman MA, Rahaman MA, Eshaque TB, Dity NJ, Sarker S, Amin MR, Hossain MM, Lopa M, Jahan N, Hossain S, Islam A, Mondol A, Faruk MO, Saha N, Kundu GK, Kanta SI, Kazal RK, Fatema K, Rahman MA, Hasan M, Hossain Mollah MA, Hosen MI, Karuvantevida N, Begum G, Zehra B, Nassir N, Nabi AHMN, Uddin KMF, Uddin M. Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders. Front Genet 2023; 14:955631. [PMID: 36959829 PMCID: PMC10028086 DOI: 10.3389/fgene.2023.955631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction: Copy number variations (CNVs) play a critical role in the pathogenesis of neurodevelopmental disorders (NDD) among children. In this study, we aim to identify clinically relevant CNVs, genes and their phenotypic characteristics in an ethnically underrepresented homogenous population of Bangladesh. Methods: We have conducted chromosomal microarray analysis (CMA) for 212 NDD patients with male to female ratio of 2.2:1.0 to identify rare CNVs. To identify candidate genes within the rare CNVs, gene constraint metrics [i.e., "Critical-Exon Genes (CEGs)"] were applied to the population data. Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) was followed in a subset of 95 NDD patients to assess the severity of autism and all statistical tests were performed using the R package. Results: Of all the samples assayed, 12.26% (26/212) and 57.08% (121/212) patients carried pathogenic and variant of uncertain significance (VOUS) CNVs, respectively. While 2.83% (6/212) patients' pathogenic CNVs were found to be located in the subtelomeric regions. Further burden test identified females are significant carriers of pathogenic CNVs compared to males (OR = 4.2; p = 0.0007). We have observed an increased number of Loss of heterozygosity (LOH) within cases with 23.85% (26/109) consanguineous parents. Our analyses on imprinting genes show, 36 LOH variants disrupting 69 unique imprinted genes and classified these variants as VOUS. ADOS-2 subset shows severe social communication deficit (p = 0.014) and overall ASD symptoms severity (p = 0.026) among the patients carrying duplication CNV compared to the CNV negative group. Candidate gene analysis identified 153 unique CEGs in pathogenic CNVs and 31 in VOUS. Of the unique genes, 18 genes were found to be in smaller (<1 MB) focal CNVs in our NDD cohort and we identified PSMC3 gene as a strong candidate gene for Autism Spectrum Disorder (ASD). Moreover, we hypothesized that KMT2B gene duplication might be associated with intellectual disability. Conclusion: Our results show the utility of CMA for precise genetic diagnosis and its integration into the diagnosis, therapy and management of NDD patients.
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Affiliation(s)
- Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Muhammad Mizanur Rahman
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shaoli Sarker
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammed Basiruzzaman
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Mazharul Islam
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Atikur Rahaman
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | | | | | - Nushrat Jahan Dity
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shouvik Sarker
- Institute of Plant Genetics, Department of Plant Biotechnology, Leibniz University Hannover, Hanover, Germany
| | - Md. Robed Amin
- Department of Medicine, Dhaka Medical College, Dhaka, Bangladesh
| | - Mohammad Monir Hossain
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Maksuda Lopa
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Nargis Jahan
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shafaat Hossain
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Amirul Islam
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Cellular Intelligence Lab, GenomeArc Inc, Toronto, ON, Canada
| | | | - Md Omar Faruk
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Narayan Saha
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Gopen kumar Kundu
- Department of Child Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shayla Imam Kanta
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Rezaul Karim Kazal
- Department of Obstetrics and Gynaecology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Kanij Fatema
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md. Ashrafur Rahman
- Department of Pharmaceutical Sciences, Wilkes University, Pennsylvania, PA, United States
| | - Maruf Hasan
- Department of Biomedical Engineering, Military Institute of Science and Technology, Dhaka, Bangladesh
| | | | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - A. H. M. Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - K. M. Furkan Uddin
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry, Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence (Ci) Lab, GenomeArc Inc, Toronto, ON, Canada
- *Correspondence: Mohammed Uddin,
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23
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Eftekhar M, Panahi Y, Eskandari MR, Pedram M. Association Study between DUF1220 Copy Number and Severity of Social Impairment in Sex-balanced Simplex Cases of Autism. Noro Psikiyatr Ars 2023; 60:43-48. [PMID: 36911566 PMCID: PMC9999218 DOI: 10.29399/npa.28020] [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: 09/16/2021] [Accepted: 04/01/2022] [Indexed: 11/07/2022] Open
Abstract
Introduction Copy number variations (CNVs), which are genetic factors responsible for human evolution, have emerged as underlying pathogenic factors for a number of diseases such as autism spectrum disorders (ASD). DUF1220 coding sequences have been shown to be positively associated with the severity of symptoms in familial/multiplex cases of autism. However, this association has not been confirmed in simplex autism, and the potential impact of gender/sex has not been studied. Methods Using saliva samples taken from Iranian children with non-syndromic simplex autism, different ethnicity/race and genetic backgrounds from previous studies, we assessed the association between DUF1220 CNVs and Autism Diagnostic Interview-Revised (ADI-R) domain scores in both males and females. Results In the male and female combined group with autism, in line with previous reports, our findings showed that there were no significant associations between DUF1220 CNVs with either total ADI-R score, social, communication, or repetitive diagnostic scores in simplex autism cases. Interestingly, however, in sex classified groups, despite the insignificant results, our findings in girls with autism showed a negative trend between DUF1220 CNVs and severity of symptoms for the social interaction and communication domains. By contrast, in male children with autism, the results showed a positive trend. Conclusion It seems that association of DUF1220 CNV with the severity of symptoms in simplex children with autism may follow a sexually dimorphic pattern that needs to be re-examined in prospective studies.
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Affiliation(s)
- Mohammad Eftekhar
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Yasin Panahi
- Department of Pharmacology and Toxicology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohammad Reza Eskandari
- Department of Psychiatry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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24
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Mangan RJ, Alsina FC, Mosti F, Sotelo-Fonseca JE, Snellings DA, Au EH, Carvalho J, Sathyan L, Johnson GD, Reddy TE, Silver DL, Lowe CB. Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell 2022; 185:4587-4603.e23. [PMID: 36423581 PMCID: PMC10013929 DOI: 10.1016/j.cell.2022.10.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/08/2022] [Accepted: 10/14/2022] [Indexed: 11/24/2022]
Abstract
Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes functional elements that descended from previously neutral regions. Here, we demonstrate that the fastest-evolved regions of the human genome, which we term "human ancestor quickly evolved regions" (HAQERs), rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split, before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. We developed a multiplex, single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. We propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.
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Affiliation(s)
- Riley J Mangan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Fernando C Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Federica Mosti
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Eric H Au
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Juliana Carvalho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Laya Sathyan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Graham D Johnson
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy E Reddy
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences and Duke Regeneration Center, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA.
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25
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Malloy C, Ahern M, Lin L, Hoffman DA. Neuronal Roles of the Multifunctional Protein Dipeptidyl Peptidase-like 6 (DPP6). Int J Mol Sci 2022; 23:ijms23169184. [PMID: 36012450 PMCID: PMC9409431 DOI: 10.3390/ijms23169184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
The concerted action of voltage-gated ion channels in the brain is fundamental in controlling neuronal physiology and circuit function. Ion channels often associate in multi-protein complexes together with auxiliary subunits, which can strongly influence channel expression and function and, therefore, neuronal computation. One such auxiliary subunit that displays prominent expression in multiple brain regions is the Dipeptidyl aminopeptidase-like protein 6 (DPP6). This protein associates with A-type K+ channels to control their cellular distribution and gating properties. Intriguingly, DPP6 has been found to be multifunctional with an additional, independent role in synapse formation and maintenance. Here, we feature the role of DPP6 in regulating neuronal function in the context of its modulation of A-type K+ channels as well as its independent involvement in synaptic development. The prevalence of DPP6 in these processes underscores its importance in brain function, and recent work has identified that its dysfunction is associated with host of neurological disorders. We provide a brief overview of these and discuss research directions currently underway to advance our understanding of the contribution of DPP6 to their etiology.
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Pourtavakoli A, Ghafouri-Fard S. Calcium signaling in neurodevelopment and pathophysiology of autism spectrum disorders. Mol Biol Rep 2022; 49:10811-10823. [PMID: 35857176 DOI: 10.1007/s11033-022-07775-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD) covers a group of neurodevelopmental disorders with complex genetic background. Several genetic mutations, epigenetic alterations, copy number variations and single nucleotide polymorphisms have been reported that cause ASD or modify its phenotype. Among signaling pathways that influence pathogenesis of ASD, calcium signaling has a prominent effect. METHODS We searched PubMed and Google Scholar databases with key words "Calcium signaling" and "Autism spectrum disorder". CONCLUSION This type of signaling has essential roles in the cell physiology. Endoplasmic reticulum and mitochondria are the key organelles involved in this signaling. It is vastly accepted that organellar disorders intensely influence the central nervous system (CNS). Several lines of evidence indicate alterations in the function of calcium channels in polygenic disorders affecting CNS. In the current review, we describe the role of calcium signaling in normal function of CNS and pathophysiology of ASD.
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Affiliation(s)
- Ashkan Pourtavakoli
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Huo Y, Lu W, Tian Y, Hou Q, Man HY. Prkn knockout mice show autistic-like behaviors and aberrant synapse formation. iScience 2022; 25:104573. [PMID: 35789851 PMCID: PMC9249611 DOI: 10.1016/j.isci.2022.104573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/26/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high genetic heterogeneity, affecting one in 44 children in the United States. Recent genomic sequencing studies from autistic human individuals indicate that PARK2, a gene that has long been considered in the pathogenesis of Parkinson's disease, is involved in ASD. Here, we report that Prkn knockout (KO) mice demonstrate autistic-like behaviors including impaired social interaction, elevated repetitive behaviors, and deficits in communication. In addition, Prkn KO mice show reduced neuronal activity in the context of sociability in the prelimbic cortex. Cell morphological examination of layer 5 prelimbic cortical neurons shows a reduction in dendritic arborization and spine number. Furthermore, biochemistry and immunocytochemistry analyses reveal alterations in synapse density and the molecular composition of synapses. These findings indicate that Prkn is implicated in brain development and suggest the potential use of the Prkn KO mouse as a model for autism research.
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Affiliation(s)
- Yuda Huo
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Wen Lu
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Yuan Tian
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Qingming Hou
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02215, USA
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28
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Jiang CC, Lin LS, Long S, Ke XY, Fukunaga K, Lu YM, Han F. Signalling pathways in autism spectrum disorder: mechanisms and therapeutic implications. Signal Transduct Target Ther 2022; 7:229. [PMID: 35817793 PMCID: PMC9273593 DOI: 10.1038/s41392-022-01081-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a prevalent and complex neurodevelopmental disorder which has strong genetic basis. Despite the rapidly rising incidence of autism, little is known about its aetiology, risk factors, and disease progression. There are currently neither validated biomarkers for diagnostic screening nor specific medication for autism. Over the last two decades, there have been remarkable advances in genetics, with hundreds of genes identified and validated as being associated with a high risk for autism. The convergence of neuroscience methods is becoming more widely recognized for its significance in elucidating the pathological mechanisms of autism. Efforts have been devoted to exploring the behavioural functions, key pathological mechanisms and potential treatments of autism. Here, as we highlight in this review, emerging evidence shows that signal transduction molecular events are involved in pathological processes such as transcription, translation, synaptic transmission, epigenetics and immunoinflammatory responses. This involvement has important implications for the discovery of precise molecular targets for autism. Moreover, we review recent insights into the mechanisms and clinical implications of signal transduction in autism from molecular, cellular, neural circuit, and neurobehavioural aspects. Finally, the challenges and future perspectives are discussed with regard to novel strategies predicated on the biological features of autism.
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Affiliation(s)
- Chen-Chen Jiang
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Li-Shan Lin
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Sen Long
- Department of Pharmacy, Hangzhou Seventh People's Hospital, Mental Health Center Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Xiao-Yan Ke
- Child Mental Health Research Center, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Kohji Fukunaga
- Department of CNS Drug Innovation, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
| | - Feng Han
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
- Institute of Brain Science, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China.
- Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215002, China.
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29
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Velmans C, O'Donnell-Luria AH, Argilli E, Tran Mau-Them F, Vitobello A, Chan MC, Fung JLF, Rech M, Abicht A, Aubert Mucca M, Carmichael J, Chassaing N, Clark R, Coubes C, Denommé-Pichon AS, de Dios JK, England E, Funalot B, Gerard M, Joseph M, Kennedy C, Kumps C, Willems M, van de Laar IMBH, Aarts-Tesselaar C, van Slegtenhorst M, Lehalle D, Leppig K, Lessmeier L, Pais LS, Paterson H, Ramanathan S, Rodan LH, Superti-Furga A, Chung BHY, Sherr E, Netzer C, Schaaf CP, Erger F. O'Donnell-Luria-Rodan syndrome: description of a second multinational cohort and refinement of the phenotypic spectrum. J Med Genet 2022; 59:697-705. [PMID: 34321323 DOI: 10.1136/jmedgenet-2020-107470] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/02/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND O'Donnell-Luria-Rodan syndrome (ODLURO) is an autosomal-dominant neurodevelopmental disorder caused by pathogenic, mostly truncating variants in KMT2E. It was first described by O'Donnell-Luria et al in 2019 in a cohort of 38 patients. Clinical features encompass macrocephaly, mild intellectual disability (ID), autism spectrum disorder (ASD) susceptibility and seizure susceptibility. METHODS Affected individuals were ascertained at paediatric and genetic centres in various countries by diagnostic chromosome microarray or exome/genome sequencing. Patients were collected into a case cohort and were systematically phenotyped where possible. RESULTS We report 18 additional patients from 17 families with genetically confirmed ODLURO. We identified 15 different heterozygous likely pathogenic or pathogenic sequence variants (14 novel) and two partial microdeletions of KMT2E. We confirm and refine the phenotypic spectrum of the KMT2E-related neurodevelopmental disorder, especially concerning cognitive development, with rather mild ID and macrocephaly with subtle facial features in most patients. We observe a high prevalence of ASD in our cohort (41%), while seizures are present in only two patients. We extend the phenotypic spectrum by sleep disturbances. CONCLUSION Our study, bringing the total of known patients with ODLURO to more than 60 within 2 years of the first publication, suggests an unexpectedly high relative frequency of this syndrome worldwide. It seems likely that ODLURO, although just recently described, is among the more common single-gene aetiologies of neurodevelopmental delay and ASD. We present the second systematic case series of patients with ODLURO, further refining the mutational and phenotypic spectrum of this not-so-rare syndrome.
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Affiliation(s)
- Clara Velmans
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Anne H O'Donnell-Luria
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Emanuela Argilli
- Brain Development Research Program, Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Frederic Tran Mau-Them
- UFR Des Sciences de Santé, INSERM UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université de Bourgogne, Dijon, Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- UFR Des Sciences de Santé, INSERM UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université de Bourgogne, Dijon, Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Marcus Cy Chan
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Jasmine Lee-Fong Fung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Megan Rech
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Marion Aubert Mucca
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, Midi-Pyrénées, France
| | - Jason Carmichael
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Nicolas Chassaing
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, Midi-Pyrénées, France
| | - Robin Clark
- Pediatrics Specialty Clinics, Loma Linda University Medical Center, Loma Linda, California, USA
| | - Christine Coubes
- Department of Medical Genetics, University Hospital Center Montpellier, Montpellier, Languedoc-Roussillon, France
| | - Anne-Sophie Denommé-Pichon
- UFR Des Sciences de Santé, INSERM UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université de Bourgogne, Dijon, Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - John Karl de Dios
- Department of Medical Genetics, Dayton Children's Hospital, Dayton, Ohio, USA
| | - Eleina England
- Center for Mendelian Genomics and Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Benoit Funalot
- Department of Clinical Genetics, Hopital Henri Mondor, Creteil, Île-de-France, France
| | - Marion Gerard
- Service de Génétique, Centre Hospitalier Universitaire de Caen, Caen, Basse-Normandie, France
| | - Maries Joseph
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Colleen Kennedy
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Camille Kumps
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, VD, Switzerland
| | - Marjolaine Willems
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Groupe DI, Inserm U1298, Montpellier University, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daphné Lehalle
- Department of Clinical Genetics, Hopital Henri Mondor, Creteil, Île-de-France, France
| | - Kathleen Leppig
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | - Lennart Lessmeier
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Lynn S Pais
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Heather Paterson
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Subhadra Ramanathan
- Pediatrics Specialty Clinics, Loma Linda University Medical Center, Loma Linda, California, USA
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, VD, Switzerland
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Elliott Sherr
- Brain Development Research Program, Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Christian Netzer
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Christian P Schaaf
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Florian Erger
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
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30
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The Roles of Par3, Par6, and aPKC Polarity Proteins in Normal Neurodevelopment and in Neurodegenerative and Neuropsychiatric Disorders. J Neurosci 2022; 42:4774-4793. [PMID: 35705493 DOI: 10.1523/jneurosci.0059-22.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 11/21/2022] Open
Abstract
Normal neural circuits and functions depend on proper neuronal differentiation, migration, synaptic plasticity, and maintenance. Abnormalities in these processes underlie various neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Neural development and maintenance are regulated by many proteins. Among them are Par3, Par6 (partitioning defective 3 and 6), and aPKC (atypical protein kinase C) families of evolutionarily conserved polarity proteins. These proteins perform versatile functions by forming tripartite or other combinations of protein complexes, which hereafter are collectively referred to as "Par complexes." In this review, we summarize the major findings on their biophysical and biochemical properties in cell polarization and signaling pathways. We next summarize their expression and localization in the nervous system as well as their versatile functions in various aspects of neurodevelopment, including neuroepithelial polarity, neurogenesis, neuronal migration, neurite differentiation, synaptic plasticity, and memory. These versatile functions rely on the fundamental roles of Par complexes in cell polarity in distinct cellular contexts. We also discuss how cell polarization may correlate with subcellular polarization in neurons. Finally, we review the involvement of Par complexes in neuropsychiatric and neurodegenerative disorders, such as schizophrenia and Alzheimer's disease. While emerging evidence indicates that Par complexes are essential for proper neural development and maintenance, many questions on their in vivo functions have yet to be answered. Thus, Par3, Par6, and aPKC continue to be important research topics to advance neuroscience.
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31
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Rare CACNA1H and RELN variants interact through mTORC1 pathway in oligogenic autism spectrum disorder. Transl Psychiatry 2022; 12:234. [PMID: 35668055 PMCID: PMC9170683 DOI: 10.1038/s41398-022-01997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/09/2022] Open
Abstract
Oligogenic inheritance of autism spectrum disorder (ASD) has been supported by several studies. However, little is known about how the risk variants interact and converge on causative neurobiological pathways. We identified in an ASD proband deleterious compound heterozygous missense variants in the Reelin (RELN) gene, and a de novo splicing variant in the Cav3.2 calcium channel (CACNA1H) gene. Here, by using iPSC-derived neural progenitor cells (NPCs) and a heterologous expression system, we show that the variant in Cav3.2 leads to increased calcium influx into cells, which overactivates mTORC1 pathway and, consequently, further exacerbates the impairment of Reelin signaling. Also, we show that Cav3.2/mTORC1 overactivation induces proliferation of NPCs and that both mutant Cav3.2 and Reelin cause abnormal migration of these cells. Finally, analysis of the sequencing data from two ASD cohorts-a Brazilian cohort of 861 samples, 291 with ASD; the MSSNG cohort of 11,181 samples, 5,102 with ASD-revealed that the co-occurrence of risk variants in both alleles of Reelin pathway genes and in one allele of calcium channel genes confer significant liability for ASD. Our results support the notion that genes with co-occurring deleterious variants tend to have interconnected pathways underlying oligogenic forms of ASD.
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32
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Mishra A, Prabha PK, Singla R, Kaur G, Sharma AR, Joshi R, Suroy B, Medhi B. Epigenetic Interface of Autism Spectrum Disorders (ASDs): Implications of Chromosome 15q11-q13 Segment. ACS Chem Neurosci 2022; 13:1684-1696. [PMID: 35635007 DOI: 10.1021/acschemneuro.2c00060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Autism spectrum disorders (ASDs) are multifactorial in nature and include both genetic and environmental factors. The increasing evidence advocates an important role of epigenetics in ASD etiology. One of the most common forms of epigenetic changes observed in the case of neurodevelopmental disorders is imprinting which is tightly regulated by developmental and tissue-specific mechanisms. Interestingly, many of these disorders that demonstrate autism-like phenotypes at varying degrees have found involvement of chromosome 15q11-q13 segment. Numerous studies demonstrate occurrence of ASD in the presence of chromosomal abnormalities located mainly in Chr15q11-q13 region. Several plausible candidate genes associated with ASD are in this chromosomal segment, including gamma aminobutyric acid A (GABAA) receptor genes GABRB3, GABRA5 and GABRG3, UBE3A, ATP 10A, MKRN3, ZNF, MAGEL2, Necdin (NDN), and SNRPN. The main objective of this review is to highlight the contribution of epigenetic modulations in chromosome 15q11-q13 segment toward the genetic etiology and pathophysiology of ASD. The present review reports the abnormalities in epigenetic regulation on genes and genomic regions located on chromosome 15 in relation to either syndromic (15q11-q13 maternal duplication) or nonsyndromic forms of ASD. Furthermore, studies reviewed in this article demonstrate conditions in which epigenetic dysregulation has been found to be a pathological factor for ASD development, thereby supporting a role for epigenetics in the multifactorial etiologies of ASD. Also, on the basis of the evidence found so far, we strongly emphasize the need to develop future therapeutic strategies as well as screening procedures for ASD that target mechanisms involving genes located on the chromosomal 15q11-q13 segment.
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Affiliation(s)
- Abhishek Mishra
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Praisy K Prabha
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Rubal Singla
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Gurjeet Kaur
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Amit Raj Sharma
- Dept. of Neurology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Rupa Joshi
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Benjamin Suroy
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Bikash Medhi
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
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33
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Išerić H, Alkan C, Hach F, Numanagić I. Fast characterization of segmental duplication structure in multiple genome assemblies. Algorithms Mol Biol 2022; 17:4. [PMID: 35303886 PMCID: PMC8932185 DOI: 10.1186/s13015-022-00210-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
MOTIVATION The increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural elements, such as common repeats and segmental duplications (SDs), increase genome plasticity that stimulates further evolution by changing the genomic structure and inventing new genes. Optimal computation of SDs within a genome requires quadratic-time local alignment algorithms that are impractical due to the size of most genomes. Additionally, to perform evolutionary analysis, one needs to characterize SDs in multiple genomes and find relations between those SDs and unique (non-duplicated) segments in other genomes. A naïve approach consisting of multiple sequence alignment would make the optimal solution to this problem even more impractical. Thus there is a need for fast and accurate algorithms to characterize SD structure in multiple genome assemblies to better understand the evolutionary forces that shaped the genomes of today. RESULTS Here we introduce a new approach, BISER, to quickly detect SDs in multiple genomes and identify elementary SDs and core duplicons that drive the formation of such SDs. BISER improves earlier tools by (i) scaling the detection of SDs with low homology to multiple genomes while introducing further 7-33[Formula: see text] speed-ups over the existing tools, and by (ii) characterizing elementary SDs and detecting core duplicons to help trace the evolutionary history of duplications to as far as 300 million years. AVAILABILITY AND IMPLEMENTATION BISER is implemented in Seq programming language and is publicly available at https://github.com/0xTCG/biser .
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Affiliation(s)
- Hamza Išerić
- Department of Computer Science, University of Victoria, Victoria, BC, V8P 5C2, Canada
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, 06800, Ankara, Turkey
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, BC, V6H 3Z6, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Ibrahim Numanagić
- Department of Computer Science, University of Victoria, Victoria, BC, V8P 5C2, Canada.
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34
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Impaired Subcortical Processing of Amplitude-Modulated Tones in Mice Deficient for Cacna2d3, a Risk Gene for Autism Spectrum Disorders in Humans. eNeuro 2022; 9:ENEURO.0118-22.2022. [PMID: 35410870 PMCID: PMC9034753 DOI: 10.1523/eneuro.0118-22.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/18/2022] Open
Abstract
Temporal processing of complex sounds is a fundamental and complex task in hearing and a prerequisite for processing and understanding vocalization, speech, and prosody. Here, we studied response properties of neurons in the inferior colliculus (IC) in mice lacking Cacna2d3, a risk gene for autism spectrum disorders (ASDs). The α2δ3 auxiliary Ca2+ channel subunit encoded by Cacna2d3 is essential for proper function of glutamatergic synapses in the auditory brainstem. Recent evidence has shown that much of auditory feature extraction is performed in the auditory brainstem and IC, including processing of amplitude modulation (AM). We determined both spectral and temporal properties of single- and multi-unit responses in the IC of anesthetized mice. IC units of α2δ3−/− mice showed normal tuning properties yet increased spontaneous rates compared with α2δ3+/+. When stimulated with AM tones, α2δ3−/− units exhibited less precise temporal coding and reduced evoked rates to higher modulation frequencies (fm). Whereas first spike latencies (FSLs) were increased for only few modulation frequencies, population peak latencies were increased for fm ranging from 20 to 100 Hz in α2δ3−/− IC units. The loss of precision of temporal coding with increasing fm from 70 to 160 Hz was characterized using a normalized offset-corrected (Pearson-like) correlation coefficient, which appeared more appropriate than the metrics of vector strength. The processing deficits of AM sounds analyzed at the level of the IC indicate that α2δ3−/− mice exhibit a subcortical auditory processing disorder (APD). Similar deficits may be present in other mouse models for ASDs.
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35
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Zhu Y, Gomez JA, Laufer BI, Mordaunt CE, Mouat JS, Soto DC, Dennis MY, Benke KS, Bakulski KM, Dou J, Marathe R, Jianu JM, Williams LA, Gutierrez Fugón OJ, Walker CK, Ozonoff S, Daniels J, Grosvenor LP, Volk HE, Feinberg JI, Fallin MD, Hertz-Picciotto I, Schmidt RJ, Yasui DH, LaSalle JM. Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. Genome Biol 2022; 23:46. [PMID: 35168652 PMCID: PMC8848662 DOI: 10.1186/s13059-022-02613-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/16/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. RESULTS We use whole genome bisulfite sequencing in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene, LOC105373085, renamed NHIP. Out of 134 differentially methylated regions associated with ASD in placental samples, a cluster at 22q13.33 corresponds to a 118-kb hypomethylated block that replicates in two additional cohorts. Within this locus, NHIP is functionally characterized as a nuclear peptide-encoding transcript with high expression in brain, and increased expression following neuronal differentiation or hypoxia, but decreased expression in ASD placenta and brain. NHIP overexpression increases cellular proliferation and alters expression of genes regulating synapses and neurogenesis, overlapping significantly with known ASD risk genes and NHIP-associated genes in ASD brain. A common structural variant disrupting the proximity of NHIP to a fetal brain enhancer is associated with NHIP expression and methylation levels and ASD risk, demonstrating a common genetic influence. CONCLUSIONS Together, these results identify and initially characterize a novel environmentally responsive ASD risk gene relevant to brain development in a hitherto under-characterized region of the human genome.
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Affiliation(s)
- Yihui Zhu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Julia S Mouat
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Daniela C Soto
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Megan Y Dennis
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Kelly S Benke
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ria Marathe
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Logan A Williams
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Orangel J Gutierrez Fugón
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Cheryl K Walker
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Sally Ozonoff
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, Davis, CA, USA
| | - Jason Daniels
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Luke P Grosvenor
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Irva Hertz-Picciotto
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA.
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA.
- Genome Center, University of California, Davis, CA, USA.
- MIND Institute, School of Medicine, University of California, Davis, CA, USA.
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Liu Y, Lv Y, Zarrei M, Dong R, Yang X, Higginbotham EJ, Li Y, Zhao D, Song F, Yang Y, Zhang H, Wang Y, Scherer SW, Gai Z. Chromosomal microarray analysis of 410 Han Chinese patients with autism spectrum disorder or unexplained intellectual disability and developmental delay. NPJ Genom Med 2022; 7:1. [PMID: 35022430 PMCID: PMC8755789 DOI: 10.1038/s41525-021-00271-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Copy number variants (CNVs) are recognized as a crucial genetic cause of neurodevelopmental disorders (NDDs). Chromosomal microarray analysis (CMA), the first-tier diagnostic test for individuals with NDDs, has been utilized to detect CNVs in clinical practice, but most reports are still from populations of European ancestry. To contribute more worldwide clinical genomics data, we investigated the genetic etiology of 410 Han Chinese patients with NDDs (151 with autism and 259 with unexplained intellectual disability (ID) and developmental delay (DD)) using CMA (Affymetrix) after G-banding karyotyping. Among all the NDD patients, 109 (26.6%) carried clinically relevant CNVs or uniparental disomies (UPDs), and 8 (2.0%) had aneuploidies (6 with trisomy 21 syndrome, 1 with 47,XXY, 1 with 47,XYY). In total, we found 129 clinically relevant CNVs and UPDs, including 32 CNVs in 30 ASD patients, and 92 CNVs and 5 UPDs in 79 ID/DD cases. When excluding the eight patients with aneuploidies, the diagnostic yield of pathogenic and likely pathogenic CNVs and UPDs was 20.9% for all NDDs (84/402), 3.3% in ASD (5/151), and 31.5% in ID/DD (79/251). When aneuploidies were included, the diagnostic yield increased to 22.4% for all NDDs (92/410), and 33.6% for ID/DD (87/259). We identified a de novo CNV in 14.9% (60/402) of subjects with NDDs. Interestingly, a higher diagnostic yield was observed in females (31.3%, 40/128) compared to males (16.1%, 44/274) for all NDDs (P = 4.8 × 10-4), suggesting that a female protective mechanism exists for deleterious CNVs and UPDs.
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Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Edward J Higginbotham
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Yue Li
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Dongmei Zhao
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Fengling Song
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Yali Yang
- Rehabilitation Center, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Haiyan Zhang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Stephen W Scherer
- The Centre for Applied Genomics and Department of 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 1A1, Canada.
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China.
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Hua Tan CS, Ang SF, Yeoh E, Goh BX, Loh WJ, Shum CF, May Ping Eng M, Yan Lun Liu A, Wan Ting Chan L, Goh LX, Subramaniam T, Sum CF, Lim SC. MODY5 Hepatocyte Nuclear Factor 1ß (HNF1ß)-Associated Nephropathy: experience from a regional monogenic diabetes referral centre in Singapore. J Investig Med High Impact Case Rep 2022; 10:23247096211065626. [PMID: 35038894 PMCID: PMC8784948 DOI: 10.1177/23247096211065626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/11/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
From our monogenic diabetes registry set-up at a secondary-care diabetes center, we identified a nontrivial subpopulation (~15%) of maturity-onset diabetes of the young (MODY) among people with young-onset diabetes. In this report, we describe the diagnostic caveats, clinical features and long-term renal-trajectory of people with HNF1B mutations (HNF1B-MODY). Between 2013 and 2020, we received 267 referrals to evaluate MODY from endocrinologists in both public and private practice. Every participant was subjected to a previously reported structured evaluation process, high-throughput nucleotide sequencing and gene-dosage analysis. Out of 40 individuals with confirmed MODY, 4 (10%) had HNF1B-MODY (harboring either a HNF1B whole-gene deletion or duplication). Postsequencing follow-up biochemical and radiological evaluations revealed the known HNF1B-MODY associated systemic-features, such as transaminitis and structural renal-lesions. These anomalies could have been missed without prior knowledge of the nucleotide-sequencing results. Interestingly, preliminary longitudinal observation (up to 15 years) suggested possibly 2 distinct patterns of renal-deterioration (albuminuric vs. nonalbuminuric chronic kidney disease). Monogenic diabetes like HNF1B-MODY may be missed among young-onset diabetes in a resource-limited routine-care clinic. Collaboration with a MODY-evaluation center may fill the care-gap. The long-term renal-trajectories of HNF1B-MODY will require further studies by dedicated registries and international consortium.
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Affiliation(s)
| | - Su Fen Ang
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | - Ester Yeoh
- Diabetes Centre, Admiralty Medical Centre, Singapore
| | - Bing Xing Goh
- Diabetes Centre, Admiralty Medical Centre, Singapore
| | - Wann Jia Loh
- Department of Endocrinology, Changi General Hospital, Singapore
| | - Cheuk Fan Shum
- Department of Surgery, Woodlands Health Campus, Singapore
| | | | | | | | - Li Xian Goh
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | | | - Chee Fang Sum
- Diabetes Centre, Admiralty Medical Centre, Singapore
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
- Diabetes Centre, Admiralty Medical Centre, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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Zhang Z, Pan L, Chen K, Tan R. Prenatal ultrasound features and genetic analysis for 17q12 microdeletion syndrome. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:1370-1374. [PMID: 35232906 PMCID: PMC10930568 DOI: 10.11817/j.issn.1672-7347.2021.210412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVES The 17q12 microdeletion syndrome is a type of syndrome caused by a deletion of 1.4 to 1.8 Mb in the 17q12 region of the chromosome. The main clinical features of the syndrome are structural or functional abnormalities in the kidney and urethra, type 5 diabetes, and neurodevelopmental or neuropsychiatric disorders. The diverse range of phenotypes associated with 17q12 microdeletion limited clinical recognition and diagnosis. In addition, the phenotypic description of this microdeletion is mainly about postpartum. Due to the rarity of the 17q12 microdeletion itself, studies on the prenatal phenotype of the 17q12 microdeletion are limited. This study aims to analyze the prenatal ultrasound features of 17q12 microdeletion, and to investigate the possibility of genotype-phenotype relationship for providing evidence for genetic counseling in such pregnancies. METHODS A total of 3 320 pregnant women and their fetuses were collected for the detection of chromosome copy number variation sequencing (CNV-Seq) due to different ultrasound anomalies in Xiangya Hospital of Central South University. The clinical data of pregnant women and their fetuses who were found to harbor 17q12 microdeletion were reviewed, including maternal age, fetus ultrasound findings, gestational week of the invasive procedure, CNV-Seq results, and the pregnancy outcome. CNV-Seq was tested in the parents to verify whether the abnormality was de novo or inherited. The prenatal ultrasound features and CNV-Seq test results of these 12 fetuses were analyzed and their pregnancy outcomes were followed up. RESULTS Approximately 0.36% (12/3 320) of fetuses were detected to have 17q12 microdeletion, all characterized as renal abnormalities, accounting for 4.2% (12/288) of all prenatal ultrasound with renal abnormalities, accounting for 48% (12/25) of prenatal ultrasound with renal abnormalities and pathogenic chromosomal abnormalities. The sizes of 17q12 deletion ranged from 1.4 to 1.7 Mb, and all of them included the HNF1B gene. Nine cases were de novo, 2 inherited from the mother, and 1 inherited from father. Among 12 fetuses with 17q12 deletion, 11 cases of prenatal ultrasound suggested bilateral hyperechogenic kidneys and 1 case only showed renal cyst, in which 3 fetuses with enlarged kidneys, 1 with clubfeet, and 1 with subependymal cyst. Pregnancy outcomes were available for 11 of the 12 fetuses. Of them, the parents of 9 fetuses with de novo deletion chose to terminate the pregnancy, and 2 live birth babies inherited from their mother with normal renal function had persistent renal echogenicity enhancement after birth. CONCLUSIONS Bilateral hyperechogenic kidneys show strikingly correlation with 17q12 microdeletion, suggesting the necessity of chromosome copy numbers detection for fetuses with hyperechogenic kidneys.
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Affiliation(s)
- Zhenhui Zhang
- Department of Obstetrics, First Hospital of Changsha, Changsha 410005.
| | - Lijuan Pan
- Department of Obstetrics, Xiangya Hospital, Central South University, Changsha 410008.
| | - Kuifang Chen
- Department of Obstetrics, Xiangya Hospital, Central South University, Changsha 410008
| | - Rong Tan
- Department of Ultrasonography, First Hospital of Changsha, Changsha 410005, China
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Tal-Ben Ishay R, Shil A, Solomon S, Sadigurschi N, Abu-Kaf H, Meiri G, Flusser H, Michaelovski A, Dinstein I, Golan H, Davidovitch N, Menashe I. Diagnostic Yield and Economic Implications of Whole-Exome Sequencing for ASD Diagnosis in Israel. Genes (Basel) 2021; 13:genes13010036. [PMID: 35052376 PMCID: PMC8774872 DOI: 10.3390/genes13010036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Whole-exome sequencing (WES) is an effective approach to identify the susceptibility of genetic variants of autism spectrum disorder (ASD). The Israel Ministry of Health supports WES as an adjunct tool for ASD diagnosis, despite its unclear diagnostic yield and cost effectiveness. To address this knowledge gap, we applied WES to a population-based sample of 182 Bedouin and Jewish children with ASD from southern Israel, and assessed its yield in a gene panel of 205 genes robustly associated with ASD. We then compared the incremental cost-effectiveness ratios (ICERs) for an ASD diagnosis by WES, chromosomal microarray analysis (CMA), and CMA + WES. Overall, 32 ASD candidate variants were detected in 28 children, corresponding to an overall WES diagnostic yield of 15.4%. Interestingly, the diagnostic yield was significantly higher for the Bedouin children than for the Jewish children, i.e., 27.6% vs. 11.1% (p = 0.036). The most cost-effective means for genetic testing was the CMA alone, followed closely by the CMA + WES strategy (ICER = USD 117 and USD 124.8 per child). Yet, WES alone could become more cost effective than the other two approaches if there was to be a 25% increase in its yield or a 50% decrease in its cost. These findings suggest that WES should be recommended to facilitate ASD diagnosis in Israel, especially for highly consanguineous populations, such as the Bedouin.
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Affiliation(s)
- Rotem Tal-Ben Ishay
- Department of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (R.T.-B.I.); (A.S.)
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
| | - Apurba Shil
- Department of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (R.T.-B.I.); (A.S.)
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
| | - Shirley Solomon
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
| | - Noa Sadigurschi
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
| | - Hadeel Abu-Kaf
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
| | - Gal Meiri
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Preschool Psychiatric Unit, Soroka University Medical Center, Beer-Sheva 84100, Israel
| | - Hagit Flusser
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Child Development Center, Soroka University Medical Center, Beer-Sheva 84100, Israel
| | - Analya Michaelovski
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Child Development Center, Soroka University Medical Center, Beer-Sheva 84100, Israel
| | - Ilan Dinstein
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
- Psychology Department, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
| | - Hava Golan
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
| | - Nadav Davidovitch
- Department of Health Systems Management, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel;
| | - Idan Menashe
- Department of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (R.T.-B.I.); (A.S.)
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel; (S.S.); (N.S.); (H.A.-K.); (G.M.); (H.F.); (A.M.); (I.D.); (H.G.)
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 84100, Israel
- Correspondence: ; Tel.: +972-8-6477456
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Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan. Medicina (B Aires) 2021; 58:medicina58010015. [PMID: 35056323 PMCID: PMC8779646 DOI: 10.3390/medicina58010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background and Objectives: Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNVs) and is recommended for the initial genetic testing of patients with autism spectrum disorder (ASD). This study aims to determine the diagnostic yield of array comparative genomic hybridization (array-CGH) in ASD patients from a cohort of Chinese patients in Taiwan. Materials and Methods: Enrolled in this study were 80 ASD children (49 males and 31 females; 2–16 years old) followed up at Taipei MacKay Memorial Hospital between January 2010 and December 2020. The genomic DNA extracted from blood samples was analyzed by array-CGH via the Affymetrix GeneChip Genome-Wide Human single nucleotide polymorphism (SNP) and NimbleGen International Standards for Cytogenomic Arrays (ISCA) Plus Cytogenetic Arrays. The CNVs were classified into five groups: pathogenic (pathologic variant), likely pathogenic (potential pathologic variant), likely benign (potential normal genomic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance), according to the American College of Medical Genetics (ACMG) guidelines. Results: We identified 47 CNVs, 31 of which in 27 patients were clinically significant. The overall diagnostic yield was 33.8%. The most frequently clinically significant CNV was 15q11.2 deletion, which was present in 4 (5.0%) patients. Conclusions: In this study, a satisfactory diagnostic yield of array-CGH was demonstrated in a Taiwanese ASD patient cohort, supporting the clinical usefulness of array-CGH as the first-line testing of ASD in Taiwan.
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Liu L, Feng X, Li H, Cheng Li S, Qian Q, Wang Y. Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5. Brief Bioinform 2021; 22:bbab207. [PMID: 34109382 PMCID: PMC8575025 DOI: 10.1093/bib/bbab207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Attention deficit hyperactivity disorder (ADHD) is a common neurodevelopmental disorder. Although genome-wide association studies (GWAS) identify the risk ADHD-associated variants and genes with significant P-values, they may neglect the combined effect of multiple variants with insignificant P-values. Here, we proposed a convolutional neural network (CNN) to classify 1033 individuals diagnosed with ADHD from 950 healthy controls according to their genomic data. The model takes the single nucleotide polymorphism (SNP) loci of P-values $\le{1\times 10^{-3}}$, i.e. 764 loci, as inputs, and achieved an accuracy of 0.9018, AUC of 0.9570, sensitivity of 0.8980 and specificity of 0.9055. By incorporating the saliency analysis for the deep learning network, a total of 96 candidate genes were found, of which 14 genes have been reported in previous ADHD-related studies. Furthermore, joint Gene Ontology enrichment and expression Quantitative Trait Loci analysis identified a potential risk gene for ADHD, EPHA5 with a variant of rs4860671. Overall, our CNN deep learning model exhibited a high accuracy for ADHD classification and demonstrated that the deep learning model could capture variants' combining effect with insignificant P-value, while GWAS fails. To our best knowledge, our model is the first deep learning method for the classification of ADHD with SNPs data.
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Affiliation(s)
- Lu Liu
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
| | - Xikang Feng
- School of Software, Northwestern Polytechnical University, Xi’an, 710072, Shaanxi, China
| | - Haimei Li
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Qiujin Qian
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
| | - Yufeng Wang
- Peking University Sixth Hospital/Institute of Mental Health, National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital) & the Key Laboratory of Mental Health, Ministry of Health (Peking University), 100191, Beijing, China
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Kava R, Peripolli E, Berton MP, Lemos M, Lobo RB, Stafuzza NB, Pereira AS, Baldi F. Genome-wide structural variations in Brazilian Senepol cattle, a tropically adapted taurine breed. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mucosa-associated specific bacterial species disrupt the intestinal epithelial barrier in the autism phenome. Brain Behav Immun Health 2021; 15:100269. [PMID: 34589774 PMCID: PMC8474478 DOI: 10.1016/j.bbih.2021.100269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/20/2022] Open
Abstract
Gut-Brain Axis provides a bidirectional communicational route, an imbalance of which can have pathophysiological consequences. Differential gut microbiome studies have become a frontier in autism research, affecting 85% of autistic children. The present study aims to understand how gut microbiota of autism subjects differ from their neurotypical counterparts. This study would help to identify the abundance of bacterial signature species in autism and their associated metabolites. 16S rRNA metagenomic sequence datasets of 30 out of 206 autism subjects were selected from the American Gut Project Archive. First, the taxonomic assignment was inferred by similarity-based methods using the Quantitative Insights into Microbial Ecology (QIIME) toolkit. Next, species abundance was characterized, and a co-occurrence network was built to infer species interaction using measures of diversity. Thirdly, statistical parameters were incorporated to validate the findings. Finally, the identification of metabolites associated with these bacterial signature species connects with biological processes in the host through pathway analysis. Gut microbiome data revealed Akkermansia sp. and Faecalibacterium prausnitzii to be statistically lower in abundance in autistic children than their neurotypical peers with a five and two-fold decrease, respectively. While Prevotella sp. and Sutterella sp. showed a five and a two-fold increase in cases, respectively. The constructed pathway revealed succinate and butyrate as the significant metabolites for the bacterial signature species identified. The present study throws light on the role of mucosa-associated bacterial species: Veillonella sp., Prevotella sp., Akkermansia sp., Sutterella sp., Faecalibacterium prausnitzii, Lactobacillus sp., which can act as diagnostic criteria for detection of gut dysbiosis in autism. Bacteroidetes/Firmicutes ratio is significantly higher in autistic children due to differential lifestyle habits in the present study. Mucosal associated bacteria, namely Prevotella, Akkermansia, Veillonella, Sutterella, and Faecalibacterium are indicated as potential diagnostic criteria for gut dysbiosis in autism. Elevated Proteobacteria levels is contrasting with reported inclinations towards gut related functionality in mouse models. The authors report unique link for autism and Prevotella sp. phylotype with higher relative abundance in autism cases. Pathway revealed succinate and butyrate as the significant metabolites for the identified bacterial signatures.
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Cuttler K, Hassan M, Carr J, Cloete R, Bardien S. Emerging evidence implicating a role for neurexins in neurodegenerative and neuropsychiatric disorders. Open Biol 2021; 11:210091. [PMID: 34610269 PMCID: PMC8492176 DOI: 10.1098/rsob.210091] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Synaptopathies are brain disorders characterized by dysfunctional synapses, which are specialized junctions between neurons that are essential for the transmission of information. Synaptic dysfunction can occur due to mutations that alter the structure and function of synaptic components or abnormal expression levels of a synaptic protein. One class of synaptic proteins that are essential to their biology are cell adhesion proteins that connect the pre- and post-synaptic compartments. Neurexins are one type of synaptic cell adhesion molecule that have, recently, gained more pathological interest. Variants in both neurexins and their common binding partners, neuroligins, have been associated with several neuropsychiatric disorders. In this review, we summarize some of the key physiological functions of the neurexin protein family and the protein networks they are involved in. Furthermore, examination of published literature has implicated neurexins in both neuropsychiatric and neurodegenerative disorders. There is a clear link between neurexins and neuropsychiatric disorders, such as autism spectrum disorder and schizophrenia. However, multiple expression studies have also shown changes in neurexin expression in several neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. Therefore, this review highlights the potential importance of neurexins in brain disorders and the importance of doing more targeted studies on these genes and proteins.
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Affiliation(s)
- Katelyn Cuttler
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Maryam Hassan
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Jonathan Carr
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Cape Town, South Africa
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Cape Town, South Africa
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Madencioglu DA, Çalışkan G, Yuanxiang P, Rehberg K, Demiray YE, Kul E, Engler A, Hayani H, Bergado-Acosta JR, Kummer A, Müller I, Song I, Dityatev A, Kähne T, Kreutz MR, Stork O. Transgenic modeling of Ndr2 gene amplification reveals disturbance of hippocampus circuitry and function. iScience 2021; 24:102868. [PMID: 34381982 PMCID: PMC8340122 DOI: 10.1016/j.isci.2021.102868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/19/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022] Open
Abstract
Duplications and deletions of short chromosomal fragments are increasingly recognized as the cause for rare neurodevelopmental conditions and disorders. The NDR2 gene encodes a protein kinase important for neuronal development and is part of a microduplication region on chromosome 12 that is associated with intellectual disabilities, autism, and epilepsy. We developed a conditional transgenic mouse with increased Ndr2 expression in postmigratory forebrain neurons to study the consequences of an increased gene dosage of this Hippo pathway kinase on brain circuitry and cognitive functions. Our analysis reveals reduced terminal fields and synaptic transmission of hippocampal mossy fibers, altered hippocampal network activity, and deficits in mossy fiber-dependent behaviors. Reduced doublecortin expression and protein interactome analysis indicate that transgenic Ndr2 disturbs the maturation of granule cells in the dentate gyrus. Together, our data suggest that increased expression of Ndr2 may critically contribute to the development of intellectual disabilities upon gene amplification.
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Affiliation(s)
- Deniz A. Madencioglu
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
| | - Gürsel Çalışkan
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39102Magdeburg, Germany
| | - Pingan Yuanxiang
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39112Magdeburg, Germany
| | - Kati Rehberg
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
| | - Yunus E. Demiray
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
| | - Emre Kul
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
| | - Alexander Engler
- Institute of Experimental Internal Medicine, Otto-von-Guericke-University, 39120Magdeburg, Germany
| | - Hussam Hayani
- Molecular Neuroplasticity Group, German Center for Neurodegenerative Diseases, 39120Magdeburg, Germany
| | - Jorge R. Bergado-Acosta
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39102Magdeburg, Germany
| | - Anne Kummer
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
| | - Iris Müller
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39102Magdeburg, Germany
| | - Inseon Song
- Molecular Neuroplasticity Group, German Center for Neurodegenerative Diseases, 39120Magdeburg, Germany
| | - Alexander Dityatev
- Molecular Neuroplasticity Group, German Center for Neurodegenerative Diseases, 39120Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39102Magdeburg, Germany
- Medical Faculty, Otto-von-Guericke-University, 39120Magdeburg, Germany
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto-von-Guericke-University, 39120Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39102Magdeburg, Germany
| | - Michael R. Kreutz
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39112Magdeburg, Germany
- Leibniz Group 'Dendritic Organelles and Synaptic Function', University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, 20251Hamburg, Germany
- Center for Behavioral Brain Sciences, 39102Magdeburg, Germany
| | - Oliver Stork
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39102Magdeburg, Germany
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Radhakrishna U. Artificial intelligence and placental DNA methylation: newborn prediction and molecular mechanisms of autism in preterm children. J Matern Fetal Neonatal Med 2021; 35:8150-8159. [PMID: 34404318 DOI: 10.1080/14767058.2021.1963704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Autism Spectrum Disorder (ASD) represents a heterogeneous group of disorders with a complex genetic and epigenomic etiology. DNA methylation is the most extensively studied epigenomic mechanism and correlates with altered gene expression. Artificial intelligence (AI) is a powerful tool for group segregation and for handling the large volume of data generated in omics experiments. METHODS We performed genome-wide methylation analysis for differential methylation of cytosine nucleotide (CpG) was performed in 20 postpartum placental tissue samples from preterm births. Ten newborns went on to develop autism (Autistic Disorder subtype) and there were 10 unaffected controls. AI including Deep Learning (AI-DL) platforms were used to identify and rank cytosine methylation markers for ASD detection. Ingenuity Pathway Analysis (IPA) to identify genes and molecular pathways that were dysregulated in autism. RESULTS We identified 4870 CpG loci comprising 2868 genes that were significantly differentially methylated in ASD compared to controls. Of these 431 CpGs met the stringent EWAS threshold (p-value <5 × 10-8) along with ≥10% methylation difference between CpGs in cases and controls. DL accurately predicted autism with an AUC (95% CI) of 1.00 (1-1) and sensitivity and specificity of 100% using a combination of 5 CpGs [cg13858611 (NRN1), cg09228833 (ZNF217), cg06179765 (GPNMB), cg08814105 (NKX2-5), cg27092191 (ZNF267)] CpG markers. IPA identified five prenatally dysregulated molecular pathways linked to ASD. CONCLUSIONS The present study provides substantial evidence that epigenetic differences in placental tissue are associated with autism development and raises the prospect of early and accurate detection of the disorder.
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Affiliation(s)
- Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, USA
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
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Padhi EM, Hayeck TJ, Cheng Z, Chatterjee S, Mannion BJ, Byrska-Bishop M, Willems M, Pinson L, Redon S, Benech C, Uguen K, Audebert-Bellanger S, Le Marechal C, Férec C, Efthymiou S, Rahman F, Maqbool S, Maroofian R, Houlden H, Musunuri R, Narzisi G, Abhyankar A, Hunter RD, Akiyama J, Fries LE, Ng JK, Mehinovic E, Stong N, Allen AS, Dickel DE, Bernier RA, Gorkin DU, Pennacchio LA, Zody MC, Turner TN. Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. Hum Genomics 2021; 15:44. [PMID: 34256850 PMCID: PMC8278787 DOI: 10.1186/s40246-021-00342-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. RESULTS We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 × 10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. CONCLUSIONS In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.
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Affiliation(s)
- Evin M Padhi
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Tristan J Hayeck
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Zhang Cheng
- Center for Epigenomics, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sumantra Chatterjee
- Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY, 10016, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Marjolaine Willems
- University of Montpellier, département de Génétique, maladies rares médecine personnalisée, U 1298, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Lucile Pinson
- University of Montpellier, département de Génétique, maladies rares médecine personnalisée, U 1298, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Sylvia Redon
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Caroline Benech
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Kevin Uguen
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | | | - Cédric Le Marechal
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Claude Férec
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Fatima Rahman
- Development and Behavioral Pediatrics Department, Institute of Child Health and Children Hospital, Lahore, Pakistan
| | - Shazia Maqbool
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Development and Behavioral Pediatrics Department, Institute of Child Health and Children Hospital, Lahore, Pakistan
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | | | | | - Riana D Hunter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lauren E Fries
- Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY, 10016, USA
| | - Jeffrey K Ng
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Elvisa Mehinovic
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Nick Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, 10027, USA
| | - Andrew S Allen
- Center for Statistical Genetics and Genomics, Duke University, Durham, NC, 27708, USA
- Division of Integrative Genomics, Duke University, Durham, NC, 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
| | - David U Gorkin
- Center for Epigenomics, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.
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Koire A, Katsonis P, Kim YW, Buchovecky C, Wilson SJ, Lichtarge O. A method to delineate de novo missense variants across pathways prioritizes genes linked to autism. Sci Transl Med 2021; 13:13/594/eabc1739. [PMID: 34011629 DOI: 10.1126/scitranslmed.abc1739] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 03/01/2021] [Indexed: 12/31/2022]
Abstract
Genotype-phenotype relationships shape health and population fitness but remain difficult to predict and interpret. Here, we apply an evolutionary action method to de novo missense variants in whole-exome sequences of individuals with autism spectrum disorder (ASD) to unravel genes and pathways connected to ASD. Evolutionary action predicts the impact of missense variants on protein function by measuring the fitness effect based on phylogenetic distances and substitution odds in homologous gene sequences. By examining de novo missense variants in 2384 individuals with ASD (probands) compared to matched siblings without ASD, we found missense variants in 398 genes representing 23 pathways that were biased toward higher evolutionary action scores than expected by random chance; these pathways were involved in axonogenesis, synaptic transmission, and neurodevelopment. The predicted fitness impact of de novo and inherited missense variants in candidate genes correlated with the IQ of individuals with ASD, even for new gene candidates. Taking an evolutionary action method, we detected those missense variants most likely to contribute to ASD pathogenesis and elucidated their phenotypic impact. This approach could be applied to integrate missense variants across a patient cohort to identify genes contributing to a shared phenotype in other complex diseases.
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Affiliation(s)
- Amanda Koire
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA.,Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Young Won Kim
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Christie Buchovecky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Division of Carrier Screening and Prenatal Testing, SEMA4, Stamford, CT, USA
| | - Stephen J Wilson
- Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA
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Frei JA, Niescier RF, Bridi MS, Durens M, Nestor JE, Kilander MBC, Yuan X, Dykxhoorn DM, Nestor MW, Huang S, Blatt GJ, Lin YC. Regulation of Neural Circuit Development by Cadherin-11 Provides Implications for Autism. eNeuro 2021; 8:ENEURO.0066-21.2021. [PMID: 34135003 PMCID: PMC8266214 DOI: 10.1523/eneuro.0066-21.2021] [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: 02/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurologic condition characterized by alterations in social interaction and communication, and restricted and/or repetitive behaviors. The classical Type II cadherins cadherin-8 (Cdh8, CDH8) and cadherin-11 (Cdh11, CDH11) have been implicated as autism risk gene candidates. To explore the role of cadherins in the etiology of autism, we investigated their expression patterns during mouse brain development and in autism-specific human tissue. In mice, expression of cadherin-8 and cadherin-11 was developmentally regulated and enriched in the cortex, hippocampus, and thalamus/striatum during the peak of dendrite formation and synaptogenesis. Both cadherins were expressed in synaptic compartments but only cadherin-8 associated with the excitatory synaptic marker neuroligin-1. Induced pluripotent stem cell (iPSC)-derived cortical neural precursor cells (NPCs) and cortical organoids generated from individuals with autism showed upregulated CDH8 expression levels, but downregulated CDH11. We used Cdh11 knock-out (KO) mice of both sexes to analyze the function of cadherin-11, which could help explain phenotypes observed in autism. Cdh11-/- hippocampal neurons exhibited increased dendritic complexity along with altered neuronal and synaptic activity. Similar to the expression profiles in human tissue, levels of cadherin-8 were significantly elevated in Cdh11 KO brains. Additionally, excitatory synaptic markers neuroligin-1 and postsynaptic density (PSD)-95 were both increased. Together, these results strongly suggest that cadherin-11 is involved in regulating the development of neuronal circuitry and that alterations in the expression levels of cadherin-11 may contribute to the etiology of autism.
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Affiliation(s)
- Jeannine A Frei
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Robert F Niescier
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Morgan S Bridi
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Madel Durens
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Jonathan E Nestor
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | | | - Xiaobing Yuan
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Michael W Nestor
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Shiyong Huang
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Gene J Blatt
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Yu-Chih Lin
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
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50
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Okay K, Varış PÜ, Miral S, Ekinci B, Yaraş T, Karakülah G, Oktay Y. Alternative splicing and gene co-expression network-based analysis of dizygotic twins with autism-spectrum disorder and their parents. Genomics 2021; 113:2561-2571. [PMID: 34087420 DOI: 10.1016/j.ygeno.2021.05.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/25/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high heritability, however, understanding the complexity of the underlying genetic basis has proven to be a challenging task. We hypothesized that dissecting the aberrations in alternative splicing (AS) and their effects on expression networks might provide insight. Therefore, we performed AS and co-expression analyses of total RNA isolated from Peripheral Blood Mononuclear Cells (PBMCs) of two pairs of dizygotic (DZ) twins with non-syndromic autism and their parents. We identified 183 differential AS events in 146 genes, seven of them being Simons Foundation Autism Research Initiative (SFARI) Category 1-3 genes, three of which had previously been reported to be alternatively spliced in ASD post-mortem brains. Gene co-expression analysis identified 7 modules with 513 genes, 5 of which were SFARI Category 1 or Category 2 genes. Among differentially AS genes within the modules, ZNF322 and NR4A1 could be potentially interesting targets for further investigations.
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Affiliation(s)
- Kaan Okay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Pelin Ünal Varış
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey; Barış Psychiatric Hospital, Nicosia, Cyprus
| | - Süha Miral
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey
| | - Burcu Ekinci
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Tutku Yaraş
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey.
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey; Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey.
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