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Ng JK, Chen Y, Akinwe TM, Heins HB, Mehinovic E, Chang Y, Payne ZL, Manuel JG, Karchin R, Turner TN. Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.02.24302238. [PMID: 38352539 PMCID: PMC10863034 DOI: 10.1101/2024.02.02.24302238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Missense de novo variants (DNVs) and missense somatic variants contribute to neurodevelopmental disorders (NDDs) and cancer, respectively. Proteins with statistical enrichment based on analyses of these variants exhibit convergence in the differing NDD and cancer phenotypes. Herein, the question of why some of the same proteins are identified in both phenotypes is examined through investigation of clustering of missense variation at the protein level. Our hypothesis is that missense variation is present in different protein locations in the two phenotypes leading to the distinct phenotypic outcomes. We tested this hypothesis in 1D protein space using our software CLUMP. Furthermore, we newly developed 3D-CLUMP that uses 3D protein structures to spatially test clustering of missense variation for proteome-wide significance. We examined missense DNVs in 39,883 parent-child sequenced trios with NDDs and missense somatic variants from 10,543 sequenced tumors covering five TCGA cancer types and two COSMIC pan-cancer aggregates of tissue types. There were 57 proteins with proteome-wide significant missense variation clustering in NDDs when compared to cancers and 79 proteins with proteome-wide significant missense clustering in cancers compared to NDDs. While our main objective was to identify differences in patterns of missense variation, we also identified a novel NDD protein BLTP2. Overall, our study is innovative, provides new insights into differential missense variation in NDDs and cancer at the protein-level, and contributes necessary information toward building a framework for thinking about prognostic and therapeutic aspects of these proteins.
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Affiliation(s)
- Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yilin Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Titilope M. Akinwe
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hillary B. Heins
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elvisa Mehinovic
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoonhoo Chang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Human & Statistical Genetics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary L. Payne
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juana G. Manuel
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
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Mariano V, Kanellopoulos AK, Ricci C, Di Marino D, Borrie SC, Dupraz S, Bradke F, Achsel T, Legius E, Odent S, Billuart P, Bienvenu T, Bagni C. Intellectual Disability and Behavioral Deficits Linked to CYFIP1 Missense Variants Disrupting Actin Polymerization. Biol Psychiatry 2024; 95:161-174. [PMID: 37704042 DOI: 10.1016/j.biopsych.2023.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND 15q11.2 deletions and duplications have been linked to autism spectrum disorder, schizophrenia, and intellectual disability. Recent evidence suggests that dysfunctional CYFIP1 (cytoplasmic FMR1 interacting protein 1) contributes to the clinical phenotypes observed in individuals with 15q11.2 deletion/duplication syndrome. CYFIP1 plays crucial roles in neuronal development and brain connectivity, promoting actin polymerization and regulating local protein synthesis. However, information about the impact of single nucleotide variants in CYFIP1 on neurodevelopmental disorders is limited. METHODS Here, we report a family with 2 probands exhibiting intellectual disability, autism spectrum disorder, spastic tetraparesis, and brain morphology defects and who carry biallelic missense point mutations in the CYFIP1 gene. We used skin fibroblasts from one of the probands, the parents, and typically developing individuals to investigate the effect of the variants on the functionality of CYFIP1. In addition, we generated Drosophila knockin mutants to address the effect of the variants in vivo and gain insight into the molecular mechanism that underlies the clinical phenotype. RESULTS Our study revealed that the 2 missense variants are in protein domains responsible for maintaining the interaction within the wave regulatory complex. Molecular and cellular analyses in skin fibroblasts from one proband showed deficits in actin polymerization. The fly model for these mutations exhibited abnormal brain morphology and F-actin loss and recapitulated the core behavioral symptoms, such as deficits in social interaction and motor coordination. CONCLUSIONS Our findings suggest that the 2 CYFIP1 variants contribute to the clinical phenotype in the probands that reflects deficits in actin-mediated brain development processes.
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Affiliation(s)
- Vittoria Mariano
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland; Department of Human Genetics, KU Leuven, Belgium
| | | | - Carlotta Ricci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center, Polytechnic University of Marche, Ancona, Italy; Department of Neuroscience, Neuronal Death and Neuroprotection Unit, Mario Negri Institute for Pharmacological Research-IRCCS, Milan, Italy
| | | | - Sebastian Dupraz
- Axonal Growth and Regeneration Group, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Frank Bradke
- Axonal Growth and Regeneration Group, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Eric Legius
- Department of Human Genetics, KU Leuven, Belgium
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Labellisé pour les Anomalies du Développement Ouest, Centre Hospitalier Universitaire de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS, UMR 6290, Université de Rennes, ERN-ITHACA, France
| | - Pierre Billuart
- Institut de Psychiatrie et de Neurosciences de Paris, Institut National de la Santé et de la Recherche Médicale U1266, Université de Paris Cité (UPC), Paris, France
| | - Thierry Bienvenu
- Institut de Psychiatrie et de Neurosciences de Paris, Institut National de la Santé et de la Recherche Médicale U1266, Université de Paris Cité (UPC), Paris, France
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
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3
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Fang Y, Cui Y, Yin Z, Hou M, Guo P, Wang H, Liu N, Cai C, Wang M. Comprehensive systematic review and meta-analysis of the association between common genetic variants and autism spectrum disorder. Gene 2023; 887:147723. [PMID: 37598788 DOI: 10.1016/j.gene.2023.147723] [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: 04/03/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is neurodevelopmental disorder characterized by stereotyped behavior and deficits in communication and social interactions. To date, numerous studies have investigated the associations between genetic variants and ASD risk. However, the results of these published studies lack a clear consensus. In the present study, we performed a systematic review on the association between genetic variants and ASD risk. Meanwhile, we conducted a meta-analysis on available data to identify the association between the single nucleotide polymorphisms (SNPs) of candidate genes and ASD risk. METHODS We systematically searched public databases including English and Chinese from their inception to August 1, 2022. Two independent reviewers extracted data and assessed study quality. Odds ratio and 95 % confidence interval were used as effect indexes to evaluate the association between the SNPs of candidate genes and the risk of ASD. Heterogeneity was explored through subgroup, sensitivity, and meta-regression analyses. Publication bias was assessed by using Egger's and Begg's tests for funnel plot asymmetry. In addition, TSA analysis were performed to confirm the study findings. RESULTS We summarized 84 SNPs of 32 candidate genes from 81 articles included in the study. Subsequently, we analyzed 16 SNPs of eight genes by calculating pooled ORs, and identified eight significant SNPs of contactin associated protein 2 (CNTNAP2), methylentetrahydrofolate reductase (MTHFR), oxytocin receptor (OXTR), and vitamin D receptor (VDR). Results showed that seven SNPs, including the CNTNAP2 rs2710102 (homozygote, heterozygote, dominant and allelic models) and rs7794745 (heterozygote and dominant models), MTHFR C677T (homozygote, heterozygote, dominant, recessive and allelic models) and A1298C (dominant and allelic models), OXTR rs2254298 (homozygote and recessive models), VDR rs731236 (homozygote, dominant, recessive and allelic models) and rs2228570 (homozygote and recessive models), were showed to be correlated with an increased ASD risk. By contrast, the VDR rs7975232 was correlated with a decreased the risk of ASD under the homozygote and allelic models. CONCLUSION Our study summarized research evidence on the genetic variants of ASD and provides a broad and detailed overview of ASD risk genes. The C677T and A1298C polymorphisms of MTHFR, rs2710102 and rs7794745 polymorphisms of CNTNAP2, rs2254298 polymorphism of OXTR, and rs731236 and rs2228570 polymorphisms of VDR were genetic risk factors. The rs7975232 polymorphism of VDR was a genetic protective factor for ASD. Our study provides novel clues to clinicians and healthcare decision-makers to predict ASD susceptibility.
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Affiliation(s)
- Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Yaqiong Cui
- Tianjin Pediatric Research Institute, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Zhaoqing Yin
- Division of Pediatrics, The People's Hospital of Dehong Autonomous Prefecture, Dehong Hospital of Kunming Medical University, Mangshi, Yunnan 678400, China
| | - Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Pan Guo
- Tianjin Pediatric Research Institute, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Hanjie Wang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin 300072, China
| | - Nan Liu
- Marshall Laboratory of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China; Institute of Environment and Health, South China Hospital, Medical School, Shenzhen 518116, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China.
| | - Mingbang Wang
- Marshall Laboratory of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China; Microbiome Therapy Center, South China Hospital, Medical School, Shenzhen University, Shenzhen, Guangdong 518116, China; Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China.
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4
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Woodbury-Smith M, D'Abate L, Stavropoulos DJ, Howe J, Drmic I, Hoang N, Zarrei M, Trost B, Iaboni A, Anagnostou E, Scherer SW. The Phenotypic variability of 16p11.2 distal BP2-BP3 deletion in a transgenerational family and in neurodevelopmentally ascertained samples. J Med Genet 2023; 60:1153-1160. [PMID: 37290907 PMCID: PMC10715508 DOI: 10.1136/jmg-2022-108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 05/03/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND We present genomic and phenotypic findings of a transgenerational family consisting of three male offspring, each with a maternally inherited distal 220 kb deletion at locus 16p11.2 (BP2-BP3). Genomic analysis of all family members was prompted by a diagnosis of autism spectrum disorder (ASD) in the eldest child, who also presented with a low body mass index. METHODS All male offspring underwent extensive neuropsychiatric evaluation. Both parents were also assessed for social functioning and cognition. The family underwent whole-genome sequencing. Further data curation was undertaken from samples ascertained for neurodevelopmental disorders and congenital abnormalities. RESULTS On medical examination, both the second and third-born male offspring presented with obesity. The second-born male offspring met research diagnostic criteria for ASD at 8 years of age and presented with mild attention deficits. The third-born male offspring was only noted as having motor deficits and received a diagnosis of developmental coordination disorder. Other than the 16p11.2 distal deletion, no additional contributing variants of clinical significance were observed. The mother was clinically evaluated and noted as having a broader autism phenotype. CONCLUSION In this family, the phenotypes observed are most likely caused by the 16p11.2 distal deletion. The lack of other overt pathogenic mutations identified by genomic sequencing reinforces the variable expressivity that should be heeded in a clinical setting. Importantly, distal 16p11.2 deletions can present with a highly variable phenotype even within a single family. Our additional data curation provides further evidence on the variable clinical presentation among those with pathogenetic 16p11.2 (BP2-BP3) mutations.
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Affiliation(s)
- Marc Woodbury-Smith
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Irene Drmic
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Ron Joyce Children's Health Centre, Autism Spectrum Disorder (ASD) Program and Child and Youth Mental Health Program, McMaster Autism Research Team, McMaster University, Hamilton, Hamilton, Ontario, Canada
| | - Ny Hoang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alana Iaboni
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Centre, Toronto, Ontario, Canada
| | - Evdokia Anagnostou
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Centre, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
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5
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Miller CJ, Golovina E, Wicker JS, Jacobsen JC, O'Sullivan JM. De novo network analysis reveals autism causal genes and developmental links to co-occurring traits. Life Sci Alliance 2023; 6:e202302142. [PMID: 37553252 PMCID: PMC10410065 DOI: 10.26508/lsa.202302142] [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: 05/08/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023] Open
Abstract
Autism is a complex neurodevelopmental condition that manifests in various ways. Autism is often accompanied by other conditions, such as attention-deficit/hyperactivity disorder and schizophrenia, which can complicate diagnosis and management. Although research has investigated the role of specific genes in autism, their relationship with co-occurring traits is not fully understood. To address this, we conducted a two-sample Mendelian randomisation analysis and identified four genes located at the 17q21.31 locus that are putatively causal for autism in fetal cortical tissue (LINC02210, LRRC37A4P, RP11-259G18.1, and RP11-798G7.6). LINC02210 was also identified as putatively causal for autism in adult cortical tissue. By integrating data from expression quantitative trait loci, genes and protein interactions, we identified that the 17q21.31 locus contributes to the intersection between autism and other neurological traits in fetal cortical tissue. We also identified a distinct cluster of co-occurring traits, including cognition and worry, linked to the genetic loci at 3p21.1. Our findings provide insights into the relationship between autism and co-occurring traits, which could be used to develop predictive models for more accurate diagnosis and better clinical management.
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Affiliation(s)
- Catriona J Miller
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Evgeniia Golovina
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Joerg S Wicker
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Jessie C Jacobsen
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Justin M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, Zealand
- Garvan Institute of Medical Research, Sydney, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
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6
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Costa CIS, da Silva Campos G, da Silva Montenegro EM, Wang JYT, Scliar M, Monfardini F, Zachi EC, Lourenço NCV, Chan AJS, Pereira SL, Engchuan W, Thiruvahindrapuram B, Zarrei M, Scherer SW, Passos-Bueno MR. Three generation families: Analysis of de novo variants in autism. Eur J Hum Genet 2023; 31:1017-1022. [PMID: 37280359 PMCID: PMC10474020 DOI: 10.1038/s41431-023-01398-6] [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: 09/19/2022] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023] Open
Abstract
De novo variants (DNVs) analysis has proven to be a powerful approach to gene discovery in Autism Spectrum Disorder (ASD), which has not yet been shown in a Brazilian ASD cohort. The relevance of inherited rare variants has also been suggested, particularly in oligogenic models. We hypothesized that three-generation analyses of DNVs could provide new insights into the relevance of de novo and inherited variants across generations. To accomplish this goal, we performed whole-exome sequencing of 33 septet families composed of probands, parents, and grandparents (n = 231 individuals) and compared DNV rates (DNVr) between generations and those from two control cohorts. The DNVr in the probands (DNVr = 1.16) was marginally higher than in parents (DNVr = 0.60; p = 0.054), and in controls (DNVr = 0.68; p = 0.035, congenital heart disorder and DNVr = 0.70; p = 0.047, unaffected ASD siblings from Simons Simplex Collection). Moreover, most of the DNVs were found to have paternal origin in both generations (84.6%). Finally, we observed that 40% (6/15) of the DNVs in parents transmitted for probands are in ASD or ASD candidate genes, representing recently emerged risk variants to ASD in their families and suggest ZNF536, MSL2 and HDAC9 as ASD candidate genes. We did not observe an enrichment of risk variants nor sex bias of transmitted variants in the three generations, that can be due to sample size. These results further reinforce the relevance of de novo variants in ASD.
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Affiliation(s)
- Claudia I Samogy Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Gabriele da Silva Campos
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Eduarda Morgana da Silva Montenegro
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Jaqueline Yu Ting Wang
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Marília Scliar
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Frederico Monfardini
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Elaine Cristina Zachi
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Naila C V Lourenço
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Ada J S Chan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil.
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7
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Caballero M, Koren A. The landscape of somatic mutations in lymphoblastoid cell lines. CELL GENOMICS 2023; 3:100305. [PMID: 37388907 PMCID: PMC10300552 DOI: 10.1016/j.xgen.2023.100305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/03/2023] [Accepted: 03/28/2023] [Indexed: 07/01/2023]
Abstract
Somatic mutations have important biological ramifications while exerting substantial rate, type, and genomic location heterogeneity. Yet, their sporadic occurrence makes them difficult to study at scale and across individuals. Lymphoblastoid cell lines (LCLs), a model system for human population and functional genomics, harbor large numbers of somatic mutations and have been extensively genotyped. By comparing 1,662 LCLs, we report that the mutational landscape of the genome varies across individuals in terms of the number of mutations, their genomic locations, and their spectra; this variation may itself be modulated by somatic trans-acting mutations. Mutations attributed to the translesion DNA polymerase η follow two different modes of formation, with one mode accounting for the hypermutability of the inactive X chromosome. Nonetheless, the distribution of mutations along the inactive X chromosome appears to follow an epigenetic memory of the active form.
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Affiliation(s)
- Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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8
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Revisiting mutagenesis at non-B DNA motifs in the human genome. Nat Struct Mol Biol 2023; 30:417-424. [PMID: 36914796 DOI: 10.1038/s41594-023-00936-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/03/2023] [Indexed: 03/16/2023]
Abstract
Non-B DNA structures formed by repetitive sequence motifs are known instigators of mutagenesis in experimental systems. Analyzing this phenomenon computationally in the human genome requires careful disentangling of intrinsic confounding factors, including overlapping and interrupted motifs and recurrent sequencing errors. Here, we show that accounting for these factors eliminates all signals of repeat-induced mutagenesis that extend beyond the motif boundary, and eliminates or dramatically shrinks the magnitude of mutagenesis within some motifs, contradicting previous reports. Mutagenesis not attributable to artifacts revealed several biological mechanisms. Polymerase slippage generates frequent indels within every variety of short tandem repeat motif, implicating slipped-strand structures. Interruption-correcting single nucleotide variants within short tandem repeats may originate from error-prone polymerases. Secondary-structure formation promotes single nucleotide variants within palindromic repeats and duplications within direct repeats. G-quadruplex motifs cause recurrent sequencing errors, whereas mutagenesis at Z-DNAs is conspicuously absent.
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9
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Bergeron LA, Besenbacher S, Zheng J, Li P, Bertelsen MF, Quintard B, Hoffman JI, Li Z, St Leger J, Shao C, Stiller J, Gilbert MTP, Schierup MH, Zhang G. Evolution of the germline mutation rate across vertebrates. Nature 2023; 615:285-291. [PMID: 36859541 PMCID: PMC9995274 DOI: 10.1038/s41586-023-05752-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/23/2023] [Indexed: 03/03/2023]
Abstract
The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies2. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis3. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.
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Affiliation(s)
- Lucie A Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | | | | | | | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Judy St Leger
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | | | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Centre for Evolutionary & Organismal Biology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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10
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SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing. Hum Genet 2023; 142:201-216. [PMID: 36376761 PMCID: PMC9918589 DOI: 10.1007/s00439-022-02494-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022]
Abstract
Copy number variants (CNVs) represent major etiologic factors in rare genetic diseases. Current clinical CNV interpretation workflows require extensive back-and-forth with multiple tools and databases. This increases complexity and time burden, potentially resulting in missed genetic diagnoses. We present the Suite for CNV Interpretation and Prioritization (SCIP), a software package for the clinical interpretation of CNVs detected by whole-genome sequencing (WGS). The SCIP Visualization Module near-instantaneously displays all information necessary for CNV interpretation (variant quality, population frequency, inheritance pattern, and clinical relevance) on a single page-supported by modules providing variant filtration and prioritization. SCIP was comprehensively evaluated using WGS data from 1027 families with congenital cardiac disease and/or autism spectrum disorder, containing 187 pathogenic or likely pathogenic (P/LP) CNVs identified in previous curations. SCIP was efficient in filtration and prioritization: a median of just two CNVs per case were selected for review, yet it captured all P/LP findings (92.5% of which ranked 1st). SCIP was also able to identify one pathogenic CNV previously missed. SCIP was benchmarked against AnnotSV and a spreadsheet-based manual workflow and performed superiorly than both. In conclusion, SCIP is a novel software package for efficient clinical CNV interpretation, substantially faster and more accurate than previous tools (available at https://github.com/qd29/SCIP , a video tutorial series is available at https://bit.ly/SCIPVideos ).
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11
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Xie Y, Wang H, Hu B, Zhang X, Liu A, Cai C, Li S, Chen C, Wang Z, Yin Z, Wang M. Dendritic Spine in Autism Genetics: Whole-Exome Sequencing Identifying De Novo Variant of CTTNBP2 in a Quad Family Affected by Autism Spectrum Disorder. CHILDREN (BASEL, SWITZERLAND) 2022; 10:children10010080. [PMID: 36670631 PMCID: PMC9856540 DOI: 10.3390/children10010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/05/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023]
Abstract
Autism spectrum disorder (ASD) affects around 1% of children with no effective blood test or cure. Recent studies have suggested that these are neurological disorders with a strong genetic basis and that they are associated with the abnormal formation of dendritic spines. Chromosome microarray (CMA) together with high-throughput sequencing technology has been used as a powerful tool to identify new candidate genes for ASD. In the present study, CMA was first used to scan for genome-wide copy number variants in a proband, and no clinically significant copy number variants were found. Whole-exome sequencing (WES) was used further for genetic testing of the whole quad family affected by ASD, including the proband, his non-autistic sister, and his parents. Sanger sequencing and MassARRAY-based validation were used to identify and confirm variants associated with ASD. WES yielded a 151-fold coverage depth for each sample. A total of 98.65% of the targeted whole-exome region was covered at >20-fold depth. A de novo variant in CTTNBP2, p.M115T, was identified. The CTTNBP2 gene belongs to a family of ankyrin repeat domain-containing proteins associated with dendritic spine formation. Although CTTNBP2 has been associated with ASD, limited studies have been developed to identify clinically relevant de novo mutations of CTTNBP2 in children with ASD; family-based WES successfully identified a clinically relevant mutation in the CTTNBP2 gene in a quad family affected by ASD. Considering the neuron-specific expression of CTTNBP2 and its role in dendritic spine formation, our results suggest a correlation between the CTTNBP2 mutation and ASD, providing genetic evidence for ASD spine pathology. Although the present study is currently insufficient to support the assertion that the de novo mutation M115T in CTTNBP2 directly causes the autism phenotype, our study provides support for the assertion that this mutation is a candidate clinically relevant variant in autism.
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Affiliation(s)
- Yingmei Xie
- Division of Neonatology, Longgang District Maternal and Child Health Hospital, Shenzhen 518172, China
| | - Hui Wang
- Division of Child Health Care, Xiamen Branch of Children’s Hospital of Fudan University (Xiamen Children’s Hospital), Xiamen 361006, China
| | - Bing Hu
- Division of Neonatology, Longgang District Maternal and Child Health Hospital, Shenzhen 518172, China
| | - Xueli Zhang
- Division of Neonatology, Shenzhen Longhua People’s Hospital, Shenzhen 518109, China
| | - Aiping Liu
- The Department of Laboratory, Baoan Public Health Service Center of Shenzhen, Shenzhen 518108, China
| | - Chunquan Cai
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children’s Hospital (Children’s Hospital of Tianjin University), Tianjin Pediatric Research Institute, Tianjin 300134, China
| | - Shijun Li
- First Medical Center, Chinese PLA General Hospital, Department of Radiology, Beijing 100853, China
| | - Cheng Chen
- Division of Neonatology, Longgang District Maternal and Child Health Hospital, Shenzhen 518172, China
| | - Zhangxing Wang
- Division of Neonatology, Shenzhen Longhua People’s Hospital, Shenzhen 518109, China
| | - Zhaoqing Yin
- The People’s Hospital of Dehong Autonomous Prefecture, Division of Pediatrics, Dehong Hospital of Kun-ming Medical University, Mangshi 678400, China
- Correspondence: (Z.Y.); (M.W.)
| | - Mingbang Wang
- Microbiome Therapy Center, South China Hospital, Medical School, Shenzhen University, Shenzhen 518116, China
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children’s Hospital of Fudan University, National Center for Children’s Health, Shanghai 201102, China
- Correspondence: (Z.Y.); (M.W.)
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12
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Jimbo M, Kunisaki J, Ghaed M, Yu V, Flores HA, Hotaling JM. Fertility in the aging male: a systematic review. Fertil Steril 2022; 118:1022-1034. [PMID: 36509505 PMCID: PMC10914128 DOI: 10.1016/j.fertnstert.2022.10.035] [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: 08/12/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022]
Abstract
The negative effect of advanced female age on fertility and offspring health is well understood. In comparison, much less is known about the implications of male age on fertility, with many studies showing conflicting results. Nevertheless, increasing evidence suggests that advanced paternal age has negative effects on sperm parameters, reproductive success, and offspring health. Herein, we summarize the current body of knowledge on this controversial topic, with the belief that this review will serve as a resource for the clinicians providing fertility counseling to couples with older male partners.
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Affiliation(s)
- Masaya Jimbo
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jason Kunisaki
- Department of Human Genetics, University of Utah, Salt Lake City, Utah
| | - Mohammadali Ghaed
- Urology Department, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Victor Yu
- University of Nevada Reno School of Medicine, Reno, Nevada
| | - Hunter A Flores
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas
| | - James M Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah.
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13
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Martinez ME, Stohn JP, Mutina EM, Whitten RJ, Hernandez A. Thyroid hormone elicits intergenerational epigenetic effects on adult social behavior and fetal brain expression of autism susceptibility genes. Front Neurosci 2022; 16:1055116. [PMID: 36419462 PMCID: PMC9676973 DOI: 10.3389/fnins.2022.1055116] [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: 09/27/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic mutations identified in genome-wide association studies can only explain a small percentage of the cases of complex, highly heritable human conditions, including neurological and neurodevelopmental disorders. This suggests that intergenerational epigenetic effects, possibly triggered by environmental circumstances, may contribute to their etiology. We previously described altered DNA methylation signatures in the sperm of mice that experienced developmental overexposure to thyroid hormones as a result of a genetic defect in hormone clearance (DIO3 deficiency). Here we studied fetal brain gene expression and adult social behavior in genetically normal F2 generation descendants of overexposed mice. The brain of F2 generation E13.5 fetuses exhibited abnormal expression of genes associated with autism in humans, including Auts2, Disc1, Ldlr, Per2, Shank3, Oxtr, Igf1, Foxg1, Cd38, Grid2, Nrxn3, and Reln. These abnormal gene expression profiles differed depending on the sex of the exposed ancestor. In the three-chamber social box test, adult F2 generation males manifested significantly decreased interest in social interaction and social novelty, as revealed by decrease total time, distance traveled and time immobile in the area of interaction with novel strangers. F1 generation mice, compared to appropriate controls also exhibited altered profiles in fetal brain gene expression, although these profiles were substantially different to those in the F2 generation. Likewise adult F1 generation mice showed some abnormalities in social behavior that were sexually dimorphic and milder than those in F2 generation mice. Our results indicate that developmental overexposure to thyroid hormone causes intergenerational epigenetic effects impacting social behavior and the expression of autism-related genes during early brain development. Our results open the possibility that altered thyroid hormone states, by eliciting changes in the epigenetic information of the germ line, contribute to the susceptibility and the missing-but heriTables-etiology of complex neurodevelopmental conditions characterized by social deficits, including autism and schizophrenia.
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Affiliation(s)
- Maria Elena Martinez
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, United States
| | - Julia Patrizia Stohn
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, United States
| | - Elizabeth M. Mutina
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, United States
| | - Rayne J. Whitten
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, United States
| | - Arturo Hernandez
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, United States
- Graduate School for Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States
- Department of Medicine, Tufts University School of Medicine, Boston, MA, United States
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14
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Linder J, Koplik SE, Kundaje A, Seelig G. Deciphering the impact of genetic variation on human polyadenylation using APARENT2. Genome Biol 2022; 23:232. [PMID: 36335397 PMCID: PMC9636789 DOI: 10.1186/s13059-022-02799-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND 3'-end processing by cleavage and polyadenylation is an important and finely tuned regulatory process during mRNA maturation. Numerous genetic variants are known to cause or contribute to human disorders by disrupting the cis-regulatory code of polyadenylation signals. Yet, due to the complexity of this code, variant interpretation remains challenging. RESULTS We introduce a residual neural network model, APARENT2, that can infer 3'-cleavage and polyadenylation from DNA sequence more accurately than any previous model. This model generalizes to the case of alternative polyadenylation (APA) for a variable number of polyadenylation signals. We demonstrate APARENT2's performance on several variant datasets, including functional reporter data and human 3' aQTLs from GTEx. We apply neural network interpretation methods to gain insights into disrupted or protective higher-order features of polyadenylation. We fine-tune APARENT2 on human tissue-resolved transcriptomic data to elucidate tissue-specific variant effects. By combining APARENT2 with models of mRNA stability, we extend aQTL effect size predictions to the entire 3' untranslated region. Finally, we perform in silico saturation mutagenesis of all human polyadenylation signals and compare the predicted effects of [Formula: see text] million variants against gnomAD. While loss-of-function variants were generally selected against, we also find specific clinical conditions linked to gain-of-function mutations. For example, we detect an association between gain-of-function mutations in the 3'-end and autism spectrum disorder. To experimentally validate APARENT2's predictions, we assayed clinically relevant variants in multiple cell lines, including microglia-derived cells. CONCLUSIONS A sequence-to-function model based on deep residual learning enables accurate functional interpretation of genetic variants in polyadenylation signals and, when coupled with large human variation databases, elucidates the link between functional 3'-end mutations and human health.
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Affiliation(s)
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, USA
- Department of Computer Science, Stanford University, Stanford, USA
| | - Georg Seelig
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, USA
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15
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Holt GS, Batty LE, Alobaidi BKS, Smith HE, Oud MS, Ramos L, Xavier MJ, Veltman JA. Phasing of de novo mutations using a scaled-up multiple amplicon long-read sequencing approach. Hum Mutat 2022; 43:1545-1556. [PMID: 36047340 PMCID: PMC9826063 DOI: 10.1002/humu.24450] [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: 05/06/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
De novo mutations (DNMs) play an important role in severe genetic disorders that reduce fitness. To better understand their role in disease, it is important to determine the parent-of-origin and timing of mutational events that give rise to these mutations, especially in sex-specific developmental disorders such as male infertility. However, currently available short-read sequencing approaches are not ideally suited for phasing, as this requires long continuous DNA strands that span both the DNM and one or more informative single-nucleotide polymorphisms. To overcome these challenges, we optimized and implemented a multiplexed long-read sequencing approach using Oxford Nanopore technologies MinION platform. We focused on improving target amplification, integrating long-read sequenced data with high-quality short-read sequence data, and developing an anchored phasing computational method. This approach handled the inherent phasing challenges of long-range target amplification and the normal accumulation of sequencing error associated with long-read sequencing. In total, 77 of 109 DNMs (71%) were successfully phased and parent-of-origin identified. The majority of phased DNMs were prezygotic (90%), the accuracy of which is highlighted by an average mutant allele frequency of 49.6% and standard error of 0.84%. This study demonstrates the benefits of employing an integrated short-read and long-read sequencing approach for large-scale DNM phasing.
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Affiliation(s)
- Giles S. Holt
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Lois E. Batty
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Bilal K. S. Alobaidi
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Hannah E. Smith
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Manon S. Oud
- Department of Human Genetics, Donders Institute for BrainCognition and Behaviour, RadboudumcNijmegenThe Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynecology, Division of Reproductive MedicineRadboudumcNijmegenThe Netherlands
| | - Miguel J. Xavier
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Joris A. Veltman
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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16
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Kim IB, Lee T, Lee J, Kim J, Lee S, Koh IG, Kim JH, An JY, Lee H, Kim WK, Ju YS, Cho Y, Yu SJ, Kim SA, Oh M, Han DW, Kim E, Choi JK, Yoo HJ, Lee JH. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. Mol Psychiatry 2022; 27:4680-4694. [PMID: 35840799 DOI: 10.1038/s41380-022-01697-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
Three-dimensional chromatin interactions regulate gene expressions. The significance of de novo mutations (DNMs) in chromatin interactions remains poorly understood for autism spectrum disorder (ASD). We generated 813 whole-genome sequences from 242 Korean simplex families to detect DNMs, and identified target genes which were putatively affected by non-coding DNMs in chromatin interactions. Non-coding DNMs in chromatin interactions were significantly involved in transcriptional dysregulations related to ASD risk. Correspondingly, target genes showed spatiotemporal expressions relevant to ASD in developing brains and enrichment in biological pathways implicated in ASD, such as histone modification. Regarding clinical features of ASD, non-coding DNMs in chromatin interactions particularly contributed to low intelligence quotient levels in ASD probands. We further validated our findings using two replication cohorts, Simons Simplex Collection (SSC) and MSSNG, and showed the consistent enrichment of non-coding DNM-disrupted chromatin interactions in ASD probands. Generating human induced pluripotent stem cells in two ASD families, we were able to demonstrate that non-coding DNMs in chromatin interactions alter the expression of target genes at the stage of early neural development. Taken together, our findings indicate that non-coding DNMs in ASD probands lead to early neurodevelopmental disruption implicated in ASD risk via chromatin interactions.
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Affiliation(s)
- Il Bin Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, Hanyang University Guri Hospital, Guri, 11923, Republic of Korea
| | - Taeyeop Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea
| | - In Gyeong Koh
- Industry-University Cooperation Foundation, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunseong Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05030, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongseong Cho
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Seok Jong Yu
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, Eulji University, Daejeon, 13135, Republic of Korea
| | - Miae Oh
- Department of Psychiatry, Kyung Hee University Hospital, Seoul, 02447, Republic of Korea
| | - Dong Wook Han
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.,Organoid sciences, Ltd., Bundang-gu, Seongnam, 13488, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea. .,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea. .,Department of Psychiatry, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Sovargen Co. Ltd., Daejeon, 34051, Republic of Korea.
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17
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Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder. Nat Commun 2022; 13:6463. [PMID: 36309498 PMCID: PMC9617891 DOI: 10.1038/s41467-022-34112-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/13/2022] [Indexed: 02/06/2023] Open
Abstract
Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorize 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We develop a method for calculating a patient-level, genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD have a significantly higher GRVS compared to those with nondysmorphic ASD (P = 0.03). Using the polygenic transmission disequilibrium test, we observe an over-transmission of ASD-associated common variants in nondysmorphic ASD probands (P = 2.9 × 10-3). These findings replicate using WGS data from 442 ASD probands with accompanying morphology data from the Simons Simplex Collection. Our results provide support for an alternative genomic classification of ASD subgroups using morphology data, which may inform intervention protocols.
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18
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Unni P, Friend J, Weinberg J, Okur V, Hochscherf J, Dominguez I. Predictive functional, statistical and structural analysis of CSNK2A1 and CSNK2B variants linked to neurodevelopmental diseases. Front Mol Biosci 2022; 9:851547. [PMID: 36310603 PMCID: PMC9608649 DOI: 10.3389/fmolb.2022.851547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022] Open
Abstract
Okur-Chung Neurodevelopmental Syndrome (OCNDS) and Poirier-Bienvenu Neurodevelopmental Syndrome (POBINDS) were recently identified as rare neurodevelopmental disorders. OCNDS and POBINDS are associated with heterozygous mutations in the CSNK2A1 and CSNK2B genes which encode CK2α, a serine/threonine protein kinase, and CK2β, a regulatory protein, respectively, which together can form a tetrameric enzyme called protein kinase CK2. A challenge in OCNDS and POBINDS is to understand the genetic basis of these diseases and the effect of the various CK2⍺ and CK2β mutations. In this study we have collected all variants available to date in CSNK2A1 and CSNK2B, and identified hotspots. We have investigated CK2⍺ and CK2β missense mutations through prediction programs which consider the evolutionary conservation, functionality and structure or these two proteins, compared these results with published experimental data on CK2α and CK2β mutants, and suggested prediction programs that could help predict changes in functionality of CK2α mutants. We also investigated the potential effect of CK2α and CK2β mutations on the 3D structure of the proteins and in their binding to each other. These results indicate that there are functional and structural consequences of mutation of CK2α and CK2β, and provide a rationale for further study of OCNDS and POBINDS-associated mutations. These data contribute to understanding the genetic and functional basis of these diseases, which is needed to identify their underlying mechanisms.
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Affiliation(s)
- Prasida Unni
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Jack Friend
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston University, Boston, MA, United States
| | - Volkan Okur
- New York Genome Center, New York, NY, United States
| | - Jennifer Hochscherf
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Isabel Dominguez
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
- *Correspondence: Isabel Dominguez,
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19
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Tian H, Jiao Y, Guo M, Wang Y, Wang R, Wang C, Chen X, Tian W. Krüppel-like factor 7 deficiency causes autistic-like behavior in mice via regulating Clock gene. Cell Biosci 2022; 12:166. [PMID: 36207723 PMCID: PMC9547400 DOI: 10.1186/s13578-022-00903-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Krüppel-like factor 7 (klf7), a transcription factor in the nervous system to regulate cell proliferation and differentiation, has been recently identified as a causal gene for autism spectrum disorder (ASD), but the mechanism behind remains unknown. RESULT To uncover this mechanism, in this study we characterized the involvement of klf7 in circadian rhythm by knocking down klf7 in N2A cells and examining the rhythmic expression of circadian genes, especially Clock gene. We constructed klf7-/- mice and then investigated into klf7 regulation on the expression of rhythm genes in vivo as well as the use of melatonin to rescue the autism behavior. Our results illustrated that circadian rhythm was disrupted in klf7 knockdown cells and that klf7-/- mice showed autism-like behavior. Also, we found that Clock gene was downregulated in the brain of these klf7-/- mice and that the downstream rhythm genes of Clock were disturbed. Melatonin, as a circadian regulation drug, could regulate the expression level and amplitude of rhythm genes in klf7 knockout cells and further rescue the autistic behavior of klf7-/- mice. CONCLUSION Klf7 deficiency causes ASD by disrupting circadian rhythm related genes to trigger rhythm oscillations. To treat ASD, maintaining circadian homeostasis is promising with the use of melatonin.
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Affiliation(s)
- Hui Tian
- grid.19373.3f0000 0001 0193 3564School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080 China
| | - Yanwen Jiao
- grid.19373.3f0000 0001 0193 3564School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080 China
| | - Mingyue Guo
- grid.19373.3f0000 0001 0193 3564School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080 China
| | - Yilin Wang
- grid.19373.3f0000 0001 0193 3564School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080 China
| | - Ruiqi Wang
- grid.19373.3f0000 0001 0193 3564School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080 China
| | - Cao Wang
- grid.19373.3f0000 0001 0193 3564School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080 China
| | - Xiongbiao Chen
- grid.25152.310000 0001 2154 235XDepartment of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9 Canada
| | - Weiming Tian
- grid.19373.3f0000 0001 0193 3564School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080 China
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20
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Ben-Mahmoud A, Jun KR, Gupta V, Shastri P, de la Fuente A, Park Y, Shin KC, Kim CA, da Cruz AD, Pinto IP, Minasi LB, Silva da Cruz A, Faivre L, Callier P, Racine C, Layman LC, Kong IK, Kim CH, Kim WY, Kim HG. A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders. Front Mol Neurosci 2022; 15:979061. [PMID: 36277487 PMCID: PMC9582330 DOI: 10.3389/fnmol.2022.979061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.
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Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Pinang Shastri
- Department of Cardiovascular Medicine, Cape Fear Valley Medical Center, Fayetteville, NC, United States
| | - Alberto de la Fuente
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Yongsoo Park
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Chul Shin
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Chong Ae Kim
- Faculdade de Medicina, Unidade de Genética do Instituto da Criança – Hospital das Clínicas HCFMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Aparecido Divino da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Irene Plaza Pinto
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Lysa Bernardes Minasi
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Alex Silva da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental Disorders, Université de Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d’Enfants, Dijon, France
| | - Patrick Callier
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Caroline Racine
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Hyung-Goo Kim,
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21
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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22
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Kushima I, Imaeda M, Tanaka S, Kato H, Oya-Ito T, Nakatochi M, Aleksic B, Ozaki N. Contribution of copy number variations to the risk of severe eating disorders. Psychiatry Clin Neurosci 2022; 76:423-428. [PMID: 35611833 PMCID: PMC9546291 DOI: 10.1111/pcn.13430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/10/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
Abstract
AIM Eating disorders (EDs) are complex, multifactorial psychiatric conditions. Previous studies identified pathogenic copy number variations associated with NDDs (NDD-CNVs) in ED patients. However, no statistical evidence for an association between NDD-CNVs and EDs has been demonstrated. Therefore, we examined whether NDD-CNVs confer risk for EDs. METHODS Using array comparative genomic hybridization (aCGH), we conducted a high-resolution CNV analysis of 71 severe female ED patients and 1045 female controls. According to the American College of Medical Genetics guidelines, we identified NDD-CNVs or pathogenic/likely pathogenic CNVs in NDD-linked loci. Gene set analysis was performed to examine the involvement of synaptic dysfunction in EDs. Clinical data were retrospectively examined for ED patients with NDD-CNVs. RESULTS Of the samples analyzed with aCGH, 70 severe ED patients (98.6%) and 1036 controls (99.1%) passed our quality control filtering. We obtained 189 and 2539 rare CNVs from patients and controls, respectively. NDD-CNVs were identified in 10.0% (7/70) of patients and 2.3% (24/1036) of controls. Statistical analysis revealed a significant association between NDD-CNVs and EDs (odds ratio = 4.69, P = 0.0023). NDD-CNVs in ED patients included 45,X and deletions at KATNAL2, DIP2A, PTPRT, RBFOX1, CNTN4, MACROD2, and FAM92B. Four of these genes were related to synaptic function. In gene set analysis, we observed a nominally significant enrichment of rare exonic CNVs in synaptic signaling in ED patients (odds ratio = 2.55, P = 0.0254). CONCLUSION Our study provides the first preliminary evidence that NDD-CNVs may confer risk for severe EDs. The pathophysiology may involve synaptic dysfunction.
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Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Miho Imaeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Clinical Oncology and Chemotherapy, Nagoya University Hospital, Nagoya, Japan
| | - Satoshi Tanaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,National Hospital Organization Higashiowari National Hospital, Nagoya, Japan.,The Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoko Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Nutrition, Shubun University, Nagoya, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
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23
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Drevet JR, Hallak J, Nasr-Esfahani MH, Aitken RJ. Reactive Oxygen Species and Their Consequences on the Structure and Function of Mammalian Spermatozoa. Antioxid Redox Signal 2022; 37:481-500. [PMID: 34913729 DOI: 10.1089/ars.2021.0235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Among the 200 or so cell types that comprise mammals, spermatozoa have an ambiguous relationship with the reactive oxygen species (ROS) inherent in the consumption of oxygen that supports aerobic metabolism. Recent Advances: In this review, we shall see that spermatozoa need the action of ROS to reach their structural and functional maturity, but that due to intrinsic unique characteristics, they are, perhaps more than any other cell type, susceptible to oxidative damage. Recent studies have improved our knowledge of how oxidative damage affects sperm structures and functions. The focus of this review will be on how genetic and epigenetic oxidative alterations to spermatozoa can have dramatic unintended consequences in terms of both the support and the suppression of sperm function. Critical Issues: Oxidative stress can have dramatic consequences not only for the spermatozoon itself, but also, and above all, on its primary objective, which is to carry out fertilization and to ensure, in part, that the embryonic development program should lead to a healthy progeny. Future Directions: Sperm oxidative DNA damage largely affects the integrity of the paternal genetic material to such an extent that the oocyte may have difficulties in correcting it. Diagnostic and therapeutic actions should be considered more systematically, especially in men with difficulties to conceive. Research is underway to determine whether the epigenetic information carried by spermatozoa is also subject to changes mediated by pro-oxidative situations. Antioxid. Redox Signal. 37, 481-500.
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Affiliation(s)
- Joël R Drevet
- Faculty of Medicine, GReD Institute, INSERM U1103-CNRS UMR6293-Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jorge Hallak
- Androscience, Science and Innovation Center in Andrology and High-Complex Clinical and Research Andrology Laboratory, São Paulo, Brazil.,Division of Urology, University of São Paulo, São Paulo, Brazil.,Men's Health Study Group, Institute for Advanced Studies, University of São Paulo, São Paulo, Brazil.,Reproductive Toxicology Unit, Department of Pathology, University of São Paulo, São Paulo, Brazil
| | - Mohammad-Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.,Isfahan Fertility and Infertility Center, Isfahan, Iran
| | - Robert J Aitken
- Faculty of Science and Priority Research Center for Reproductive Sciences, The University of Newcastle, Callaghan, Australia.,Faculty of Health and Medicine, Priority Research Center for Reproductive Sciences, The University of Newcastle, Callaghan, Australia.,Hunter Medical Research Institute, New Lambton Heights, Australia
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24
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Wang T, Zhao PA, Eichler EE. Rare variants and the oligogenic architecture of autism. Trends Genet 2022; 38:895-903. [PMID: 35410794 PMCID: PMC9378350 DOI: 10.1016/j.tig.2022.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
Most large-scale genetic studies of autism have focused on the discovery of genes by proving an enrichment of de novo mutations (DNMs) in autism probands or characterizing polygenic risk based on the association of common variants. We present evidence in support of an oligogenic model where two or more ultrarare mutations of more modest effect are preferentially transmitted to children with autism. Such private gene-disruptive mutations are enriched in families where there are multiple affected individuals, emerged two or three generations ago, and map to genes not previously associated with autism. Although no single gene has reached statistical significance, this class of variation should be considered along with genetic and nongenetic factors to better explain the etiology of this complex trait.
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Affiliation(s)
- Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Peiyao A Zhao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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25
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Ramirez M, Badayeva Y, Yeung J, Wu J, Abdalla-Wyse A, Yang E, Trost B, Scherer SW, Goldowitz D. Temporal analysis of enhancers during mouse cerebellar development reveals dynamic and novel regulatory functions. eLife 2022; 11:74207. [PMID: 35942939 PMCID: PMC9398453 DOI: 10.7554/elife.74207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
We have identified active enhancers in the mouse cerebellum at embryonic and postnatal stages which provides a view of novel enhancers active during cerebellar development. The majority of cerebellar enhancers have dynamic activity between embryonic and postnatal development. Cerebellar enhancers were enriched for neural transcription factor binding sites with temporally specific expression. Putative gene targets displayed spatially restricted expression patterns, indicating cell-type specific expression regulation. Functional analysis of target genes indicated that enhancers regulate processes spanning several developmental epochs such as specification, differentiation and maturation. We use these analyses to discover one novel regulator and one novel marker of cerebellar development: Bhlhe22 and Pax3, respectively. We identified an enrichment of de novo mutations and variants associated with autism spectrum disorder in cerebellar enhancers. Furthermore, by comparing our data with relevant brain development ENCODE histone profiles and cerebellar single-cell datasets we have been able to generalize and expand on the presented analyses, respectively. We have made the results of our analyses available online in the Developing Mouse Cerebellum Enhancer Atlas (https://goldowitzlab.shinyapps.io/developing_mouse_cerebellum_enhancer_atlas/), where our dataset can be efficiently queried, curated and exported by the scientific community to facilitate future research efforts. Our study provides a valuable resource for studying the dynamics of gene expression regulation by enhancers in the developing cerebellum and delivers a rich dataset of novel gene-enhancer associations providing a basis for future in-depth studies in the cerebellum.
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Yuliya Badayeva
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Erin Yang
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | -
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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26
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Cai C, Yin Z, Liu A, Wang H, Zeng S, Wang Z, Qiu H, Li S, Zhou J, Wang M. Identifying Rare Genetic Variants of Immune Mediators as Risk Factors for Autism Spectrum Disorder. Genes (Basel) 2022; 13:1098. [PMID: 35741860 PMCID: PMC9223212 DOI: 10.3390/genes13061098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/30/2022] Open
Abstract
Autism spectrum disorder (ASD) affects more than 1% of children, and there is no viable pharmacotherapeutic agent to treat the core symptoms of ASD. Studies have shown that children with ASD show changes in their levels of immune response molecules. Our previous studies have shown that ASD is more common in children with folate receptor autoantibodies. We also found that children with ASD have abnormal gut immune function, which was characterized by a significant increase in the content of immunoglobulin A and an increase in gut-microbiota-associated epitope diversity. These studies suggest that the immune mechanism plays an important role in the occurrence of ASD. The present study aims to systematically assess gene mutations in immune mediators in patients with ASD. We collected genetic samples from 72 children with ASD (2−12 years old) and 107 healthy controls without ASD (20−78 years old). We used our previously-designed immune gene panel, which can capture cytokine and receptor genes, the coding regions of MHC genes, and genes of innate immunity. Target region sequencing (500×) and bioinformatics analytical methods were used to identify variants in immune response genes associated with patients with ASD. A total of 4 rare variants were found to be associated with ASD, including HLA-B: p.A93G, HLA-DQB1: p.S229N, LILRB2: p.R322H, and LILRB2: c.956-4C>T. These variants were present in 44.44% (32/72) of the ASD patients and were detected in 3.74% (4/107) of the healthy controls. We expect these genetic variants will serve as new targets for the clinical genetic assessment of ASD, and our findings suggest that immune abnormalities in children with ASD may have a genetic basis.
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Affiliation(s)
- Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children’s Hospital (Children’s Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China;
| | - Zhaoqing Yin
- Division of Neonatology, The People’s Hospital of Dehong Autonomous Prefecture, Mangshi 678400, China;
| | - Aiping Liu
- The Department of Laboratory, Public Health Service Center of Bao’an District, Bao’an District, Shenzhen 518018, China;
| | - Hui Wang
- Xiamen Branch of Children’s Hospital of Fudan University (Xiamen Children’s Hospital), Xiamen 361006, China;
| | - Shujuan Zeng
- Division of Neonatology, Longgang Central Hospital of Shenzhen, Shenzhen 518116, China; (S.Z.); (H.Q.)
| | - Zhangxing Wang
- Division of Neonatology, Shenzhen Longhua People’s Hospital, Shenzhen 518109, China;
| | - Huixian Qiu
- Division of Neonatology, Longgang Central Hospital of Shenzhen, Shenzhen 518116, China; (S.Z.); (H.Q.)
| | - Shijun Li
- Department of Radiology, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Jiaxiu Zhou
- Division of Psychology, Shenzhen Children’s Hospital, Shenzhen 518038, China
| | - Mingbang Wang
- Microbiome Therapy Center, South China Hospital of Shenzhen University, Shenzhen 518111, China
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children’s Hospital of Fudan University, Shanghai 201102, China
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27
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Smits RM, Xavier MJ, Oud MS, Astuti GDN, Meijerink AM, de Vries PF, Holt GS, Alobaidi BKS, Batty LE, Khazeeva G, Sablauskas K, Vissers LELM, Gilissen C, Fleischer K, Braat DDM, Ramos L, Veltman JA. De novo mutations in children born after medical assisted reproduction. Hum Reprod 2022; 37:1360-1369. [PMID: 35413117 PMCID: PMC9156847 DOI: 10.1093/humrep/deac068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/08/2022] [Indexed: 01/23/2023] Open
Abstract
STUDY QUESTION Are there more de novo mutations (DNMs) present in the genomes of children born through medical assisted reproduction (MAR) compared to spontaneously conceived children? SUMMARY ANSWER In this pilot study, no statistically significant difference was observed in the number of DNMs observed in the genomes of MAR children versus spontaneously conceived children. WHAT IS KNOWN ALREADY DNMs are known to play a major role in sporadic disorders with reduced fitness such as severe developmental disorders, including intellectual disability and epilepsy. Advanced paternal age is known to place offspring at increased disease risk, amongst others by increasing the number of DNMs in their genome. There are very few studies reporting on the effect of MAR on the number of DNMs in the offspring, especially when male infertility is known to be affecting the potential fathers. With delayed parenthood an ongoing epidemiological trend in the 21st century, there are more children born from fathers of advanced age and more children born through MAR every day. STUDY DESIGN, SIZE, DURATION This observational pilot study was conducted from January 2015 to March 2019 in the tertiary care centre at Radboud University Medical Center. We included a total of 53 children and their respective parents, forming 49 trios (mother, father and child) and two quartets (mother, father and two siblings). One group of children was born after spontaneous conception (n = 18); a second group of children born after IVF (n = 17) and a third group of children born after ICSI combined with testicular sperm extraction (ICSI-TESE) (n = 18). In this pilot study, we also subdivided each group by paternal age, resulting in a subgroup of children born to younger fathers (<35 years of age at conception) and older fathers (>45 years of age at conception). PARTICIPANTS/MATERIALS, SETTING, METHODS Whole-genome sequencing (WGS) was performed on all parent-offspring trios to identify DNMs. For 34 of 53 trios/quartets, WGS was performed twice to independently detect and validate the presence of DNMs. Quality of WGS-based DNM calling was independently assessed by targeted Sanger sequencing. MAIN RESULTS AND THE ROLE OF CHANCE No significant differences were observed in the number of DNMs per child for the different methods of conception, independent of parental age at conception (multi-factorial ANOVA, f(2) = 0.17, P-value = 0.85). As expected, a clear paternal age effect was observed after adjusting for method of conception and maternal age at conception (multiple regression model, t = 5.636, P-value = 8.97 × 10-7), with on average 71 DNMs in the genomes of children born to young fathers (<35 years of age) and an average of 94 DNMs in the genomes of children born to older fathers (>45 years of age). LIMITATIONS, REASONS FOR CAUTION This is a pilot study and other small-scale studies have recently reported contrasting results. Larger unbiased studies are required to confirm or falsify these results. WIDER IMPLICATIONS OF THE FINDINGS This pilot study did not show an effect for the method of conception on the number of DNMs per genome in offspring. Given the role that DNMs play in disease risk, this negative result is good news for IVF and ICSI-TESE born children, if replicated in a larger cohort. STUDY FUNDING/COMPETING INTEREST(S) This research was funded by the Netherlands Organisation for Scientific Research (918-15-667) and by an Investigator Award in Science from the Wellcome Trust (209451). The authors have no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- R M Smits
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - M J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - G D N Astuti
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - A M Meijerink
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - P F de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - G S Holt
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - B K S Alobaidi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - L E Batty
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G Khazeeva
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - K Sablauskas
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - L E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - K Fleischer
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - D D M Braat
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - L Ramos
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - J A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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28
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Melliou S, Sangster KT, Kao J, Zarrei M, Lam KHB, Howe J, Papaioannou MD, Tsang QPL, Borhani OA, Sajid RS, Bonnet C, Leheup B, Shannon P, Scherer SW, Stavropoulos DJ, Djuric U, Diamandis P. Regionally defined proteomic profiles of human cerebral tissue and organoids reveal conserved molecular modules of neurodevelopment. Cell Rep 2022; 39:110846. [PMID: 35613588 DOI: 10.1016/j.celrep.2022.110846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/01/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022] Open
Abstract
Cerebral organoids have emerged as robust models for neurodevelopmental and pathological processes, as well as a powerful discovery platform for less-characterized neurobiological programs. Toward this prospect, we leverage mass-spectrometry-based proteomics to molecularly profile precursor and neuronal compartments of both human-derived organoids and mid-gestation fetal brain tissue to define overlapping programs. Our analysis includes recovery of precursor-enriched transcriptional regulatory proteins not found to be differentially expressed in previous transcriptomic datasets. To highlight the discovery potential of this resource, we show that RUVBL2 is preferentially expressed in the SOX2-positive compartment of organoids and that chemical inactivation leads to precursor cell displacement and apoptosis. To explore clinicopathological correlates of this cytoarchitectural disruption, we interrogate clinical datasets and identify rare de novo genetic variants involving RUVBL2 in patients with neurodevelopmental impairments. Together, our findings demonstrate how cell-type-specific profiling of organoids can help nominate previously unappreciated genes in neurodevelopment and disease.
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Affiliation(s)
- Sofia Melliou
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kevin T Sangster
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Jennifer Kao
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mehdi Zarrei
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - K H Brian Lam
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jennifer Howe
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Queenie P L Tsang
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Okty Abbasi Borhani
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Rifat Shahriar Sajid
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Céline Bonnet
- Department of Clinical Genetics, Nancy University Hospital, Nancy, France
| | - Bruno Leheup
- Department of Clinical Genetics, Nancy University Hospital, Nancy, France
| | - Patrick Shannon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON M5G 1X5, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Dimitri James Stavropoulos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Ugljesa Djuric
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON M5G 2C4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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29
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Jegathisawaran J, Tsiplova K, Hayeems RZ, Marshall CR, Stavropoulos DJ, Pereira SL, Thiruvahindrapuram B, Liston E, Reuter MS, Manshaei R, Cohn I, Jobling R, Kim RH, Mital S, Ungar WJ. Trio genome sequencing for developmental delay and pediatric heart conditions: A comparative microcost analysis. Genet Med 2022; 24:1027-1036. [PMID: 35219592 DOI: 10.1016/j.gim.2022.01.020] [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: 10/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Genome sequencing (GS) can aid clinical management of multiple pediatric conditions. Insurers require accurate cost information to inform funding and implementation decisions. The objective was to compare the laboratory workflows and microcosts of trio GS testing in children with developmental delay (DD) and in children with cardiac conditions. METHODS Cost items related to each step in trio GS (child and 2 parents) for both populations were identified and measured. Program costs over 5 years were estimated. Probabilistic and deterministic analyses were conducted. RESULTS The mean cost per trio GS was CAD$6634.11 (95% CI = 6352.29-6913.40) for DD and CAD$8053.10 (95% CI = 7699.30-8558.10) for cardiac conditions. The 5-year program cost was CAD$28.11 million (95% CI = 26.91-29.29) for DD and CAD$5.63 million (95% CI = 5.38-5.98) for cardiac conditions. Supplies constituted the largest cost component for both populations. The higher cost per sample for the population with cardiac conditions was due to the inclusion of pharmacogenomics, higher bioinformatics labor costs, and a more labor intensive case review. CONCLUSION This analysis indicated important variation in trio GS workflow and costs between pediatric populations in a single institution. Enhanced understanding of the clinical utility and costs of GS can inform harmonization and implementation decision-making.
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Affiliation(s)
- Jathishinie Jegathisawaran
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Kate Tsiplova
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Robin Z Hayeems
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christian R Marshall
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Eriskay Liston
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Miriam S Reuter
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Iris Cohn
- Clinical Pharmacology and Toxicology & Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raymond H Kim
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Toronto, Ontario, Canada; Department of Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Seema Mital
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Toronto, Ontario, Canada; Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
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30
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Cummings CT, Rowley MJ. Implications of Dosage Deficiencies in CTCF and Cohesin on Genome Organization, Gene Expression, and Human Neurodevelopment. Genes (Basel) 2022; 13:583. [PMID: 35456389 PMCID: PMC9030571 DOI: 10.3390/genes13040583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Properly organizing DNA within the nucleus is critical to ensure normal downstream nuclear functions. CTCF and cohesin act as major architectural proteins, working in concert to generate thousands of high-intensity chromatin loops. Due to their central role in loop formation, a massive research effort has been dedicated to investigating the mechanism by which CTCF and cohesin create these loops. Recent results lead to questioning the direct impact of CTCF loops on gene expression. Additionally, results of controlled depletion experiments in cell lines has indicated that genome architecture may be somewhat resistant to incomplete deficiencies in CTCF or cohesin. However, heterozygous human genetic deficiencies in CTCF and cohesin have illustrated the importance of their dosage in genome architecture, cellular processes, animal behavior, and disease phenotypes. Thus, the importance of considering CTCF or cohesin levels is especially made clear by these heterozygous germline variants that characterize genetic syndromes, which are increasingly recognized in clinical practice. Defined primarily by developmental delay and intellectual disability, the phenotypes of CTCF and cohesin deficiency illustrate the importance of architectural proteins particularly in neurodevelopment. We discuss the distinct roles of CTCF and cohesin in forming chromatin loops, highlight the major role that dosage of each protein plays in the amplitude of observed effects on gene expression, and contrast these results to heterozygous mutation phenotypes in murine models and clinical patients. Insights highlighted by this comparison have implications for future research into these newly emerging genetic syndromes.
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Affiliation(s)
- Christopher T. Cummings
- Munroe-Meyer Institute, Department of Genetic Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - M. Jordan Rowley
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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31
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Fischer FP, Kasture AS, Hummel T, Sucic S. Molecular and Clinical Repercussions of GABA Transporter 1 Variants Gone Amiss: Links to Epilepsy and Developmental Spectrum Disorders. Front Mol Biosci 2022; 9:834498. [PMID: 35295842 PMCID: PMC7612498 DOI: 10.3389/fmolb.2022.834498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
The human γ-aminobutyric acid (GABA) transporter 1 (hGAT-1) is the first member of the solute carrier 6 (SLC6) protein superfamily. GAT-1 (SLC6A1) is one of the main GABA transporters in the central nervous system. Its principal physiological role is retrieving GABA from the synapse into neurons and astrocytes, thus swiftly terminating neurotransmission. GABA is a key inhibitory neurotransmitter and shifts in GABAergic signaling can lead to pathological conditions, from anxiety and epileptic seizures to schizophrenia. Point mutations in the SLC6A1 gene frequently give rise to epilepsy, intellectual disability or autism spectrum disorders in the afflicted individuals. The mechanistic routes underlying these are still fairly unclear. Some loss-of-function variants impair the folding and intracellular trafficking of the protein (thus retaining the transporter in the endoplasmic reticulum compartment), whereas others, despite managing to reach their bona fide site of action at the cell surface, nonetheless abolish GABA transport activity (plausibly owing to structural/conformational defects). Whatever the molecular culprit(s), the physiological aftermath transpires into the absence of functional transporters, which in turn perturbs GABAergic actions. Dozens of mutations in the kin SLC6 family members are known to exhort protein misfolding. Such events typically elicit severe ailments in people, e.g., infantile parkinsonism-dystonia or X-linked intellectual disability, in the case of dopamine and creatine transporters, respectively. Flaws in protein folding can be rectified by small molecules known as pharmacological and/or chemical chaperones. The search for such apt remedies calls for a systematic investigation and categorization of the numerous disease-linked variants, by biochemical and pharmacological means in vitro (in cell lines and primary neuronal cultures) and in vivo (in animal models). We here give special emphasis to the utilization of the fruit fly Drosophila melanogaster as a versatile model in GAT-1-related studies. Jointly, these approaches can portray indispensable insights into the molecular factors underlying epilepsy, and ultimately pave the way for contriving efficacious therapeutic options for patients harboring pathogenic mutations in hGAT-1.
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Affiliation(s)
- Florian P. Fischer
- Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
- Department of Epileptology and Neurology, University of Aachen, Aachen, Germany
| | - Ameya S. Kasture
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Thomas Hummel
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
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32
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Pugsley K, Scherer SW, Bellgrove MA, Hawi Z. Environmental exposures associated with elevated risk for autism spectrum disorder may augment the burden of deleterious de novo mutations among probands. Mol Psychiatry 2022; 27:710-730. [PMID: 34002022 PMCID: PMC8960415 DOI: 10.1038/s41380-021-01142-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022]
Abstract
Although the full aetiology of autism spectrum disorder (ASD) is unknown, familial and twin studies demonstrate high heritability of 60-90%, indicating a predominant role of genetics in the development of the disorder. The genetic architecture of ASD consists of a complex array of rare and common variants of all classes of genetic variation usually acting additively to augment individual risk. The relative contribution of heredity in ASD persists despite selective pressures against the classic autistic phenotype; a phenomenon thought to be explained, in part, by the incidence of spontaneous (or de novo) mutations. Notably, environmental exposures attributed as salient risk factors for ASD may play a causal role in the emergence of deleterious de novo variations, with several ASD-associated agents having significant mutagenic potential. To explore this hypothesis, this review article assesses published epidemiological data with evidence derived from assays of mutagenicity, both in vivo and in vitro, to determine the likely role such agents may play in augmenting the genetic liability in ASD. Broadly, these exposures were observed to elicit genomic alterations through one or a combination of: (1) direct interaction with genetic material; (2) impaired DNA repair; or (3) oxidative DNA damage. However, the direct contribution of these factors to the ASD phenotype cannot be determined without further analysis. The development of comprehensive prospective birth cohorts in combination with genome sequencing is essential to forming a causal, mechanistic account of de novo mutations in ASD that links exposure, genotypic alterations, and phenotypic consequences.
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Affiliation(s)
- Kealan Pugsley
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC Australia
| | - Stephen W. Scherer
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Mark A. Bellgrove
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia.
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33
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Zaghi M, Banfi F, Bellini E, Sessa A. Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era. Biomolecules 2021; 11:1713. [PMID: 34827709 PMCID: PMC8616022 DOI: 10.3390/biom11111713] [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: 10/18/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022] Open
Abstract
The advent of next-generation sequencing (NGS) is heavily changing both the diagnosis of human conditions and basic biological research. It is now possible to dig deep inside the genome of hundreds of thousands or even millions of people and find both common and rare genomic variants and to perform detailed phenotypic characterizations of both physiological organs and experimental models. Recent years have seen the introduction of multiple techniques using NGS to profile transcription, DNA and chromatin modifications, protein binding, etc., that are now allowing us to profile cells in bulk or even at a single-cell level. Although rare and ultra-rare diseases only affect a few people, each of these diseases represent scholarly cases from which a great deal can be learned about the pathological and physiological function of genes, pathways, and mechanisms. Therefore, for rare diseases, state-of-the-art investigations using NGS have double valence: their genomic cause (new variants) and the characterize the underlining the mechanisms associated with them (discovery of gene function) can be found. In a non-exhaustive manner, this review will outline the main usage of NGS-based techniques for the diagnosis and characterization of neurodevelopmental disorders (NDDs), under whose umbrella many rare and ultra-rare diseases fall.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
- CNR Institute of Neuroscience, 20129 Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
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34
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Loureiro LO, Howe JL, Reuter MS, Iaboni A, Calli K, Roshandel D, Pritišanac I, Moses A, Forman-Kay JD, Trost B, Zarrei M, Rennie O, Lau LYS, Marshall CR, Srivastava S, Godlewski B, Buttermore ED, Sahin M, Hartley D, Frazier T, Vorstman J, Georgiades S, Lewis SME, Szatmari P, Bradley CAL, Tabet AC, Willems M, Lumbroso S, Piton A, Lespinasse J, Delorme R, Bourgeron T, Anagnostou E, Scherer SW. A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder. NPJ Genom Med 2021; 6:91. [PMID: 34737294 PMCID: PMC8568906 DOI: 10.1038/s41525-021-00254-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/23/2021] [Indexed: 01/22/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is genetically complex with ~100 copy number variants and genes involved. To try to establish more definitive genotype and phenotype correlations in ASD, we searched genome sequence data, and the literature, for recurrent predicted damaging sequence-level variants affecting single genes. We identified 18 individuals from 16 unrelated families carrying a heterozygous guanine duplication (c.3679dup; p.Ala1227Glyfs*69) occurring within a string of 8 guanines (genomic location [hg38]g.50,721,512dup) affecting SHANK3, a prototypical ASD gene (0.08% of ASD-affected individuals carried the predicted p.Ala1227Glyfs*69 frameshift variant). Most probands carried de novo mutations, but five individuals in three families inherited it through somatic mosaicism. We scrutinized the phenotype of p.Ala1227Glyfs*69 carriers, and while everyone (17/17) formally tested for ASD carried a diagnosis, there was the variable expression of core ASD features both within and between families. Defining such recurrent mutational mechanisms underlying an ASD outcome is important for genetic counseling and early intervention.
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Affiliation(s)
- Livia O Loureiro
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer L Howe
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- Canada's Genomics Enterprise (CGEn), The Hospital for Sick Children, Toronto, ON, Canada
| | - Alana Iaboni
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | - Kristina Calli
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Iva Pritišanac
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alan Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Brett Trost
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Zarrei
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Olivia Rennie
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lynette Y S Lau
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brianna Godlewski
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth D Buttermore
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Thomas Frazier
- Autism Speaks and Department of Psychology, John Carroll University, Cleveland, OH, USA
| | - Jacob Vorstman
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Peter Szatmari
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Clarrisa A Lisa Bradley
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne-Claude Tabet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
- Genetics Department, Cytogenetic Unit, Robert Debré Hospital, APHP, F-75019, Paris, France
| | | | - Serge Lumbroso
- Biochimie et Biologie Moléculaire, CHU Nimes, Univ. Montpellier, Nimes, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
- Unité de Génétique Moléculaire, IGMA, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
- Institut Universitaire de France, Paris, France
| | | | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
- Child and Adolescent Psychiatry Department, Robert Debré Hospital, APHP, F-75019, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, ON, Canada.
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35
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Kaiser VB, Talmane L, Kumar Y, Semple F, MacLennan M, FitzPatrick DR, Taylor MS, Semple CA. Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome. Genome Res 2021; 31:1994-2007. [PMID: 34417209 PMCID: PMC8559717 DOI: 10.1101/gr.275407.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022]
Abstract
Mutation in the germline is the ultimate source of genetic variation, but little is known about the influence of germline chromatin structure on mutational processes. Using ATAC-seq, we profile the open chromatin landscape of human spermatogonia, the most proliferative cell type of the germline, identifying transcription factor binding sites (TFBSs) and PRDM9 binding sites, a subset of which will initiate meiotic recombination. We observe an increase in rare structural variant (SV) breakpoints at PRDM9-bound sites, implicating meiotic recombination in the generation of structural variation. Many germline TFBSs, such as NRF1, are also associated with increased rates of SV breakpoints, apparently independent of recombination. Singleton short insertions (≥5 bp) are highly enriched at TFBSs, particularly at sites bound by testis active TFs, and their rates correlate with those of structural variant breakpoints. Short insertions often duplicate the TFBS motif, leading to clustering of motif sites near regulatory regions in this male-driven evolutionary process. Increased mutation loads at germline TFBSs disproportionately affect neural enhancers with activity in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.
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Affiliation(s)
- Vera B Kaiser
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Lana Talmane
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Yatendra Kumar
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Fiona Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Marie MacLennan
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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36
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Prediction of genetic alteration of phospholipase C isozymes in brain disorders: Studies with deep learning. Adv Biol Regul 2021; 82:100833. [PMID: 34773889 DOI: 10.1016/j.jbior.2021.100833] [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: 10/06/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022]
Abstract
Genetic mutations leading to the development of various diseases, such as cancer, diabetes, and neurodegenerative disorders, can be attributed to multiple mechanisms and exposure to diverse environments. These disorders further increase gene mutation rates and affect the activity of translated proteins, both phenomena associated with cellular responses. Therefore, maintaining the integrity of genetic and epigenetic information is critical for disease suppression and prevention. With the advent of genome sequencing technologies, large-scale genomic data-based machine learning tools, including deep learning, have been used to predict and identify somatic inactivation or negative dominant expression of target genes in various diseases. Although deep learning studies have recently been highlighted for their ability to distinguish between the genetic information of diseases, conventional wisdom is also necessary to explain the correlation between genotype and phenotype. Herein, we summarize the current understanding of phosphoinositide-specific phospholipase C isozymes (PLCs) and an overview of their associations with genetic variation, as well as their emerging roles in several diseases. We also predicted and discussed new findings of cryptic PLC splice variants by deep learning and the clinical implications of the PLC genetic variations predicted using these tools.
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37
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Ostrom KF, LaVigne JE, Brust TF, Seifert R, Dessauer CW, Watts VJ, Ostrom RS. Physiological Roles of Mammalian Transmembrane Adenylyl Cyclase Isoforms. Physiol Rev 2021; 102:815-857. [PMID: 34698552 DOI: 10.1152/physrev.00013.2021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adenylyl cyclases (ACs) catalyze the conversion of ATP to the ubiquitous second messenger cAMP. Mammals possess nine isoforms of transmembrane ACs, dubbed AC1-9, that serve as major effector enzymes of G protein-coupled receptors. The transmembrane ACs display varying expression patterns across tissues, giving potential for them having a wide array of physiologic roles. Cells express multiple AC isoforms, implying that ACs have redundant functions. Furthermore, all transmembrane ACs are activated by Gαs so it was long assumed that all ACs are activated by Gαs-coupled GPCRs. AC isoforms partition to different microdomains of the plasma membrane and form prearranged signaling complexes with specific GPCRs that contribute to cAMP signaling compartments. This compartmentation allows for a diversity of cellular and physiological responses by enabling unique signaling events to be triggered by different pools of cAMP. Isoform specific pharmacological activators or inhibitors are lacking for most ACs, making knockdown and overexpression the primary tools for examining the physiological roles of a given isoform. Much progress has been made in understanding the physiological effects mediated through individual transmembrane ACs. GPCR-AC-cAMP signaling pathways play significant roles in regulating functions of every cell and tissue, so understanding each AC isoform's role holds potential for uncovering new approaches for treating a vast array of pathophysiological conditions.
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Affiliation(s)
- Katrina F Ostrom
- W. M. Keck Science Department, Claremont McKenna College, Claremont, CA, United States
| | - Justin E LaVigne
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States
| | - Tarsis F Brust
- Department of Pharmaceutical Sciences, Palm Beach Atlantic University, West Palm Beach, FL, United States
| | - Roland Seifert
- Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Carmen W Dessauer
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas, United States
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States.,Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, United States
| | - Rennolds S Ostrom
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
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38
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Somatic Mosaicism and Autism Spectrum Disorder. Genes (Basel) 2021; 12:genes12111699. [PMID: 34828306 PMCID: PMC8619103 DOI: 10.3390/genes12111699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a genetically heterogenous neurodevelopmental disorder. In the early years of next-generation sequencing, de novo germline variants were shown to contribute to ASD risk. These germline mutations are present in all of the cells of an affected individual and can be detected in any tissue, including clinically accessible DNA sources such as blood or saliva. In recent years, studies have also implicated de novo somatic variants in ASD risk. These somatic mutations arise postzygotically and are present in only a subset of the cells of an affected individual. Depending on the developmental time and progenitor cell in which a somatic mutation occurs, it may be detectable in some tissues and not in others. Somatic mutations detectable at relatively low sequencing coverage in clinically accessible tissues are suggested to contribute to 3-5% of simplex ASD diagnoses, and "brain limited" somatic mutations have been identified in postmortem ASD brain tissue. Somatic mutations likely represent the genetic diagnosis in a proportion of otherwise unexplained individuals with ASD, and brain limited somatic mutations can be used as markers to discover risk genes, cell types, brain regions, and cellular pathways important for ASD pathogenesis and to potentially target for therapeutics.
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39
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Qaiser F, Sadoway T, Yin Y, Zulfiqar Ali Q, Nguyen CM, Shum N, Backstrom I, Marques PT, Tabarestani S, Munhoz RP, Krings T, Pearson CE, Yuen RKC, Andrade DM. Genome sequencing identifies rare tandem repeat expansions and copy number variants in Lennox-Gastaut syndrome. Brain Commun 2021; 3:fcab207. [PMID: 34622207 PMCID: PMC8491034 DOI: 10.1093/braincomms/fcab207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 11/22/2022] Open
Abstract
Epilepsies are a group of common neurological disorders with a substantial
genetic basis. Despite this, the molecular diagnosis of epilepsies remains
challenging due to its heterogeneity. Studies utilizing whole-genome sequencing
may provide additional insights into genetic causes of epilepsies of unknown
aetiology. Whole-genome sequencing was used to evaluate a cohort of adults with
unexplained developmental and epileptic encephalopathies (n
= 30), for whom prior genetic tests, including whole-exome sequencing in
some cases, were negative or inconclusive. Rare single nucleotide variants,
insertions/deletions, copy number variants and tandem repeat expansions were
analysed. Seven pathogenic or likely pathogenic single nucleotide variants, and
two pathogenic deleterious copy number variants were identified in nine patients
(32.1% of the cohort). One of the copy number variants, identified in a
patient with Lennox–Gastaut syndrome, was too small to be detected by
chromosomal microarray techniques. We also identified two tandem repeat
expansions with clinical implications in two other patients with
Lennox–Gastaut syndrome: a CGG repeat expansion in the
5′untranslated region of DIP2B, and a CTG expansion in
ATXN8OS (previously implicated in spinocerebellar ataxia
type 8). Three patients had KCNA2 pathogenic variants. One of
them died of sudden unexpected death in epilepsy. The other two patients had, in
addition to a KCNA2 variant, a second de novo
variant impacting potential epilepsy-relevant genes (KCNIP4 and
UBR5). Overall, whole-genome sequencing provided a genetic
explanation in 32.1% of the total cohort. This is also the first report
of coding and non-coding tandem repeat expansions identified in patients with
Lennox–Gastaut syndrome. This study demonstrates that using whole-genome
sequencing, the examination of multiple types of rare genetic variation,
including those found in the non-coding region of the genome, can help resolve
unexplained epilepsies.
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Affiliation(s)
- Farah Qaiser
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada.,Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Tara Sadoway
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Yue Yin
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Quratulain Zulfiqar Ali
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Charlotte M Nguyen
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Natalie Shum
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ian Backstrom
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Paula T Marques
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Sepideh Tabarestani
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Renato P Munhoz
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, Canada.,Neuromodulation Unit and Ataxia Clinic, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Timo Krings
- Department of Medical Imaging, University of Toronto, Toronto, Canada.,Division of Neuroradiology, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Christopher E Pearson
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ryan K C Yuen
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Danielle M Andrade
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, Canada.,Epilepsy Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Canada
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40
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Jiang Y, Urresti J, Pagel KA, Pramod AB, Iakoucheva LM, Radivojac P. Prioritizing de novo autism risk variants with calibrated gene- and variant-scoring models. Hum Genet 2021; 141:1595-1613. [PMID: 34549350 DOI: 10.1007/s00439-021-02356-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 12/17/2022]
Abstract
Whole-exome and whole-genome sequencing studies in autism spectrum disorder (ASD) have identified hundreds of thousands of exonic variants. Only a handful of them, primarily loss-of-function variants, have been shown to increase the risk for ASD, while the contributory roles of other variants, including most missense variants, remain unknown. New approaches that combine tissue-specific molecular profiles with patients' genetic data can thus play an important role in elucidating the functional impact of exonic variation and improve understanding of ASD pathogenesis. Here, we integrate spatio-temporal gene co-expression networks from the developing human brain and protein-protein interaction networks to first reach accurate prioritization of ASD risk genes based on their connectivity patterns with previously known high-confidence ASD risk genes. We subsequently integrate these gene scores with variant pathogenicity predictions to further prioritize individual exonic variants based on the positive-unlabeled learning framework with gene- and variant-score calibration. We demonstrate that this approach discriminates among variants between cases and controls at the high end of the prediction range. Finally, we experimentally validate our top-scoring de novo mutation NP_001243143.1:p.Phe309Ser in the sodium/potassium-transporting ATPase ATP1A3 to disrupt protein binding with different partners.
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Affiliation(s)
- Yuxiang Jiang
- Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - Jorge Urresti
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Kymberleigh A Pagel
- Department of Computer Science, Indiana University, Bloomington, IN, USA.,Institute for Computational Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Akula Bala Pramod
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
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41
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Yoon S, Munoz A, Yamrom B, Lee YH, Andrews P, Marks S, Wang Z, Reeves C, Winterkorn L, Krieger AM, Buja A, Pradhan K, Ronemus M, Baldwin KK, Levy D, Wigler M, Iossifov I. Rates of contributory de novo mutation in high and low-risk autism families. Commun Biol 2021; 4:1026. [PMID: 34471188 PMCID: PMC8410909 DOI: 10.1038/s42003-021-02533-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Autism arises in high and low-risk families. De novo mutation contributes to autism incidence in low-risk families as there is a higher incidence in the affected of the simplex families than in their unaffected siblings. But the extent of contribution in low-risk families cannot be determined solely from simplex families as they are a mixture of low and high-risk. The rate of de novo mutation in nearly pure populations of high-risk families, the multiplex families, has not previously been rigorously determined. Moreover, rates of de novo mutation have been underestimated from studies based on low resolution microarrays and whole exome sequencing. Here we report on findings from whole genome sequence (WGS) of both simplex families from the Simons Simplex Collection (SSC) and multiplex families from the Autism Genetic Resource Exchange (AGRE). After removing the multiplex samples with excessive cell-line genetic drift, we find that the contribution of de novo mutation in multiplex is significantly smaller than the contribution in simplex. We use WGS to provide high resolution CNV profiles and to analyze more than coding regions, and revise upward the rate in simplex autism due to an excess of de novo events targeting introns. Based on this study, we now estimate that de novo events contribute to 52-67% of cases of autism arising from low risk families, and 30-39% of cases of all autism.
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Affiliation(s)
- Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Adriana Munoz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Yoon-Ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Steven Marks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | | | - Abba M Krieger
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Andreas Buja
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Kith Pradhan
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Kristin K Baldwin
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA.,Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA. .,New York Genome Center, New York, NY, USA.
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42
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Trost B, Loureiro LO, Scherer SW. Discovery of genomic variation across a generation. Hum Mol Genet 2021; 30:R174-R186. [PMID: 34296264 PMCID: PMC8490016 DOI: 10.1093/hmg/ddab209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Over the past 30 years (the timespan of a generation), advances in genomics technologies have revealed tremendous and unexpected variation in the human genome and have provided increasingly accurate answers to long-standing questions of how much genetic variation exists in human populations and to what degree the DNA complement changes between parents and offspring. Tracking the characteristics of these inherited and spontaneous (or de novo) variations has been the basis of the study of human genetic disease. From genome-wide microarray and next-generation sequencing scans, we now know that each human genome contains over 3 million single nucleotide variants when compared with the ~ 3 billion base pairs in the human reference genome, along with roughly an order of magnitude more DNA—approximately 30 megabase pairs (Mb)—being ‘structurally variable’, mostly in the form of indels and copy number changes. Additional large-scale variations include balanced inversions (average of 18 Mb) and complex, difficult-to-resolve alterations. Collectively, ~1% of an individual’s genome will differ from the human reference sequence. When comparing across a generation, fewer than 100 new genetic variants are typically detected in the euchromatic portion of a child’s genome. Driven by increasingly higher-resolution and higher-throughput sequencing technologies, newer and more accurate databases of genetic variation (for instance, more comprehensive structural variation data and phasing of combinations of variants along chromosomes) of worldwide populations will emerge to underpin the next era of discovery in human molecular genetics.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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43
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Choi L, An JY. Genetic architecture of autism spectrum disorder: Lessons from large-scale genomic studies. Neurosci Biobehav Rev 2021; 128:244-257. [PMID: 34166716 DOI: 10.1016/j.neubiorev.2021.06.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. Recently developed genomic technologies, including microarray and next-generation sequencing (NGS), have enabled researchers to genetic analyses aimed at identifying genetic variations associated with ASD and to elucidate the genetic architecture of the disorder. Large-scale microarray, exome sequencing analyses, and robust statistical methods have resulted in successful gene discovery and identification of high-confidence ASD genes from among de novo and inherited variants. Efforts have been made to understand the genetic architecture of ASD using whole-genome sequencing and genome-wide association studies aimed at identifying noncoding mutations and common variants associated with ASD. In addition, the development of systems biology approaches has resulted in the integration of genetic findings with functional genomic datasets, thereby providing a unique insight into the functional convergence of ASD risk genes and their neurobiology. In this review, we summarize the latest findings of ASD genetic studies involving large cohorts and discuss their implications in ASD neurobiology and in clinical practice.
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Affiliation(s)
- Leejee Choi
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea; Transdisciplinary Major in Learning Health Systems, Department of Healthcare Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.
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44
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Vogel Ciernia A, Laufer BI, Hwang H, Dunaway KW, Mordaunt CE, Coulson RL, Yasui DH, LaSalle JM. Epigenomic Convergence of Neural-Immune Risk Factors in Neurodevelopmental Disorder Cortex. Cereb Cortex 2021; 30:640-655. [PMID: 31240313 DOI: 10.1093/cercor/bhz115] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) affect 7-14% of all children in developed countries and are one of the leading causes of lifelong disability. Epigenetic modifications are poised at the interface between genes and environment and are predicted to reveal insight into NDD etiology. Whole-genome bisulfite sequencing was used to examine DNA cytosine methylation in 49 human cortex samples from 3 different NDDs (autism spectrum disorder, Rett syndrome, and Dup15q syndrome) and matched controls. Integration of methylation changes across NDDs with relevant genomic and genetic datasets revealed differentially methylated regions (DMRs) unique to each type of NDD but with shared regulatory functions in neurons and microglia. NDD DMRs were enriched within promoter regions and for transcription factor binding sites with identified methylation sensitivity. DMRs from all 3 disorders were enriched for ontologies related to nervous system development and genes with disrupted expression in brain from neurodevelopmental or neuropsychiatric disorders. Genes associated with NDD DMRs showed expression patterns indicating an important role for altered microglial function during brain development. These findings demonstrate an NDD epigenomic signature in human cortex that will aid in defining therapeutic targets and early biomarkers at the interface of genetic and environmental NDD risk factors.
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Affiliation(s)
- A Vogel Ciernia
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - B I Laufer
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - H Hwang
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - K W Dunaway
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - C E Mordaunt
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - R L Coulson
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - D H Yasui
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - J M LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
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45
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Yanagishita T, Hirade T, Shimojima Yamamoto K, Funatsuka M, Miyamoto Y, Maeda M, Yanagi K, Kaname T, Nagata S, Nagata M, Ishihara Y, Miyashita Y, Asano Y, Sakata Y, Kosaki K, Yamamoto T. HECW2-related disorder in four Japanese patients. Am J Med Genet A 2021; 185:2895-2902. [PMID: 34047014 DOI: 10.1002/ajmg.a.62363] [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] [Received: 02/22/2021] [Revised: 04/14/2021] [Accepted: 05/09/2021] [Indexed: 11/11/2022]
Abstract
The HECT, C2, and WW domain containing E3 ubiquitin protein ligase 2 gene (HECW2) is involved in protein ubiquitination. Several genes associated with protein ubiquitination have been linked to neurodevelopmental disorders. HECW2-related disorder has been established through the identification of de novo variants in HECW2 in patients with neurodevelopmental disorders with hypotonia, seizures, and absent language. Recently, we identified novel HECW2 variants in four Japanese patients with neurodevelopmental disorders. Regarding motor development, two of the patients cannot walk, whereas the other two can walk with an unsteady gait, owing to hypotonia. All HECW2 variants, including those that were previously reported, are missense, and no loss-of-function variants have been identified. Most of the identified variants are located around the HECT domain. These findings suggest that the dominant negative effects of missense variants around the HECT domain may be the mechanism underlying HECW2-related disorder.
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Affiliation(s)
- Tomoe Yanagishita
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Takuya Hirade
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Keiko Shimojima Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Makoto Funatsuka
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yusaku Miyamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Makiko Maeda
- Department of Pediatrics, Saga Medical and Welfare Center for the Challenged, Saga, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Satoru Nagata
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yohei Miyashita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Legal Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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46
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Tang L, Levy T, Guillory S, Halpern D, Zweifach J, Giserman-Kiss I, Foss-Feig JH, Frank Y, Lozano R, Belani P, Layton C, Lerman B, Frowner E, Breen MS, De Rubeis S, Kostic A, Kolevzon A, Buxbaum JD, Siper PM, Grice DE. Prospective and detailed behavioral phenotyping in DDX3X syndrome. Mol Autism 2021; 12:36. [PMID: 33993884 PMCID: PMC8127248 DOI: 10.1186/s13229-021-00431-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/01/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND DDX3X syndrome is a recently identified genetic disorder that accounts for 1-3% of cases of unexplained developmental delay and/or intellectual disability (ID) in females, and is associated with motor and language delays, and autism spectrum disorder (ASD). To date, the published phenotypic characterization of this syndrome has primarily relied on medical record review; in addition, the behavioral dimensions of the syndrome have not been fully explored. METHODS We carried out multi-day, prospective, detailed phenotyping of DDX3X syndrome in 14 females and 1 male, focusing on behavioral, psychological, and neurological measures. Three participants in this cohort were previously reported with limited phenotype information and were re-evaluated for this study. We compared results against population norms and contrasted phenotypes between individuals harboring either (1) protein-truncating variants or (2) missense variants or in-frame deletions. RESULTS Eighty percent (80%) of individuals met criteria for ID, 60% for ASD and 53% for attention-deficit/hyperactivity disorder (ADHD). Motor and language delays were common as were sensory processing abnormalities. The cohort included 5 missense, 3 intronic/splice-site, 2 nonsense, 2 frameshift, 2 in-frame deletions, and one initiation codon variant. Genotype-phenotype correlations indicated that, on average, missense variants/in-frame deletions were associated with more severe language, motor, and adaptive deficits in comparison to protein-truncating variants. LIMITATIONS Sample size is modest, however, DDX3X syndrome is a rare and underdiagnosed disorder. CONCLUSION This study, representing a first, prospective, detailed characterization of DDX3X syndrome, extends our understanding of the neurobehavioral phenotype. Gold-standard diagnostic approaches demonstrated high rates of ID, ASD, and ADHD. In addition, sensory deficits were observed to be a key part of the syndrome. Even with a modest sample, we observe evidence for genotype-phenotype correlations with missense variants/in-frame deletions generally associated with more severe phenotypes.
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Affiliation(s)
- Lara Tang
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Tess Levy
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Sylvia Guillory
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Danielle Halpern
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Jessica Zweifach
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Ivy Giserman-Kiss
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Jennifer H. Foss-Feig
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Yitzchak Frank
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Reymundo Lozano
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Puneet Belani
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Christina Layton
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Bonnie Lerman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Emanuel Frowner
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Michael S. Breen
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ana Kostic
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Paige M. Siper
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Dorothy E. Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Division of Tics, OCD, and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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47
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Bergeron LA, Besenbacher S, Bakker J, Zheng J, Li P, Pacheco G, Sinding MHS, Kamilari M, Gilbert MTP, Schierup MH, Zhang G. The germline mutational process in rhesus macaque and its implications for phylogenetic dating. Gigascience 2021; 10:giab029. [PMID: 33954793 PMCID: PMC8099771 DOI: 10.1093/gigascience/giab029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/05/2021] [Accepted: 03/29/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. RESULTS Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ∼76× per individual and estimated a mean rate of 0.77 × 10-8de novo mutations per site per generation (95% CI: 0.69 × 10-8 to 0.85 × 10-8). By phasing 50% of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed a mean of 81% of the de novo mutations, with a trend of an increasing male contribution for older fathers. Approximately 3.5% of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated on the basis of the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecoidea/Hominoidea molecular divergence dated at 58 Mya using our new estimate of the yearly mutation rate. CONCLUSIONS When compared to the traditional molecular clock methods, new estimated rates from pedigree samples can provide insights into the evolution of well-studied groups such as primates.
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Affiliation(s)
- Lucie A Bergeron
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Brendstrupgårdsvej 21A, 8200 Aarhus N, Denmark
| | - Jaco Bakker
- Animal Science Department, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, Netherlands
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
| | - Panyi Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Mikkel-Holger S Sinding
- Department of genetics, Trinity College Dublin, 2 college green, D02 VF25, Dublin, Ireland
- Greenland Institute of Natural Resources, Kivioq 2, 3900 Nuuk, Greenland
| | - Maria Kamilari
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, C.F.Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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48
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Swahari V, Nakamura A, Hollville E, Stroud H, Simon JM, Ptacek TS, Beck MV, Flowers C, Guo J, Plestant C, Liang J, Kurtz CL, Kanke M, Hammond SM, He YW, Anton ES, Sethupathy P, Moy SS, Greenberg ME, Deshmukh M. MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation. Cell Rep 2021; 35:108946. [PMID: 33826889 PMCID: PMC8103628 DOI: 10.1016/j.celrep.2021.108946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/09/2020] [Accepted: 03/14/2021] [Indexed: 11/27/2022] Open
Abstract
Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Ayumi Nakamura
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Emilie Hollville
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hume Stroud
- Department of Neurobiology, Harvard University, Boston, MA, USA
| | - Jeremy M Simon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Travis S Ptacek
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew V Beck
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Cornelius Flowers
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jiami Guo
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jie Liang
- Department of Immunology, Duke University, Durham, NC, USA
| | - C Lisa Kurtz
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - You-Wen He
- Department of Immunology, Duke University, Durham, NC, USA
| | - E S Anton
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | | | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.
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49
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Wang T, Zhang Y, Liu L, Wang Y, Chen H, Fan T, Li J, Xia K, Sun Z. Targeted sequencing and integrative analysis of 3,195 Chinese patients with neurodevelopmental disorders prioritized 26 novel candidate genes. J Genet Genomics 2021; 48:312-323. [PMID: 33994118 DOI: 10.1016/j.jgg.2021.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 02/06/2023]
Abstract
Neurodevelopmental disorders (NDDs) are a set of complex disorders characterized by diverse and co-occurring clinical symptoms. The genetic contribution in patients with NDDs remains largely unknown. Here, we sequence 519 NDD-related genes in 3,195 Chinese probands with neurodevelopmental phenotypes and identify 2,522 putative functional mutations consisting of 137 de novo mutations (DNMs) in 86 genes and 2,385 rare inherited mutations (RIMs) with 22 X-linked hemizygotes in 13 genes, 2 homozygous mutations in 2 genes and 23 compound heterozygous mutations in 10 genes. Furthermore, the DNMs of 16,807 probands with NDDs are retrieved from public datasets and combine in an integrated analysis with the mutation data of our Chinese NDD probands by taking 3,582 in-house controls of Chinese origin as background. We prioritize 26 novel candidate genes. Notably, six of these genes - ITSN1, UBR3, CADM1, RYR3, FLNA, and PLXNA3 - preferably contribute to autism spectrum disorders (ASDs), as demonstrated by high co-expression and/or interaction with ASD genes confirmed via rescue experiments in a mouse model. Importantly, these genes are differentially expressed in the ASD cortex in a significant manner and involved in ASD-associated networks. Together, our study expands the genetic spectrum of Chinese NDDs, further facilitating both basic and translational research.
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Affiliation(s)
- Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; DIAGenes Precision Medicine, Beijing 102600, China
| | - Yi Zhang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410083, China
| | - Liqui Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiqian Chen
- Shanghai Adeptus Biotechnology, Shanghai 200126, China
| | - Tianda Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jinchen Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410083, China; Department of Neurology, Xiangya Hospital, Central South University, Changsha Hunan, 410083, China.
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China; CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai 200031, China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, China.
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China.
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50
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Radio FC, Pang K, Ciolfi A, Levy MA, Hernández-García A, Pedace L, Pantaleoni F, Liu Z, de Boer E, Jackson A, Bruselles A, McConkey H, Stellacci E, Lo Cicero S, Motta M, Carrozzo R, Dentici ML, McWalter K, Desai M, Monaghan KG, Telegrafi A, Philippe C, Vitobello A, Au M, Grand K, Sanchez-Lara PA, Baez J, Lindstrom K, Kulch P, Sebastian J, Madan-Khetarpal S, Roadhouse C, MacKenzie JJ, Monteleone B, Saunders CJ, Jean Cuevas JK, Cross L, Zhou D, Hartley T, Sawyer SL, Monteiro FP, Secches TV, Kok F, Schultz-Rogers LE, Macke EL, Morava E, Klee EW, Kemppainen J, Iascone M, Selicorni A, Tenconi R, Amor DJ, Pais L, Gallacher L, Turnpenny PD, Stals K, Ellard S, Cabet S, Lesca G, Pascal J, Steindl K, Ravid S, Weiss K, Castle AMR, Carter MT, Kalsner L, de Vries BBA, van Bon BW, Wevers MR, Pfundt R, Stegmann APA, Kerr B, Kingston HM, Chandler KE, Sheehan W, Elias AF, Shinde DN, Towne MC, Robin NH, Goodloe D, Vanderver A, Sherbini O, Bluske K, Hagelstrom RT, Zanus C, Faletra F, Musante L, Kurtz-Nelson EC, Earl RK, Anderlid BM, Morin G, van Slegtenhorst M, Diderich KEM, Brooks AS, Gribnau J, Boers RG, Finestra TR, Carter LB, Rauch A, Gasparini P, Boycott KM, Barakat TS, Graham JM, Faivre L, Banka S, Wang T, Eichler EE, Priolo M, Dallapiccola B, Vissers LELM, Sadikovic B, Scott DA, Holder JL, Tartaglia M. SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females. Am J Hum Genet 2021; 108:502-516. [PMID: 33596411 DOI: 10.1016/j.ajhg.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.
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Affiliation(s)
| | - Kaifang Pang
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ciolfi
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Andrés Hernández-García
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lucia Pedace
- Oncohaematology Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Zhandong Liu
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Adam Jackson
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Emilia Stellacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marialetizia Motta
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Rosalba Carrozzo
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | | | | | - Christophe Philippe
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Joanne Baez
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | | | - Peggy Kulch
- Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - Jessica Sebastian
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Suneeta Madan-Khetarpal
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | | | | | - Berrin Monteleone
- Clinical genetics, NYU Langone Long Island School of Medicine, Mineola, NY 11501, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - July K Jean Cuevas
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Laura Cross
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Sarah L Sawyer
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | | | | | - Fernando Kok
- Mendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil
| | | | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Eva Morava
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | - Romano Tenconi
- Dipartimento di Pediatria, Università di Padova, 35137 Padua, Italy
| | - David J Amor
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Lynn Pais
- Medical and Populations Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | | | - Karen Stals
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sian Ellard
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sara Cabet
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Gaetan Lesca
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Joset Pascal
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Sarit Ravid
- Pediatric Neurology Unit, Ruth Children's Hospital, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa 3109601, Israel
| | - Alison M R Castle
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Melissa T Carter
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Louisa Kalsner
- Connecticut Children's Medical Center, University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marijke R Wevers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, 6229 HX Maastricht, the Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Helen M Kingston
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Willow Sheehan
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | | | | | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dana Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Omar Sherbini
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Krista Bluske
- Illumina Clinical Services Laboratory, San Diego, CA 92122, USA
| | | | - Caterina Zanus
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | | | - Rachel K Earl
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Gilles Morin
- CA de Génétique Clinique & Oncogénétique, CHU Amiens-Picardie, 80054 Amiens, France
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Teresa Robert Finestra
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Lauren B Carter
- Department of Pediatrics, Division of Medical Genetics, Levine Children's Hospital Atrium Health, Charlotte, NC 28203, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy; Department of Medicine, Surgery & Health Science, University of Trieste, 34143 Trieste, Italy
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Laurence Faivre
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD et Institut GIMI, 77908 Dijon, France; UMR 1231 GAD, Inserm - Université Bourgogne-Franche Comté, 77908 Dijon, France
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Manuela Priolo
- UOSD Genetica Medica del Grande Ospedale Metropolitano "Bianchi Melacrino Morelli" di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jimmy Lloyd Holder
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
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