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Craig O, Lee S, Pilcher C, Saoud R, Abdirahman S, Salazar C, Williams N, Ascher D, Vary R, Luu J, Cowley K, Ramm S, Li MX, Thio N, Li J, Semple T, Simpson K, Gorringe K, Holien J. A new method for network bioinformatics identifies novel drug targets for mucinous ovarian carcinoma. NAR Genom Bioinform 2024; 6:lqae096. [PMID: 39184376 PMCID: PMC11344246 DOI: 10.1093/nargab/lqae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/11/2024] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
Mucinous ovarian carcinoma (MOC) is a subtype of ovarian cancer that is distinct from all other ovarian cancer subtypes and currently has no targeted therapies. To identify novel therapeutic targets, we developed and applied a new method of differential network analysis comparing MOC to benign mucinous tumours (in the absence of a known normal tissue of origin). This method mapped the protein-protein network in MOC and then utilised structural bioinformatics to prioritise the proteins identified as upregulated in the MOC network for their likelihood of being successfully drugged. Using this protein-protein interaction modelling, we identified the strongest 5 candidates, CDK1, CDC20, PRC1, CCNA2 and TRIP13, as structurally tractable to therapeutic targeting by small molecules. siRNA knockdown of these candidates performed in MOC and control normal fibroblast cell lines identified CDK1, CCNA2, PRC1 and CDC20, as potential drug targets in MOC. Three targets (TRIP13, CDC20, CDK1) were validated using known small molecule inhibitors. Our findings demonstrate the utility of our pipeline for identifying new targets and highlight potential new therapeutic options for MOC patients.
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Affiliation(s)
- Olivia Craig
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Samuel Lee
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Carlton, VIC 3010, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Courtney Pilcher
- School of Science, STEM College, RMIT University, Bundoora, VIC 3082, Australia
| | - Rita Saoud
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Suad Abdirahman
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Carolina Salazar
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Nathan Williams
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- School of Science, STEM College, RMIT University, Bundoora, VIC 3082, Australia
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4067, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robert Vary
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Jennii Luu
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Karla J Cowley
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Susanne Ramm
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Mark Xiang Li
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
| | - Jason Li
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
| | - Tim Semple
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
| | - Kaylene J Simpson
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Jessica K Holien
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Carlton, VIC 3010, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- School of Science, STEM College, RMIT University, Bundoora, VIC 3082, Australia
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Gupta V, Ben-Mahmoud A, Ku B, Velayutham D, Jan Z, Yousef Aden A, Kubbar A, Alshaban F, Stanton LW, Jithesh PV, Layman LC, Kim HG. Identification of two novel autism genes, TRPC4 and SCFD2, in Qatar simplex families through exome sequencing. Front Psychiatry 2023; 14:1251884. [PMID: 38025430 PMCID: PMC10644705 DOI: 10.3389/fpsyt.2023.1251884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
This study investigated the genetic underpinnings of autism spectrum disorder (ASD) in a Middle Eastern cohort in Qatar using exome sequencing. The study identified six candidate autism genes in independent simplex families, including both four known and two novel autosomal dominant and autosomal recessive genes associated with ASD. The variants consisted primarily of de novo and homozygous missense and splice variants. Multiple individuals displayed more than one candidate variant, suggesting the potential involvement of digenic or oligogenic models. These variants were absent in the Genome Aggregation Database (gnomAD) and exhibited extremely low frequencies in the local control population dataset. Two novel autism genes, TRPC4 and SCFD2, were discovered in two Qatari autism individuals. Furthermore, the D651A substitution in CLCN3 and the splice acceptor variant in DHX30 were identified as likely deleterious mutations. Protein modeling was utilized to evaluate the potential impact of three missense variants in DEAF1, CLCN3, and SCFD2 on their respective structures and functions, which strongly supported the pathogenic natures of these variants. The presence of multiple de novo mutations across trios underscored the significant contribution of de novo mutations to the genetic etiology of ASD. Functional assays and further investigations are necessary to confirm the pathogenicity of the identified genes and determine their significance in ASD. Overall, this study sheds light on the genetic factors underlying ASD in Qatar and highlights the importance of considering diverse populations in ASD research.
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Affiliation(s)
- Vijay Gupta
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Afif Ben-Mahmoud
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Dinesh Velayutham
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Zainab Jan
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Abdi Yousef Aden
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Ahmad Kubbar
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Fouad Alshaban
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence W. Stanton
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Puthen Veettil Jithesh
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - 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
| | - Hyung-Goo Kim
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
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Medina E, Peterson S, Ford K, Singletary K, Peixoto L. Critical periods and Autism Spectrum Disorders, a role for sleep. Neurobiol Sleep Circadian Rhythms 2023; 14:100088. [PMID: 36632570 PMCID: PMC9826922 DOI: 10.1016/j.nbscr.2022.100088] [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: 09/21/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Brain development relies on both experience and genetically defined programs. Time windows where certain brain circuits are particularly receptive to external stimuli, resulting in heightened plasticity, are referred to as "critical periods". Sleep is thought to be essential for normal brain development. Importantly, studies have shown that sleep enhances critical period plasticity and promotes experience-dependent synaptic pruning in the developing mammalian brain. Therefore, normal plasticity during critical periods depends on sleep. Problems falling and staying asleep occur at a higher rate in Autism Spectrum Disorder (ASD) relative to typical development. In this review, we explore the potential link between sleep, critical period plasticity, and ASD. First, we review the importance of critical period plasticity in typical development and the role of sleep in this process. Next, we summarize the evidence linking ASD with deficits in synaptic plasticity in rodent models of high-confidence ASD gene candidates. We then show that the high-confidence rodent models of ASD that show sleep deficits also display plasticity deficits. Given how important sleep is for critical period plasticity, it is essential to understand the connections between synaptic plasticity, sleep, and brain development in ASD. However, studies investigating sleep or plasticity during critical periods in ASD mouse models are lacking. Therefore, we highlight an urgent need to consider developmental trajectory in studies of sleep and plasticity in neurodevelopmental disorders.
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Affiliation(s)
- Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Sarah Peterson
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Kristan Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
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McGee SR, Rajamanickam S, Adhikari S, Falayi OC, Wilson TA, Shayota BJ, Cooley Coleman JA, Skinner C, Caylor RC, Stevenson RE, Quaio CRDAC, Wilke BC, Bain JM, Anyane-Yeboa K, Brown K, Greally JM, Bijlsma EK, Ruivenkamp CAL, Politi K, Arbogast LA, Collard MW, Huggenvik JI, Elsea SH, Jensik PJ. Expansion and mechanistic insights into de novo DEAF1 variants in DEAF1-associated neurodevelopmental disorders. Hum Mol Genet 2023; 32:386-401. [PMID: 35981081 PMCID: PMC10310974 DOI: 10.1093/hmg/ddac200] [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: 05/13/2022] [Revised: 07/11/2022] [Accepted: 08/08/2022] [Indexed: 01/24/2023] Open
Abstract
De novo deleterious and heritable biallelic mutations in the DNA binding domain (DBD) of the transcription factor deformed epidermal autoregulatory factor 1 (DEAF1) result in a phenotypic spectrum of disorders termed DEAF1-associated neurodevelopmental disorders (DAND). RNA-sequencing using hippocampal RNA from mice with conditional deletion of Deaf1 in the central nervous system indicate that loss of Deaf1 activity results in the altered expression of genes involved in neuronal function, dendritic spine maintenance, development, and activity, with reduced dendritic spines in hippocampal regions. Since DEAF1 is not a dosage-sensitive gene, we assessed the dominant negative activity of previously identified de novo variants and a heritable recessive DEAF1 variant on selected DEAF1-regulated genes in 2 different cell models. While no altered gene expression was observed in cells over-expressing the recessive heritable variant, the gene expression profiles of cells over-expressing de novo variants resulted in similar gene expression changes as observed in CRISPR-Cas9-mediated DEAF1-deleted cells. Altered expression of DEAF1-regulated genes was rescued by exogenous expression of WT-DEAF1 but not by de novo variants in cells lacking endogenous DEAF1. De novo heterozygous variants within the DBD of DEAF1 were identified in 10 individuals with a phenotypic spectrum including autism spectrum disorder, developmental delays, sleep disturbance, high pain tolerance, and mild dysmorphic features. Functional assays demonstrate these variants alter DEAF1 transcriptional activity. Taken together, this study expands the clinical phenotypic spectrum of individuals with DAND, furthers our understanding of potential roles of DEAF1 on neuronal function, and demonstrates dominant negative activity of identified de novo variants.
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Affiliation(s)
- Stacey R McGee
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Shivakumar Rajamanickam
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Sandeep Adhikari
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Brian J Shayota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
- Department of Pediatrics, Division of Genetics, University of Utah, Salt Lake City, UT
| | | | | | | | | | - Caio Robledo D' Angioli Costa Quaio
- Instituto da Criança (Children’s Hospital), Hospital das Clínicas (HCFMUSP), Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório Clínico, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Jennifer M Bain
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Irving Medical Center, New York, USA
| | - Kaitlyn Brown
- Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - John M Greally
- Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY USA
- Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, PO box 9600, 2300 RC, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, PO box 9600, 2300 RC, Leiden, The Netherlands
| | | | - Lydia A Arbogast
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Michael W Collard
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Jodi I Huggenvik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
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5
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Bodunova N, Vorontsova M, Khatkov I, Baranova E, Bykova S, Degterev D, Litvinova M, Bilyalov A, Makarova M, Sagaydak O, Danishevich A. A Unique Observation of a Patient with Vulto-van Silfhout-de Vries Syndrome. Diagnostics (Basel) 2022; 12:diagnostics12081887. [PMID: 36010237 PMCID: PMC9406734 DOI: 10.3390/diagnostics12081887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction: Vulto-van Silfhout-de Vries Syndrome (VSVS; OMIM#615828) is a rare hereditary disease associated with impaired intellectual development and speech, delayed psychomotor development, and behavioral anomalies, including autistic behavioral traits and poor eye contact. To date, 27 patients with VSVS have been reported in the literature. Materials and Methods: We describe a 23-year-old male patient with autism spectrum disorder (ASD) who was admitted to the gastroenterological hospital with signs of pseudomembranous colitis. ASD was first noted in the patient at the age of 2.5 years. Later, he developed epileptic seizures and important growth retardation. Prior to the hospitalization, chromosomal aberrations, Fragile X syndrome, and aminoacidopathies/aminoacidurias associated with ASD were excluded. Whole-genome sequencing (WGS) was prescribed to the patient at 23 years old. Results: The patient had a heterozygous carrier of “de novo” variant c.662C > T (p.S221L) in exon 4 of the DEAF1 gene. c.662C > T had not been previously described in genomic databases. According to the ACMG criteria, this missense variant was considered to be pathogenic. VSVS was diagnosed in the patient. Conclusions: The phenotype of the patient is very similar to the data presented in the world literature. However, growth retardation and cachexia, which have not been described previously in the articles, are of interest.
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Affiliation(s)
- Natalia Bodunova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Maria Vorontsova
- National Medical Research Center for Endocrinology, 117292 Moscow, Russia
| | - Igor Khatkov
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Elena Baranova
- LLC Evogen, 115191 Moscow, Russia
- Russian Medical Academy of Continuous Professional Education, 125445 Moscow, Russia
| | - Svetlana Bykova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Daniil Degterev
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Maria Litvinova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
- Department of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia
| | - Airat Bilyalov
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Correspondence: ; Tel.: +7-962-560-38-02
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Gleeson J, Leger A, Prawer YDJ, Lane TA, Harrison PJ, Haerty W, Clark MB. Accurate expression quantification from nanopore direct RNA sequencing with NanoCount. Nucleic Acids Res 2022; 50:e19. [PMID: 34850115 PMCID: PMC8886870 DOI: 10.1093/nar/gkab1129] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Sequencing full-length native RNAs using long-read direct RNA sequencing (DRS) has the potential to overcome many limitations of short and long-read sequencing methods that require RNA fragmentation, cDNA synthesis or PCR. However, there are a lack of tools specifically designed for DRS and its ability to identify differential expression in complex organisms is poorly characterised. We developed NanoCount for fast, accurate transcript isoform quantification in DRS and demonstrate it outperforms similar methods. Using synthetic controls and human SH-SY5Y cell differentiation into neuron-like cells, we show that DRS accurately quantifies RNA expression and identifies differential expression of genes and isoforms. Differential expression of 231 genes, 333 isoforms, plus 27 isoform switches were detected between undifferentiated and differentiated SH-SY5Y cells and samples clustered by differentiation state at the gene and isoform level. Genes upregulated in neuron-like cells were associated with neurogenesis. NanoCount quantification of thousands of novel isoforms discovered with DRS likewise enabled identification of their differential expression. Our results demonstrate enhanced DRS isoform quantification with NanoCount and establish the ability of DRS to identify biologically relevant differential expression of genes and isoforms.
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Affiliation(s)
- Josie Gleeson
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yair D J Prawer
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Tracy A Lane
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Foundation Trust, Oxford, UK
| | - Wilfried Haerty
- The Earlham Institute, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
- Department of Psychiatry, University of Oxford, Oxford, UK
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7
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Whole genome sequencing in transposition of the great arteries and associations with clinically relevant heart, brain and laterality genes. Am Heart J 2022; 244:1-13. [PMID: 34670123 DOI: 10.1016/j.ahj.2021.10.185] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND The most common cyanotic congenital heart disease (CHD) requiring management as a neonate is transposition of great arteries (TGA). Clinically, up to 50% of TGA patients develop some form of neurodevelopmental disability (NDD), thought to have a significant genetic component. A "ciliopathy" and links with laterality disorders have been proposed. This first report of whole genome sequencing in TGA, sought to identify clinically relevant variants contributing to heart, brain and laterality defects. METHODS Initial whole genome sequencing analyses on 100 TGA patients focussed on established disease genes related to CHD (n = 107), NDD (n = 659) and heterotaxy (n = 74). Single variant as well as copy number variant analyses were conducted. Variant pathogenicity was assessed using the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. RESULTS Fifty-five putatively damaging variants were identified in established disease genes associated with CHD, NDD and heterotaxy; however, no clinically relevant variants could be attributed to disease. Notably, case-control analyses identified significantly more predicted-damaging, silent and total variants in TGA cases than healthy controls in established CHD genes (P < .001), NDD genes (P < .001) as well as across the three gene panels (P < .001). CONCLUSION We present compelling evidence that the majority of TGA is not caused by monogenic rare variants and is most likely oligogenic and/or polygenic in nature, highlighting the complex genetic architecture and multifactorial influences on this CHD sub-type and its long-term sequelae. Assessment of variant burden in key heart, brain and/or laterality genes may be required to unravel the genetic contributions to TGA and related disabilities.
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Taşkıran EZ, Karaosmanoğlu B, Koşukcu C, Ürel-Demir G, Akgün-Doğan Ö, Şimşek-Kiper PÖ, Alikaşifoğlu M, Boduroğlu K, Utine GE. Diagnostic yield of whole-exome sequencing in non-syndromic intellectual disability. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2021; 65:577-588. [PMID: 33739554 DOI: 10.1111/jir.12835] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Aetiological diagnosis in non-syndromic intellectual disability (NSID) still poses a diagnostic challenge to clinicians. METHODS Screening is currently achieved by chromosomal microarrays followed by whole-exome sequencing (WES). In search for the aetiological yield of WES in patients with NSID, 59 unrelated patients were studied. RESULTS Among the 59 patients, 44 (74.6%) were from consanguineous unions. Epilepsy was present in 11 (37.9%), behavioural problems in 12 (41.4%) and autistic features in 14 (48.3%). WES analysis resulted in molecular diagnosis in 29 patients (49.2%). Some of the genes were specific for nervous system functioning, like HERC1, TBC1D7, LINS, HECW2, DEAF1, HNMT, DLG3, NRXN1 and HUWE1. Others were ubiquitously expressed genes involved in fundamental cellular processes, like IARS, UBE3A, COQ4, TAF1, SETBP1, ARV1, ZC4H2, KAT6A, ASXL3, THOC6, HNRNPH2, TUBA8 and KIF1A. Twenty-two (75.8%) were consanguineously married; however, only 12 (41.4%) of the detected genes caused autosomal recessive phenotypes. CONCLUSIONS This cohort suggests that recessive genes probably represent an actually smaller subgroup of NSID, even among families with consanguinity. Although in societies with high consanguinity rates, considering the recessive inheritance first seems to be an advantageous strategy, de novo mutations in autosomal dominantly expressed genes represent the major aetiological group in patients with NSID, even among those patients from consanguineous families.
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Affiliation(s)
- E Z Taşkıran
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - B Karaosmanoğlu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - C Koşukcu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - G Ürel-Demir
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ö Akgün-Doğan
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - P Ö Şimşek-Kiper
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - M Alikaşifoğlu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - K Boduroğlu
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - G E Utine
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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Cederquist GY, Tchieu J, Callahan SJ, Ramnarine K, Ryan S, Zhang C, Rittenhouse C, Zeltner N, Chung SY, Zhou T, Chen S, Betel D, White RM, Tomishima M, Studer L. A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes. Cell Stem Cell 2021; 27:35-49.e6. [PMID: 32619517 DOI: 10.1016/j.stem.2020.06.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 01/12/2023]
Abstract
Autism is a clinically heterogeneous neurodevelopmental disorder characterized by impaired social interactions, restricted interests, and repetitive behaviors. Despite significant advances in the genetics of autism, understanding how genetic changes perturb brain development and affect clinical symptoms remains elusive. Here, we present a multiplex human pluripotent stem cell (hPSC) platform, in which 30 isogenic disease lines are pooled in a single dish and differentiated into prefrontal cortex (PFC) lineages to efficiently test early-developmental hypotheses of autism. We define subgroups of autism mutations that perturb PFC neurogenesis and are correlated to abnormal WNT/βcatenin responses. Class 1 mutations (8 of 27) inhibit while class 2 mutations (5 of 27) enhance PFC neurogenesis. Remarkably, autism patient data reveal that individuals carrying subclass-specific mutations differ clinically in their corresponding language acquisition profiles. Our study provides a framework to disentangle genetic heterogeneity associated with autism and points toward converging molecular and developmental pathways of diverse autism-associated mutations.
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Affiliation(s)
- Gustav Y Cederquist
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Jason Tchieu
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Scott J Callahan
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Cancer Genetics and Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Gerstner Graduate School of Biomedical Sciences, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Kiran Ramnarine
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Sean Ryan
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chelsea Rittenhouse
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Nadja Zeltner
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Center for Molecular Medicine, Department of Cellular Biology, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sun Young Chung
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Ting Zhou
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Doron Betel
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Richard M White
- Cancer Genetics and Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Mark Tomishima
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA.
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Impairments of Photoreceptor Outer Segments Renewal and Phototransduction Due to a Peripherin Rare Haplotype Variant: Insights from Molecular Modeling. Int J Mol Sci 2021; 22:ijms22073484. [PMID: 33801777 PMCID: PMC8036374 DOI: 10.3390/ijms22073484] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Retinitis pigmentosa punctata albescens (RPA) is a particular form of retinitis pigmentosa characterized by childhood onset night blindness and areas of peripheral retinal atrophy. We investigated the genetic cause of RPA in a family consisting of two affected Egyptian brothers with healthy consanguineous parents. METHODS Mutational analysis of four RPA causative genes was realized by Sanger sequencing on both probands, and detected variants were subsequently genotyped in their parents. Afterwards, found variants were deeply, statistically, and in silico characterized to determine their possible effects and association with RPA. RESULTS Both brothers carry three missense PRPH2 variants in a homozygous condition (c.910C > A, c.929G > A, and c.1013A > C) and two promoter variants in RHO (c.-26A > G) and RLBP1 (c.-70G > A) genes, respectively. Haplotype analyses highlighted a PRPH2 rare haplotype variant (GAG), determining a possible alteration of PRPH2 binding with melanoregulin and other outer segment proteins, followed by photoreceptor outer segment instability. Furthermore, an altered balance of transcription factor binding sites, due to the presence of RHO and RLBP1 promoter variants, might determine a comprehensive downregulation of both genes, possibly altering the PRPH2 shared visual-related pathway. CONCLUSIONS Despite several limitations, the study might be a relevant step towards detection of novel scenarios in RPA etiopathogenesis.
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Chen S, Deng X, Xiong J, He F, Yang L, Chen B, Chen C, Zhang C, Yang L, Peng J, Yin F. De novo variants of DEAF1 cause intellectual disability in six Chinese patients. Clin Chim Acta 2021; 518:17-21. [PMID: 33705764 DOI: 10.1016/j.cca.2021.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND It has been reported that de novo heterozygous variants of DEAF1 can cause DEAF1-associated neurodevelopmental disorder. The purpose of this article is to explore the clinical and genetic characteristics of Chinese patients harboring de novo DEAF1 variants. METHODS We assembled a cohort of six unrelated patients with de novo variants in DEAF1. Clinical and genetic features of these patients were summarized. RESULTS Each child showed intellectual disability (ID)/ global developmental delay (GDD). Severe language impairment was prominent. Behavior problems, seizures, sleep disturbance, and a high pain threshold were common features. DEAF1-related seizures were reported to be difficult to treat or intractable. Seizures in our cohort were almost all treatable. Valproic acid was the most commonly used drug. Five heterozygous missense mutations of DEAF1 gene were identified, three of which (p.W234C, p.L203P, p.H275Q) were not published in literature before. CONCLUSION Mutations of DEAF1 gene should be considered in ID/GDD patients with a nonspecific phenotype, comprising intellectual disability, prominent speech delay, abnormal behaviors, especially autism. In our study, DEAF1-related epilepsy is completely treatable in Eastern-Asian individuals when compared to patients in other regions, and valproic acid can be used as a first choice. The knowledge of DEAF1-related neurodevelopmental disorder and the de novo variant database of DEAF1 were expanded.
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Affiliation(s)
- Shimeng Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Baiyu Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ciliu Zhang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Li Yang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China.
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12
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Gene constraint and genotype-phenotype correlations in neurodevelopmental disorders. Curr Opin Genet Dev 2020; 65:69-75. [PMID: 32599522 DOI: 10.1016/j.gde.2020.05.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 11/24/2022]
Abstract
With the advent and widespread adoption of high-throughput DNA sequencing, genetic discoveries in neurodevelopmental disorders (NDDs) are advancing very rapidly. The identification of novel NDD genes and of rare, highly penetrant pathogenic variants is leading to improved understanding of genotype-phenotype correlations. Here we emphasize the importance of large-scale, reference databases such as gnomAD to determine gene and variant level constraints and facilitate gene discovery, variant interpretation, and genotype-phenotype correlations. While the majority of dominant NDD genes are highly intolerant to variation, some apparent exceptions in reference databases are related to the presence of variants in transcripts that are not brain expressed and/or genes that show acquired somatic mosaicism in blood. Multiple NDD genes are being identified where varying phenotypes depend on the mode of inheritance (e.g., dominant or recessive), the nature (e.g., missense or truncating), or location of the mutation. Ongoing genome-wide analyses and targeted functional studies provide enhancements to the annotation of genes, gene products and variants, which will continue to facilitate gene and variant discovery and variant interpretation.
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Rare genetic susceptibility variants assessment in autism spectrum disorder: detection rate and practical use. Transl Psychiatry 2020; 10:77. [PMID: 32094338 PMCID: PMC7039996 DOI: 10.1038/s41398-020-0760-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/10/2019] [Accepted: 01/10/2020] [Indexed: 12/21/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component whose knowledge evolves quickly. Next-generation sequencing is the only effective technology to deal with the high genetic heterogeneity of ASD in a clinical setting. However, rigorous criteria to classify rare genetic variants conferring ASD susceptibility are currently lacking. We have performed whole-exome sequencing to identify both nucleotide variants and copy number variants (CNVs) in 253 ASD patients, including 68 patients with intellectual disability (ID) and 90 diagnosed as Asperger syndrome. Using explicit criteria to classify both susceptibility genes and susceptibility variants we prioritized 217 genes belonging to the following categories: syndromic genes, genes with an excess of de novo protein truncating variants and genes targeted by rare CNVs. We obtained a susceptibility variant detection rate of 19.7% (95% CI: [15-25.2%]). The rate for CNVs was 7.1% (95% CI: [4.3-11%]) and 12.6% (95% CI: [8.8-17.4%]) for nucleotide variants. The highest rate (30.1%, 95% CI: [20.2-43.2%]) was obtained in the ASD + ID subgroup. A strong contributor for at risk nucleotide variants was the recently identified set of genes (n = 81) harboring an excess of de novo protein truncating variants. Since there is currently no evidence that the genes targeted here are necessary and sufficient to cause ASD, we recommend to avoid the term "causative of ASD" when delivering the information about a variant to a family and to use instead the term "genetic susceptibility factor contributing to ASD".
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Satterstrom FK, Kosmicki JA, Wang J, Breen MS, De Rubeis S, An JY, Peng M, Collins R, Grove J, Klei L, Stevens C, Reichert J, Mulhern MS, Artomov M, Gerges S, Sheppard B, Xu X, Bhaduri A, Norman U, Brand H, Schwartz G, Nguyen R, Guerrero EE, Dias C, Betancur C, Cook EH, Gallagher L, Gill M, Sutcliffe JS, Thurm A, Zwick ME, Børglum AD, State MW, Cicek AE, Talkowski ME, Cutler DJ, Devlin B, Sanders SJ, Roeder K, Daly MJ, Buxbaum JD. Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism. Cell 2020; 180:568-584.e23. [PMID: 31981491 PMCID: PMC7250485 DOI: 10.1016/j.cell.2019.12.036] [Citation(s) in RCA: 1201] [Impact Index Per Article: 300.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/08/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022]
Abstract
We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n = 35,584 total samples, 11,986 with ASD). Using an enhanced analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained to have severe neurodevelopmental delay, whereas 53 show higher frequencies in individuals ascertained to have ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In cells from the human cortex, expression of risk genes is enriched in excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.
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Affiliation(s)
- F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jiebiao Wang
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Michael S Breen
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Minshi Peng
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ryan Collins
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jennifer Reichert
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maureen S Mulhern
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mykyta Artomov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sherif Gerges
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brooke Sheppard
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Utku Norman
- Computer Engineering Department, Bilkent University, Ankara, Turkey
| | - Harrison Brand
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Grace Schwartz
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel Nguyen
- Center for Autism Research and Translation, University of California, Irvine, Irvine, CA, USA
| | - Elizabeth E Guerrero
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California, Davis, Davis, CA, USA
| | - Caroline Dias
- Division of Genetics, Boston Children's Hospital, Boston, MA, USA; Division of Developmental Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Michael Gill
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - James S Sutcliffe
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Molecular Physiology and Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Audrey Thurm
- National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Ercument Cicek
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA; Computer Engineering Department, Bilkent University, Ankara, Turkey
| | - Michael E Talkowski
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 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, USA.
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15
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Casanova EL, Konkel MK. The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements. Bioessays 2020; 42:e1900173. [PMID: 31943266 PMCID: PMC7029956 DOI: 10.1002/bies.201900173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/30/2019] [Indexed: 12/13/2022]
Abstract
Theories of the genetics underlying punctuated equilibrium (PE) have been vague to date. Here the developmental gene hypothesis is proposed, which states that: 1) developmental regulatory (DevReg) genes are responsible for the orchestration of metazoan morphogenesis and their extreme conservation and mutation intolerance generates the equilibrium or stasis present throughout much of the fossil record and 2) the accumulation of regulatory elements and recombination within these same genes-often derived from transposable elements-drives punctuated bursts of morphological divergence and speciation across metazoa. This two-part hypothesis helps to explain the features that characterize PE, providing a theoretical genetic basis for the once-controversial theory. Also see the video abstract here https://youtu.be/C-fu-ks5yDs.
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Affiliation(s)
- Emily L. Casanova
- Department of Biomedical Sciences, University of South Carolina School of Medicine at Greenville, Greenville, South Carolina, USA
| | - Miriam K. Konkel
- Department of Genetics and Biochemistry, Clemson Center for Human Genetics, Biomedical Data Science and Informatics Program, Clemson University, Clemson, South Carolina, USA
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A girl with a neurodevelopmental syndrome, adducted thumbs and frequent infections caused by novel homozygous variant in DEAF1. Clin Dysmorphol 2020; 29:107-110. [PMID: 31929336 DOI: 10.1097/mcd.0000000000000314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Exome sequencing identifies de novo splicing variant in XRCC6 in sporadic case of autism. J Hum Genet 2019; 65:287-296. [PMID: 31827253 DOI: 10.1038/s10038-019-0707-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with heterogeneity in presentation, genetic etiology, and clinical outcome. Although numerous ASD susceptibility genes have been described, they only account for a small fraction of the estimated heritability, supporting the need to identify more risk variants. This study reports the whole exome sequencing for 24 simplex families with sporadic cases of ASD. These families were selected following a rigorous family history study designed to exclude families with any history of neurodevelopmental or psychiatric disease. Fifteen rare, de novo variants, including fourteen missense variants and one splicing variant, in thirteen families were identified. We describe a splicing variant in XRCC6 which was predicted to destroy the 5' splice site in intron 9 and introduce a premature stop codon. We observed intron 9 retention in XRCC6 transcripts and reduced XRCC6 expression in the proband. Reduced XRCC6 activity and function may be relevant to ASD etiology due to XRCC6's role in nonhomologous DNA repair and interactions of the C-terminal SAP domain with DEAF1, a nuclear transcriptional regulator that is important during embryonic development.
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Impaired memory and marble burying activity in deformed epidermal autoregulatory factor 1 (Deaf1) conditional knockout mice. Behav Brain Res 2019; 380:112383. [PMID: 31783086 DOI: 10.1016/j.bbr.2019.112383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/05/2019] [Accepted: 11/23/2019] [Indexed: 11/24/2022]
Abstract
Deleterious mutations within the DNA binding domain of the transcription factor deformed epidermal autoregulatory factor 1 (DEAF1) result in a phenotypic spectrum of neurodevelopmental disorders including intellectual disabilities and autism spectrum disorders. While whole animal deletion of Deaf1 in mice is lethal, mice with conditional disruption of the gene in neuronal precursor cells can display memory deficits and increased anxiety-like behavior. This study aimed to further characterize learning and memory alterations and assess changes in marble burying activity and hippocampal size in mice with conditional deletion of Deaf1. Mice lacking DEAF1 in the CNS (NKO) displayed reduced memory in both contextual fear conditioning and a 3-day massed trials Morris water maze paradigm. NKO mice had reduced marble burying activity in full cage marble burying tests. Using a half-cage marble test, NKO mice again buried fewer marbles and spent significantly more time on the side of the cage away from the marbles compared to control animals. The area of the dorsal hippocampus of NKO mice was decreased compared to control and animals with a single Deaf1 allele. These results continue to establish the importance of DEAF1 in cognitive behavior and provide new evidence that DEAF1 regulates hippocampal morphology.
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19
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A novel autosomal recessive DEAF1 nonsense variant: expanding the clinical phenotype. Clin Dysmorphol 2019; 29:114-117. [PMID: 31688097 DOI: 10.1097/mcd.0000000000000306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Konki M, Malonzo M, Karlsson IK, Lindgren N, Ghimire B, Smolander J, Scheinin NM, Ollikainen M, Laiho A, Elo LL, Lönnberg T, Röyttä M, Pedersen NL, Kaprio J, Lähdesmäki H, Rinne JO, Lund RJ. Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease. Clin Epigenetics 2019; 11:130. [PMID: 31477183 PMCID: PMC6721173 DOI: 10.1186/s13148-019-0729-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alzheimer's disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. Environmental and lifestyle factors largely modulate the disease risk and may influence the pathogenesis through epigenetic mechanisms, such as DNA methylation. As environmental and lifestyle factors may affect multiple tissues of the body, we hypothesized that the disease-associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs. RESULTS Comparison of 23 disease discordant Finnish twin pairs with reduced representation bisulfite sequencing revealed peripheral blood DNA methylation differences in 11 genomic regions with at least 15.0% median methylation difference and FDR adjusted p value ≤ 0.05. Several of the affected genes are primarily associated with neuronal functions and pathologies and do not display disease-associated differences in gene expression in blood. The DNA methylation mark in ADARB2 gene was found to be differentially methylated also in the anterior hippocampus, including entorhinal cortex, of non-twin cases and controls. Targeted bisulfite pyrosequencing of the DNA methylation mark in ADARB2 gene in 62 Finnish and Swedish twin pairs revealed that, in addition to the disease status, DNA methylation of this region is influenced by gender, age, zygosity, APOE genotype, and smoking. Further analysis of 120 Swedish twin pairs indicated that this specific DNA methylation mark is not predictive for Alzheimer's disease and becomes differentially methylated after disease onset. CONCLUSIONS DNA methylation differences can be detected in the peripheral blood of twin pairs discordant for Alzheimer's disease. These DNA methylation signatures may have value as disease markers and provide insights into the molecular mechanisms of pathogenesis. We found no evidence that the DNA methylation marks would be associated with gene expression in blood. Further studies are needed to elucidate the potential importance of the associated genes in neuronal functions and to validate the prognostic or diagnostic value of the individual marks or marker panels.
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Affiliation(s)
- Mikko Konki
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, FI-20014, Turku, Finland
| | - Maia Malonzo
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Ida K Karlsson
- Institute of Gerontology and Aging Research Network-Jönköping (ARN-J), School of Health and Welfare, Jönköping University, SE-55111, Jönköping, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | - Noora Lindgren
- Drug Research Doctoral Program, University of Turku, FI-20014, Turku, Finland.,Turku PET Centre, University of Turku, FI-20520, Turku, Finland
| | - Bishwa Ghimire
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Noora M Scheinin
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Turku Brain and Mind Center, FinnBrain Birth Cohort Study, Institute of Clinical Medicine, University of Turku, FI-20014, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, FI-20014, Turku, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Matias Röyttä
- Department of Pathology/Neuropathology, Turku University Hospital, University of Turku, FI-20014, Turku, Finland
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden.,Department of Psychology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland.,Department of Public Health, University of Helsinki, FI-00271, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Juha O Rinne
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Division of Clinical Neurosciences, Turku University Hospital, FI-20014, Turku, Finland
| | - Riikka J Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.
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21
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Bourgeois Y, Boissinot S. Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer. Mol Ecol 2019; 28:3523-3543. [PMID: 31233650 DOI: 10.1111/mec.15162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical, and the green anole (Anolis carolinensis) constitutes an exception since it expanded into temperate North America from subtropical Florida. Thus, we used the green anole as a model to investigate signatures of selection associated with colonization of a new environment, namely temperate North America. To this end, we analysed 29 whole-genome sequences, covering the entire native range of the species. We used a combination of recent methods to quantify both positive and balancing selection in northern populations, including FST outlier methods, machine learning and ancestral recombination graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests. Strikingly, we identified many genes involved in behaviour, suggesting that the recent successful colonization of northern environments may have been linked to behavioural shifts as well as physiological adaptation. Using a candidate genes strategy, we determined that genes involved in response to cold or behaviour displayed more frequently signals of selection, while controlling for local recombination rate, gene clustering and gene length. In addition, we found signatures of balancing selection at immune genes in all investigated genetic groups, but also at genes involved in neuronal and anatomical development.
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Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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22
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Sullivan JM, De Rubeis S, Schaefer A. Convergence of spectrums: neuronal gene network states in autism spectrum disorder. Curr Opin Neurobiol 2019; 59:102-111. [PMID: 31220745 DOI: 10.1016/j.conb.2019.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/20/2019] [Accepted: 04/24/2019] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder characterized by social deficits and restrictive and/or repetitive behaviors. The breadth of ASD symptoms is paralleled by the multiplicity of genes that have been implicated in its etiology. Initial findings revealed numerous ASD risk genes that contribute to synaptic function. More recently, genomic and gene expression studies point to altered chromatin function and impaired transcriptional control as additional risk factors for ASD. The consequences of impaired transcriptional alterations in ASD involve consistent changes in synaptic gene expression and cortical neuron specification during brain development. The multiplicity of genetic and environmental factors associated with ASD risk and their convergence onto common molecular pathways in neurons point to ASD as a disorder of gene regulatory networks.
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Affiliation(s)
- Josefa M Sullivan
- Nash Family Department of Neuroscience, New York, NY, USA; Department of Psychiatry, New York, NY, USA; Friedman Brain Institute, New York, NY, USA; Seaver Autism Center for Research and Treatment, New York, NY, USA
| | - Silvia De Rubeis
- Department of Psychiatry, New York, NY, USA; Seaver Autism Center for Research and Treatment, New York, NY, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne Schaefer
- Nash Family Department of Neuroscience, New York, NY, USA; Department of Psychiatry, New York, NY, USA; Friedman Brain Institute, New York, NY, USA; Seaver Autism Center for Research and Treatment, New York, NY, USA.
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23
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The Transcription Factor Deaf1 Modulates Engrailed-1 Expression to Regulate Skin Appendage Fate. J Invest Dermatol 2019; 139:2378-2381.e4. [PMID: 31145909 DOI: 10.1016/j.jid.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/29/2019] [Accepted: 05/10/2019] [Indexed: 12/23/2022]
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24
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Nabais Sá MJ, Jensik PJ, McGee SR, Parker MJ, Lahiri N, McNeil EP, Kroes HY, Hagerman RJ, Harrison RE, Montgomery T, Splitt M, Palmer EE, Sachdev RK, Mefford HC, Scott AA, Martinez-Agosto JA, Lorenz R, Orenstein N, Berg JN, Amiel J, Heron D, Keren B, Cobben JM, Menke LA, Marco EJ, Graham JM, Pierson TM, Karimiani EG, Maroofian R, Manzini MC, Cauley ES, Colombo R, Odent S, Dubourg C, Phornphutkul C, de Brouwer APM, de Vries BBA, Vulto-vanSilfhout AT. De novo and biallelic DEAF1 variants cause a phenotypic spectrum. Genet Med 2019; 21:2059-2069. [PMID: 30923367 DOI: 10.1038/s41436-019-0473-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/15/2019] [Indexed: 01/24/2023] Open
Abstract
PURPOSE To investigate the effect of different DEAF1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and on DEAF1 activity in vitro. METHODS We assembled a cohort of 23 patients with de novo and biallelic DEAF1 variants, described the genotype-phenotype correlation, and investigated the differential effect of de novo and recessive variants on transcription assays using DEAF1 and Eif4g3 promoter luciferase constructs. RESULTS The proportion of the most prevalent phenotypic features, including intellectual disability, speech delay, motor delay, autism, sleep disturbances, and a high pain threshold, were not significantly different in patients with biallelic and pathogenic de novo DEAF1 variants. However, microcephaly was exclusively observed in patients with recessive variants (p < 0.0001). CONCLUSION We propose that different variants in the DEAF1 gene result in a phenotypic spectrum centered around neurodevelopmental delay. While a pathogenic de novo dominant variant would also incapacitate the product of the wild-type allele and result in a dominant-negative effect, a combination of two recessive variants would result in a partial loss of function. Because the clinical picture can be nonspecific, detailed phenotype information, segregation, and functional analysis are fundamental to determine the pathogenicity of novel variants and to improve the care of these patients.
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Affiliation(s)
- Maria J Nabais Sá
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Stacey R McGee
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, OPD2 Northern General Hospital, Sheffield, UK
| | - Nayana Lahiri
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust & St George's, University of London, London, UK
| | - Evan P McNeil
- Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Randi J Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis School of Medicine, Sacramento, Sacramento, CA, USA.,Department of Pediatrics, University of California Davis Medical Center, Sacramento, Sacramento, CA, USA
| | - Rachel E Harrison
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Tara Montgomery
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Rani K Sachdev
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington-Seattle, Seattle, WA, USA
| | - Abbey A Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan N Berg
- Department of Clinical Genetics, Ninewells Hospital and Medical School, Dundee, Angus, UK.,Clinical Genetics, University of Dundee, Dundee, Angus, UK
| | - Jeanne Amiel
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Delphine Heron
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Boris Keren
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Jan-Maarten Cobben
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,North West Thames Genetics NHS, Northwick Park Hospital, London, UK
| | - Leonie A Menke
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Elysa J Marco
- Department of Child Neurology, Cortica Healthcare, San Rafael, CA, USA
| | - John M Graham
- Division of Clinical Genetics and Dysmorphology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tyler Mark Pierson
- Department of Pediatrics, Department of Neurology, and the Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ehsan Ghayoor Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - M Chiara Manzini
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Edmund S Cauley
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Roberto Colombo
- Faculty of Medicine"Agostino Gemelli"Catholic University of the Sacred Heart, Rome, Italy.,Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, CLAD-Ouest CHU Rennes, Univ Rennes, CNRS 6290 Institut de Génétique et Développement de Rennes (IGDR), Rennes, France
| | | | - Chanika Phornphutkul
- Division of Human Genetics, Department of Pediatrics, Hasbro Children's Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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25
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Expanding the phenotype in autosomal dominant mental retardation-24: a novel variation in DEAF1 gene. Clin Dysmorphol 2018; 28:94-97. [PMID: 30451703 DOI: 10.1097/mcd.0000000000000252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR. Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. NPJ Genom Med 2018; 3:22. [PMID: 30109124 PMCID: PMC6089881 DOI: 10.1038/s41525-018-0061-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/14/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
Abstract
Early infantile epileptic encephalopathy (EIEE) is a devastating epilepsy syndrome with onset in the first months of life. Although mutations in more than 50 different genes are known to cause EIEE, current diagnostic yields with gene panel tests or whole-exome sequencing are below 60%. We applied whole-genome analysis (WGA) consisting of whole-genome sequencing and comprehensive variant discovery approaches to a cohort of 14 EIEE subjects for whom prior genetic tests had not yielded a diagnosis. We identified both de novo point and INDEL mutations and de novo structural rearrangements in known EIEE genes, as well as mutations in genes not previously associated with EIEE. The detection of a pathogenic or likely pathogenic mutation in all 14 subjects demonstrates the utility of WGA to reduce the time and costs of clinical diagnosis of EIEE. While exome sequencing may have detected 12 of the 14 causal mutations, 3 of the 12 patients received non-diagnostic exome panel tests prior to genome sequencing. Thus, given the continued decline of sequencing costs, our results support the use of WGA with comprehensive variant discovery as an efficient strategy for the clinical diagnosis of EIEE and other genetic conditions.
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Affiliation(s)
- Betsy E. P. Ostrander
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Russell J. Butterfield
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Brent S. Pedersen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Andrew J. Farrell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Ryan M. Layer
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Alistair Ward
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Chase Miller
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Tonya DiSera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Francis M. Filloux
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Meghan S. Candee
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Tara Newcomb
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Joshua L. Bonkowsky
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Gabor T. Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Aaron R. Quinlan
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT USA
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27
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Rao AR, Nelson SF. Calculating the statistical significance of rare variants causal for Mendelian and complex disorders. BMC Med Genomics 2018; 11:53. [PMID: 29898714 PMCID: PMC6001062 DOI: 10.1186/s12920-018-0371-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question. METHODS We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample. Based on data from 2504 individuals in the 1000 Genomes Project dataset, we calculated the number of individuals who have a rare variant in a given gene for numerous filtering threshold scenarios, which may be used for calculating the significance of an observed rare variant being causal for disease. Additionally, we calculated mutational burden data on the number of individuals with rare variants in genic regions mapping to protein domains. RESULTS We describe methods to use the mutational burden data for calculating the significance of observing rare variants in a given proportion of sequenced individuals. We present SORVA, an implementation of these methods as a web tool, and we demonstrate application to 20 relevant but diverse next-gen sequencing studies. Specifically, we calculate the statistical significance of findings involving multi-family studies with rare Mendelian disease and a large-scale study of a complex disorder, autism spectrum disorder. If we use the frequency counts to rank genes based on intolerance for variation, the ranking correlates well with pLI scores derived from the Exome Aggregation Consortium (ExAC) dataset (ρ = 0.515), with the benefit that the scores are directly interpretable. CONCLUSIONS We have presented a strategy that is useful for vetting candidate genes from NGS studies and allows researchers to calculate the significance of seeing a variant in a given gene or protein domain. This approach is an important step towards developing a quantitative, statistics-based approach for presenting clinical findings.
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Affiliation(s)
- Aliz R. Rao
- Department of Human Genetics, University of California, Los Angeles, California, Los Angeles USA
| | - Stanley F. Nelson
- Department of Human Genetics, University of California, Los Angeles, California, Los Angeles USA
- Department of Psychiatry and Biobehavioral Sciences at the David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, Los Angeles USA
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28
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Li SJ, Yu SS, Luo HY, Li X, Rao B, Wang Y, Li ZZ, Liu G, Zou LP, Zhang JS, Feng C, Liu J, Liu JW, Hu N, Chen XQ, Yu SY, Li K, He MW, Yu XG, Wang J, Guo SL, Chen ZY, Zhang L, Ma L. Two de novo variations identified by massively parallel sequencing in 13 Chinese families with children diagnosed with autism spectrum disorder. Clin Chim Acta 2018; 479:144-147. [PMID: 29366832 DOI: 10.1016/j.cca.2018.01.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 01/09/2023]
Abstract
Autism spectrum disorder (ASD) is a genetically heterogeneous neurodevelopmental disorder characterized by impairments in social interaction and communication, and by restricted and repetitive behaviors. The genetic architecture of ASD has been elucidated, including chromosomal rearrangements, de novo or inherited rare variants, and copy number variants. However, the genetic mechanism of Chinese families with ASD children is explored rarely. To identify genetic pathogenesis, we performed massively parallel sequencing on 13 Chinese ASD trio families, and found two de novo variations. The novel de novo splice alteration c.664 + 2T > G in the DEAF1 gene and the novel de novo missense mutation c.95 C > T in the AADAT gene associated with ASD may be important clues for exploring the etiology of this disorder.
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Affiliation(s)
- Shi-Jun Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China.
| | | | | | - Xin Li
- BGI-shenzhen, Shenzhen 518083, China
| | - Bin Rao
- BGI-shenzhen, Shenzhen 518083, China
| | - Yi Wang
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhen-Zhen Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China
| | - Gang Liu
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Li-Ping Zou
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Ji-Shui Zhang
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Chen Feng
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian-Wei Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Nan Hu
- Department of Rehabilitation Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiao-Qiao Chen
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Sheng-Yuan Yu
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Ke Li
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Mian-Wang He
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Xin-Guang Yu
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Jun Wang
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Sheng-Li Guo
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhi-Ye Chen
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Lei Zhang
- Department of Medical Information, Chinese PLA General Hospital, Beijing 100853, China
| | - Lin Ma
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
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29
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Jansen S, Hoischen A, Coe BP, Carvill GL, Van Esch H, Bosch DGM, Andersen UA, Baker C, Bauters M, Bernier RA, van Bon BW, Claahsen-van der Grinten HL, Gecz J, Gilissen C, Grillo L, Hackett A, Kleefstra T, Koolen D, Kvarnung M, Larsen MJ, Marcelis C, McKenzie F, Monin ML, Nava C, Schuurs-Hoeijmakers JH, Pfundt R, Steehouwer M, Stevens SJC, Stumpel CT, Vansenne F, Vinci M, van de Vorst M, Vries PD, Witherspoon K, Veltman JA, Brunner HG, Mefford HC, Romano C, Vissers LELM, Eichler EE, de Vries BBA. A genotype-first approach identifies an intellectual disability-overweight syndrome caused by PHIP haploinsufficiency. Eur J Hum Genet 2018; 26:54-63. [PMID: 29209020 PMCID: PMC5839042 DOI: 10.1038/s41431-017-0039-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/19/2017] [Accepted: 10/17/2017] [Indexed: 11/08/2022] Open
Abstract
Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetics, especially in the era of next generation sequencing. This combines the identification of individuals with mutations in the same gene and linking these to consistent (endo)phenotypes to establish disease causality. We have performed a MIP (molecular inversion probe)-based targeted re-sequencing study in 3,275 individuals with intellectual disability (ID) to facilitate a genotype-first approach for 24 genes previously implicated in ID.Combining our data with data from a publicly available database, we confirmed 11 of these 24 genes to be relevant for ID. Amongst these, PHIP was shown to have an enrichment of disruptive mutations in the individuals with ID (5 out of 3,275). Through international collaboration, we identified a total of 23 individuals with PHIP mutations and elucidated the associated phenotype. Remarkably, all 23 individuals had developmental delay/ID and the majority were overweight or obese. Other features comprised behavioral problems (hyperactivity, aggression, features of autism and/or mood disorder) and dysmorphisms (full eyebrows and/or synophrys, upturned nose, large ears and tapering fingers). Interestingly, PHIP encodes two protein-isoforms, PHIP/DCAF14 and NDRP, each involved in neurodevelopmental processes, including E3 ubiquitination and neuronal differentiation. Detailed genotype-phenotype analysis points towards haploinsufficiency of PHIP/DCAF14, and not NDRP, as the underlying cause of the phenotype.Thus, we demonstrated the use of large scale re-sequencing by MIPs, followed by reverse phenotyping, as a constructive approach to verify candidate disease genes and identify novel syndromes, highlighted by PHIP haploinsufficiency causing an ID-overweight syndrome.
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Affiliation(s)
- Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Gemma L Carvill
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Hilde Van Esch
- Centre for Human Genetics, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Daniëlle G M Bosch
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Currently working at the Department of Genetics, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Ulla A Andersen
- Department of Psychiatry, Odense, Institute of clinical research, University of Southern Denmark, J.B. Winsløwsvej 18, 5000, Odense C, Denmark
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Marijke Bauters
- Centre for Human Genetics, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle, WA, USA
| | - Bregje W van Bon
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Lucia Grillo
- Laboratory of Medical Genetics, Oasi Research Institute (IRCCS), Via Conte Ruggero, 73, Postal Code 94018, Troina, Italy
| | - Anna Hackett
- The GOLD service Hunter Genetics, University of Newcastle, Newcastle, NSW, Australia
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - David Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 77, Stockholm, Sweden
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Carlo Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Fiona McKenzie
- School of Paediatrics and Child Health, The University of Western Australia, Crawley, WA, Australia
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Marie-Lorraine Monin
- Department of Genetics, Pitié-Salpêtrière University Hospital, 47-83 Boulevard de l'Hôpital, 75651, Paris Cedex 13, France
| | - Caroline Nava
- Département de Génétique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, 75013, Paris, France
- INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, 75013, Paris, France
| | - Janneke H Schuurs-Hoeijmakers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX, Maastricht, The Netherlands
| | - Connie T Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX, Maastricht, The Netherlands
| | - Fleur Vansenne
- Department of Genetics, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - Mirella Vinci
- Laboratory of Medical Genetics, Oasi Research Institute (IRCCS), Via Conte Ruggero, 73, Postal Code 94018, Troina, Italy
| | - Maartje van de Vorst
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Petra de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Kali Witherspoon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, United Kingdom
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX, Maastricht, The Netherlands
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Corrado Romano
- Pediatrics and Medical Genetics, Oasi Research Institute (IRCCS), Via Conte Ruggero, 73, Postal Code 94018, Troina, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - 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
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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Chen L, Jensik PJ, Alaimo JT, Walkiewicz M, Berger S, Roeder E, Faqeih EA, Bernstein JA, Smith ACM, Mullegama SV, Saffen DW, Elsea SH. Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype. Hum Mutat 2017; 38:1774-1785. [PMID: 28940898 PMCID: PMC5679464 DOI: 10.1002/humu.23339] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 11/06/2022]
Abstract
Deformed epidermal autoregulatory factor-1 (DEAF1), a transcription factor essential for central nervous system and early embryonic development, has recently been implicated in a series of intellectual disability-related neurodevelopmental anomalies termed, in this study, as DEAF1-associated neurodevelopmental disorder (DAND). We identified six potentially deleterious DEAF1 variants in a cohort of individuals with DAND via clinical exome sequencing (CES) and in silico analysis, including two novel de novo variants: missense variant c.634G > A p.Gly212Ser in the SAND domain and deletion variant c.913_915del p.Lys305del in the NLS domain, as well as c.676C > T p.Arg226Trp, c.700T > A p.Trp234Arg, c.737G > C p.Arg246Thr, and c.791A > C p.Gln264Pro. Luciferase reporter, immunofluorescence staining, and electrophoretic mobility shift assays revealed that these variants had decreased transcriptional repression activity at the DEAF1 promoter and reduced affinity to consensus DEAF1 DNA binding sequences. In addition, c.913_915del p.K305del localized primarily to the cytoplasm and interacted with wild-type DEAF1. Our results demonstrate that variants located within the SAND or NLS domains significantly reduce DEAF1 transcriptional regulatory activities and are thus, likely to contribute to the underlying clinical concerns in DAND patients. These findings illustrate the importance of experimental characterization of variants with uncertain significance identified by CES to assess their potential clinical significance and possible use in diagnosis.
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Affiliation(s)
- Li Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Philip J. Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Joseph T. Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Seth Berger
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Departments of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
| | - Eissa A. Faqeih
- Department of Pediatrics Subspecialty, Children’s Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Ann C. M. Smith
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sureni V. Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - David W. Saffen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Institutes of Brain Science, Fudan University, Shanghai, China
- State Key Laboratory for Medical Neurobiology, Fudan University, Shanghai, China
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
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31
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Abstract
Smith-Magenis syndrome (SMS; OMIM #182290) is a complex genetic disorder characterized by distinctive physical features, developmental delay, cognitive impairment, and a typical behavioral phenotype. SMS is caused by interstitial 17p11.2 deletions, encompassing multiple genes and including the retinoic acid-induced 1 gene (RAI1), or by mutations in RAI1 itself. About 10% of all the SMS patients, in fact, carry an RAI1 mutation responsible for the phenotype. RAI1 (OMIM *607642) is a dosage-sensitive gene expressed in many tissues and highly conserved among species. Over the years, several studies have demonstrated that RAI1 (or its homologs in animal models) acts as a transcriptional factor implicated in embryonic neurodevelopment, neuronal differentiation, cell growth and cell cycle regulation, bone and skeletal development, lipid and glucose metabolisms, behavioral functions, and circadian activity. Patients with RAI1 pathogenic variants show some phenotypic differences when compared to those carrying the typical deletion. They usually have lower incidence of hypotonia and less cognitive impairment than those with 17p11.2 deletions but more frequently show the behavioral characteristics of the syndrome and overeating issues. These differences reflect the primary pathogenetic role of RAI1 without the pathogenetic contribution of the other genes included in the typical 17p11.2 deletion. The better comprehension of physiological roles of RAI1, its molecular co-workers and interactors, and its contribution in determining the typical SMS phenotype will certainly open a new path for therapeutic interventions.
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Affiliation(s)
- Mariateresa Falco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Sonia Amabile
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Fabio Acquaviva
- Department of Translational Medical Sciences (DISMET), Section of Pediatric Clinical Genetics, University of Naples “Federico II”, Naples, Italy
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32
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Mullegama SV, Jensik P, Li C, Dorrani N, Kantarci S, Blumberg B, Grody WW, Strom SP. Coupling clinical exome sequencing with functional characterization studies to diagnose a patient with familial Mediterranean fever and MED13L haploinsufficiency syndromes. Clin Case Rep 2017; 5:833-840. [PMID: 28588821 PMCID: PMC5458005 DOI: 10.1002/ccr3.904] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/28/2017] [Accepted: 02/11/2017] [Indexed: 02/06/2023] Open
Abstract
Clinicians should consider that clinical exome sequencing provides the unique potential to disentangle complex phenotypes into multiple genetic etiologies. Further, functional studies on variants of uncertain significance are necessary to arrive at an accurate diagnosis for the patient.
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Affiliation(s)
- Sureni V Mullegama
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Phillip Jensik
- Department of Physiology Southern Illinois University School of Medicine Carbondale Illinois
| | - Chen Li
- Department of Cellular and Genetic Medicine School of Basic Medical Sciences Fudan University Shanghai China
| | - Naghmeh Dorrani
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Sibel Kantarci
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Wayne W Grody
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Samuel P Strom
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
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33
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Huang WC, Ferris E, Cheng T, Hörndli CS, Gleason K, Tamminga C, Wagner JD, Boucher KM, Christian JL, Gregg C. Diverse Non-genetic, Allele-Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain. Neuron 2017; 93:1094-1109.e7. [PMID: 28238550 PMCID: PMC5774018 DOI: 10.1016/j.neuron.2017.01.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 11/27/2016] [Accepted: 01/30/2017] [Indexed: 01/19/2023]
Abstract
Interactions between genetic and epigenetic effects shape brain function, behavior, and the risk for mental illness. Random X inactivation and genomic imprinting are epigenetic allelic effects that are well known to influence genetic architecture and disease risk. Less is known about the nature, prevalence, and conservation of other potential epigenetic allelic effects in vivo in the mouse and primate brain. Here we devise genomics, in situ hybridization, and mouse genetics strategies to uncover diverse allelic effects in the brain that are not caused by imprinting or genetic variation. We found allelic effects that are developmental stage and cell type specific, that are prevalent in the neonatal brain, and that cause mosaics of monoallelic brain cells that differentially express wild-type and mutant alleles for heterozygous mutations. Finally, we show that diverse non-genetic allelic effects that impact mental illness risk genes exist in the macaque and human brain. Our findings have potential implications for mammalian brain genetics. VIDEO ABSTRACT.
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Affiliation(s)
- Wei-Chao Huang
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Elliott Ferris
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Tong Cheng
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Cornelia Stacher Hörndli
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kelly Gleason
- Department of Psychiatry, UT Southwestern, Dallas, TX 75390-9127, USA
| | - Carol Tamminga
- Department of Psychiatry, UT Southwestern, Dallas, TX 75390-9127, USA
| | - Janice D Wagner
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kenneth M Boucher
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Cancer Biostatistics Shared Resource, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jan L Christian
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Christopher Gregg
- Robertson Neuroscience Investigator, New York Stem Cell Foundation, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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34
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Exome analysis of Smith-Magenis-like syndrome cohort identifies de novo likely pathogenic variants. Hum Genet 2017; 136:409-420. [PMID: 28213671 DOI: 10.1007/s00439-017-1767-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/03/2017] [Indexed: 12/12/2022]
Abstract
Smith-Magenis syndrome (SMS), a neurodevelopmental disorder characterized by dysmorphic features, intellectual disability (ID), and sleep disturbances, results from a 17p11.2 microdeletion or a mutation in the RAI1 gene. We performed exome sequencing on 6 patients with SMS-like phenotypes but without chromosomal abnormalities or RAI1 variants. We identified pathogenic de novo variants in two cases, a nonsense variant in IQSEC2 and a missense variant in the SAND domain of DEAF1, and candidate de novo missense variants in an additional two cases. One candidate variant was located in an alpha helix of Necdin (NDN), phased to the paternally inherited allele. NDN is maternally imprinted within the 15q11.2 Prader-Willi Syndrome (PWS) region. This can help clarify NDN's role in the PWS phenotype. No definitive pathogenic gene variants were detected in the remaining SMS-like cases, but we report our findings for future comparison. This study provides information about the inheritance pattern and recurrence risk for patients with identified variants and demonstrates clinical and genetic overlap of neurodevelopmental disorders. Identification and characterization of ID-related genes that assist in development of common developmental pathways and/or gene-networks, may inform disease mechanism and treatment strategies.
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35
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Vulto-van Silfhout AT, Gilissen C, Goeman JJ, Jansen S, van Amen-Hellebrekers CJM, van Bon BWM, Koolen DA, Sistermans EA, Brunner HG, de Brouwer APM, de Vries BBA. Quantification of Phenotype Information Aids the Identification of Novel Disease Genes. Hum Mutat 2017; 38:594-599. [PMID: 28074630 DOI: 10.1002/humu.23176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/09/2017] [Indexed: 01/10/2023]
Abstract
Next-generation sequencing led to the identification of many potential novel disease genes. The presence of mutations in the same gene in multiple unrelated patients is, however, a priori insufficient to establish that these genes are truly involved in the respective disease. Here, we show how phenotype information can be incorporated within statistical approaches to provide additional evidence for the causality of mutations. We developed a broadly applicable statistical model that integrates gene-specific mutation rates, cohort size, mutation type, and phenotype frequency information to assess the chance of identifying de novo mutations affecting the same gene in multiple patients with shared phenotype features. We demonstrate our approach based on the frequency of phenotype features present in a unique cohort of 6,149 patients with intellectual disability. We show that our combined approach can decrease the number of patients required to identify novel disease genes, especially for patients with combinations of rare phenotypes. In conclusion, we show how integrating genotype-phenotype information can aid significantly in the interpretation of de novo mutations in potential novel disease genes.
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Affiliation(s)
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Jelle J Goeman
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Bregje W M van Bon
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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36
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Ganapathiraju MK, Karunakaran KB, Correa-Menéndez J. Predicted protein interactions of IFITMs may shed light on mechanisms of Zika virus-induced microcephaly and host invasion. F1000Res 2016; 5:1919. [PMID: 29333229 PMCID: PMC5747333 DOI: 10.12688/f1000research.9364.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2017] [Indexed: 06/16/2024] Open
Abstract
After the first reported case of Zika virus (ZIKV) in Brazil, in 2015, a significant increase in the reported cases of microcephaly was observed. Microcephaly is a neurological condition in which the infant's head is significantly smaller with complications in brain development. Recently, two small membrane-associated interferon-inducible transmembrane proteins (IFITM1 and IFITM3) have been shown to repress members of the flaviviridae family which includes ZIKV. However, the exact mechanisms leading to the inhibition of the virus are yet unknown. Here, we assembled an interactome of IFITM1 and IFITM3 with known protein-protein interactions (PPIs) collected from publicly available databases and novel PPIs predicted using the High-confidence Protein-Protein Interaction Prediction (HiPPIP) model. We analyzed the functional and pathway associations of the interacting proteins, and found that there are several immunity pathways (toll-like receptor signaling, cd28 signaling in T-helper cells, crosstalk between dendritic cells and natural killer cells), neuronal pathways (axonal guidance signaling, neural tube closure and actin cytoskeleton signaling) and developmental pathways (neural tube closure, embryonic skeletal system development) that are associated with these interactors. Our novel PPIs associate cilia dysfunction in ependymal cells to microcephaly, and may also shed light on potential targets of ZIKV for host invasion by immunosuppression and cytoskeletal rearrangements. These results could help direct future research in elucidating the mechanisms underlying host defense to ZIKV and other flaviviruses.
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Affiliation(s)
- Madhavi K. Ganapathiraju
- Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kalyani B. Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
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37
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Ganapathiraju MK, Karunakaran KB, Correa-Menéndez J. Predicted protein interactions of IFITMs may shed light on mechanisms of Zika virus-induced microcephaly and host invasion. F1000Res 2016; 5:1919. [PMID: 29333229 PMCID: PMC5747333 DOI: 10.12688/f1000research.9364.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2017] [Indexed: 12/22/2022] Open
Abstract
After the first reported case of Zika virus (ZIKV) in Brazil, in 2015, a significant increase in the reported cases of microcephaly was observed. Microcephaly is a neurological condition in which the infant’s head is significantly smaller with complications in brain development. Recently, two small membrane-associated interferon-inducible transmembrane proteins (IFITM1 and IFITM3) have been shown to repress members of the flaviviridae family which includes ZIKV. However, the exact mechanisms leading to the inhibition of the virus are yet unknown. Here, we assembled an interactome of IFITM1 and IFITM3 with known protein-protein interactions (PPIs) collected from publicly available databases and novel PPIs predicted using the High-confidence Protein-Protein Interaction Prediction (HiPPIP) model. We analyzed the functional and pathway associations of the interacting proteins, and found that there are several immunity pathways (toll-like receptor signaling, cd28 signaling in T-helper cells, crosstalk between dendritic cells and natural killer cells), neuronal pathways (axonal guidance signaling, neural tube closure and actin cytoskeleton signaling) and developmental pathways (neural tube closure, embryonic skeletal system development) that are associated with these interactors. Our novel PPIs associate cilia dysfunction in ependymal cells to microcephaly, and may also shed light on potential targets of ZIKV for host invasion by immunosuppression and cytoskeletal rearrangements. These results could help direct future research in elucidating the mechanisms underlying host defense to ZIKV and other flaviviruses.
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Affiliation(s)
- Madhavi K Ganapathiraju
- Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
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38
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Luckhart C, Philippe TJ, Le François B, Vahid-Ansari F, Geddes SD, Béïque JC, Lagace DC, Daigle M, Albert PR. Sex-dependent adaptive changes in serotonin-1A autoreceptor function and anxiety in Deaf1-deficient mice. Mol Brain 2016; 9:77. [PMID: 27488351 PMCID: PMC4973060 DOI: 10.1186/s13041-016-0254-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/23/2016] [Indexed: 12/20/2022] Open
Abstract
The C (-1019) G rs6295 promoter polymorphism of the serotonin-1A (5-HT1A) receptor gene is associated with major depression in several but not all studies, suggesting that compensatory mechanisms mediate resilience. The rs6295 risk allele prevents binding of the repressor Deaf1 increasing 5-HT1A receptor gene transcription, and the Deaf1-/- mouse model shows an increase in 5-HT1A autoreceptor expression. In this study, Deaf1-/- mice bred on a mixed C57BL6-BALB/c background were compared to wild-type littermates for 5-HT1A autoreceptor function and behavior in males and females. Despite a sustained increase in 5-HT1A autoreceptor binding levels, the amplitude of the 5-HT1A autoreceptor-mediated current in 5-HT neurons was unaltered in Deaf1-/- mice, suggesting compensatory changes in receptor function. Consistent with increased 5-HT1A autoreceptor function in vivo, hypothermia induced by the 5-HT1A agonist DPAT was augmented in early generation male but not female Deaf1-/- mice, but was reduced with succeeding generations. Loss of Deaf1 resulted in a mild anxiety phenotype that was sex-and test-dependent, with no change in depression-like behavior. Male Deaf1 knockout mice displayed anxiety-like behavior in the open field and light-dark tests, while female Deaf1-/- mice showed increased anxiety only in the elevated plus maze. These data show that altered 5-HT1A autoreceptor regulation in male Deaf1-/- mice can be compensated for by generational adaptation of receptor response that may help to normalize behavior. The sex dependence of Deaf1 function in mice is consistent with a greater role for 5-HT1A autoreceptors in sensitivity to depression in men.
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Affiliation(s)
- Christine Luckhart
- Ottawa Hospital Research Institute (Neuroscience), Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada
| | - Tristan J Philippe
- Ottawa Hospital Research Institute (Neuroscience), Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada
| | - Brice Le François
- Ottawa Hospital Research Institute (Neuroscience), Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada
| | - Faranak Vahid-Ansari
- Ottawa Hospital Research Institute (Neuroscience), Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada
| | - Sean D Geddes
- Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada
| | - Jean-Claude Béïque
- Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada
| | - Diane C Lagace
- Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada
| | - Mireille Daigle
- Ottawa Hospital Research Institute (Neuroscience), Ottawa, Canada
| | - Paul R Albert
- Ottawa Hospital Research Institute (Neuroscience), Ottawa, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H-8M5, Canada.
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39
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Mullins C, Fishell G, Tsien RW. Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops. Neuron 2016; 89:1131-1156. [PMID: 26985722 DOI: 10.1016/j.neuron.2016.02.017] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2016] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying autism spectrum disorders (ASDs) is a challenging goal. Here we review recent progress on several fronts, including genetics, proteomics, biochemistry, and electrophysiology, that raise motivation for forming a viable pathophysiological hypothesis. In place of a traditionally unidirectional progression, we put forward a framework that extends homeostatic hypotheses by explicitly emphasizing autoregulatory feedback loops and known synaptic biology. The regulated biological feature can be neuronal electrical activity, the collective strength of synapses onto a dendritic branch, the local concentration of a signaling molecule, or the relative strengths of synaptic excitation and inhibition. The sensor of the biological variable (which we have termed the homeostat) engages mechanisms that operate as negative feedback elements to keep the biological variable tightly confined. We categorize known ASD-associated gene products according to their roles in such feedback loops and provide detailed commentary for exemplar genes within each module.
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Affiliation(s)
- Caitlin Mullins
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Gord Fishell
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Richard W Tsien
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA.
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40
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Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. Genet Med 2016; 19:209-214. [DOI: 10.1038/gim.2016.88] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/16/2016] [Indexed: 12/14/2022] Open
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41
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D'haene E, Jacobs EZ, Volders PJ, De Meyer T, Menten B, Vergult S. Identification of long non-coding RNAs involved in neuronal development and intellectual disability. Sci Rep 2016; 6:28396. [PMID: 27319317 PMCID: PMC4913242 DOI: 10.1038/srep28396] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/01/2016] [Indexed: 12/15/2022] Open
Abstract
Recently, exome sequencing led to the identification of causal mutations in 16–31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies.
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Affiliation(s)
- Eva D'haene
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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42
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Casanova EL, Sharp JL, Chakraborty H, Sumi NS, Casanova MF. Genes with high penetrance for syndromic and non-syndromic autism typically function within the nucleus and regulate gene expression. Mol Autism 2016; 7:18. [PMID: 26985359 PMCID: PMC4793536 DOI: 10.1186/s13229-016-0082-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/01/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Intellectual disability (ID), autism, and epilepsy share frequent yet variable comorbidities with one another. In order to better understand potential genetic divergence underlying this variable risk, we studied genes responsible for monogenic IDs, grouped according to their autism and epilepsy comorbidities. METHODS Utilizing 465 different forms of ID with known molecular origins, we accessed available genetic databases in conjunction with gene ontology (GO) to determine whether the genetics underlying ID diverge according to its comorbidities with autism and epilepsy and if genes highly penetrant for autism or epilepsy share distinctive features that set them apart from genes that confer comparatively variable or no apparent risk. RESULTS The genetics of ID with autism are relatively enriched in terms associated with nervous system-specific processes and structural morphogenesis. In contrast, we find that ID with highly comorbid epilepsy (HCE) is modestly associated with lipid metabolic processes while ID without autism or epilepsy comorbidity (ID only) is enriched at the Golgi membrane. Highly comorbid autism (HCA) genes, on the other hand, are strongly enriched within the nucleus, are typically involved in regulation of gene expression, and, along with IDs with more variable autism, share strong ties with a core protein-protein interaction (PPI) network integral to basic patterning of the CNS. CONCLUSIONS According to GO terminology, autism-related gene products are integral to neural development. While it is difficult to draw firm conclusions regarding IDs unassociated with autism, it is clear that the majority of HCA genes are tightly linked with general dysregulation of gene expression, suggesting that disturbances to the chronology of neural maturation and patterning may be key in conferring susceptibility to autism spectrum conditions.
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Affiliation(s)
- Emily L. Casanova
- />Department of Biomedical Sciences, University of South Carolina, South Carolina, USA
- />Department of Pediatrics, Greenville Health System, Patewood Medical Campus, 200A Patewood Dr, Greenville, SC 29615 USA
| | - Julia L. Sharp
- />Department of Mathematical Sciences, Clemson University, Clemson, USA
| | - Hrishikesh Chakraborty
- />Department of Biostatistics and Epidemiology, University of South Carolina, South Carolina, USA
| | - Nahid Sultana Sumi
- />Department of Biostatistics and Epidemiology, University of South Carolina, South Carolina, USA
| | - Manuel F. Casanova
- />Department of Biomedical Sciences, University of South Carolina, South Carolina, USA
- />Department of Pediatrics, Greenville Health System, Patewood Medical Campus, 200A Patewood Dr, Greenville, SC 29615 USA
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43
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Abstract
The next-generation sequencing revolution has substantially increased our understanding of the mutated genes that underlie complex neurodevelopmental disease. Exome sequencing has enabled us to estimate the number of genes involved in the etiology of neurodevelopmental disease, whereas targeted sequencing approaches have provided the means for quick and cost-effective sequencing of thousands of patient samples to assess the significance of individual genes. By leveraging such technologies and clinical exome sequencing, a genotype-first approach has emerged in which patients with a common genotype are first identified and then clinically reassessed as a group. This approach has proven a powerful methodology for refining disease subtypes. We propose that the molecular characterization of these genetic subtypes has important implications for diagnostics and also for future drug development. Classifying patients into subgroups with a common genetic etiology and applying treatments tailored to the specific molecular defect they carry is likely to improve management of neurodevelopmental disease in the future.
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44
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Gund C, Powis Z, Alcaraz W, Desai S, Baranano K. Identification of a syndrome comprising microcephaly and intellectual disability but not white matter disease associated with a homozygous c.676C>T p.R226W DEAF1 mutation. Am J Med Genet A 2016; 170A:1330-2. [PMID: 26834045 DOI: 10.1002/ajmg.a.37580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 01/21/2016] [Indexed: 11/07/2022]
Abstract
We evaluated a 13-year-old East Pakistani male affected with microcephaly, apparent intellectual disability, hypotonia, and brisk reflexes without spasticity. His parents were first cousins. The patient also had a brother who was similarly affected and died at 10 years due to an accident. Previous SNP array testing showed a 1.63 Mb duplication at 16p13.11 of uncertain significance along with regions of homozygosity. Exome sequencing identified a known pathogenic homozygous alteration in DEAF1, c.676C>T (p.R226W), in this patient. The alteration had been reported in two individuals from a consanguineous Saudi Arabian family. Both individuals had microcephaly, intellectual disability, hypotonia, feeding difficulties, and poor growth. The patient reported here did not have evidence of white matter disease, as had been reported with prior patients. We conclude that this DEAF1 gene alteration caused this patient's symptoms and that white matter disease should not be considered a obligate feature of this syndrome.
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Affiliation(s)
| | - Zöe Powis
- Ambry Genetics, 15 Argonaut, Aliso Viejo, California
| | - Wendy Alcaraz
- Ambry Genetics, 15 Argonaut, Aliso Viejo, California
| | - Sonal Desai
- Kennedy Krieger Institute, Baltimore, Maryland
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45
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Li J, Cai T, Jiang Y, Chen H, He X, Chen C, Li X, Shao Q, Ran X, Li Z, Xia K, Liu C, Sun ZS, Wu J. Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database. Mol Psychiatry 2016; 21:290-7. [PMID: 25849321 PMCID: PMC4837654 DOI: 10.1038/mp.2015.40] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 12/16/2022]
Abstract
Currently, many studies on neuropsychiatric disorders have utilized massive trio-based whole-exome sequencing (WES) and whole-genome sequencing (WGS) to identify numerous de novo mutations (DNMs). Here, we retrieved 17,104 DNMs from 3555 trios across four neuropsychiatric disorders: autism spectrum disorder, epileptic encephalopathy, intellectual disability and schizophrenia, in addition to unaffected siblings (control), from 36 studies by WES/WGS. After eliminating non-exonic variants, we focused on 3334 exonic DNMs for evaluation of their association with these diseases. Our results revealed a higher prevalence of DNMs in the probands of all four disorders compared with the one in the controls (P<1.3 × 10(-7)). The elevated DNM frequency is dominated by loss-of-function/deleterious single-nucleotide variants and frameshift indels (that is, extreme mutations, P<4.5 × 10(-5)). With extensive annotation of these 'extreme' mutations, we prioritized 764 candidate genes in these four disorders. A combined analysis of Gene Ontology, microRNA targets and transcription factor targets revealed shared biological process and non-coding regulatory elements of candidate genes in the pathology of neuropsychiatric disorders. In addition, weighted gene co-expression network analysis of human laminar-specific neocortical expression data showed that candidate genes are convergent on eight shared modules with specific layer enrichment and biological process features. Furthermore, we identified that 53 candidate genes are associated with more than one disorder (P<0.000001), suggesting a possibly shared genetic etiology underlying these disorders. Particularly, DNMs of the SCN2A gene are frequently occurred across all four disorders. Finally, we constructed a freely available NPdenovo database, which provides a comprehensive catalog of the DNMs identified in neuropsychiatric disorders.
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Affiliation(s)
- Jinchen Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China,State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Tao Cai
- Experimental Medicine Section, NIDCR/NIH, Bethesda, Maryland, USA
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Huiqian Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, USA
| | - Chao Chen
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China,Department of Psychiatry, University of Illinois at Chicago, Chicago, USA
| | - Xianfeng Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Qianzhi Shao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xia Ran
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Chunyu Liu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China,Department of Psychiatry, University of Illinois at Chicago, Chicago, USA,Correspondence should be addressed to: Jinyu Wu (), Zhong Sheng Sun (), or Chunyu Liu ()
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China,Correspondence should be addressed to: Jinyu Wu (), Zhong Sheng Sun (), or Chunyu Liu ()
| | - Jinyu Wu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China,Correspondence should be addressed to: Jinyu Wu (), Zhong Sheng Sun (), or Chunyu Liu ()
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46
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De novo loss-of-function mutations in WAC cause a recognizable intellectual disability syndrome and learning deficits in Drosophila. Eur J Hum Genet 2016; 24:1145-53. [PMID: 26757981 DOI: 10.1038/ejhg.2015.282] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 12/04/2015] [Accepted: 12/16/2015] [Indexed: 01/15/2023] Open
Abstract
Recently WAC was reported as a candidate gene for intellectual disability (ID) based on the identification of a de novo mutation in an individual with severe ID. WAC regulates transcription-coupled histone H2B ubiquitination and has previously been implicated in the 10p12p11 contiguous gene deletion syndrome. In this study, we report on 10 individuals with de novo WAC mutations which we identified through routine (diagnostic) exome sequencing and targeted resequencing of WAC in 2326 individuals with unexplained ID. All but one mutation was expected to lead to a loss-of-function of WAC. Clinical evaluation of all individuals revealed phenotypic overlap for mild ID, hypotonia, behavioral problems and distinctive facial dysmorphisms, including a square-shaped face, deep set eyes, long palpebral fissures, and a broad mouth and chin. These clinical features were also previously reported in individuals with 10p12p11 microdeletion syndrome. To investigate the role of WAC in ID, we studied the importance of the Drosophila WAC orthologue (CG8949) in habituation, a non-associative learning paradigm. Neuronal knockdown of Drosophila CG8949 resulted in impaired learning, suggesting that WAC is required in neurons for normal cognitive performance. In conclusion, we defined a clinically recognizable ID syndrome, caused by de novo loss-of-function mutations in WAC. Independent functional evidence in Drosophila further supported the role of WAC in ID. On the basis of our data WAC can be added to the list of ID genes with a role in transcription regulation through histone modification.
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47
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Evidence for genetic regulation of mRNA expression of the dosage-sensitive gene retinoic acid induced-1 (RAI1) in human brain. Sci Rep 2016; 6:19010. [PMID: 26743651 PMCID: PMC4705554 DOI: 10.1038/srep19010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/02/2015] [Indexed: 12/12/2022] Open
Abstract
RAI1 (retinoic acid induced-1) is a dosage-sensitive gene that causes Smith-Magenis syndrome (SMS) when mutated or deleted and Potocki-Lupski Syndrome (PTLS) when duplicated, with psychiatric features commonly observed in both syndromes. How common genetic variants regulate this gene, however, is unknown. In this study, we found that RAI1 mRNA expression in Chinese prefrontal and temporal cortex correlate with genotypes of common single nucleotide polymorphisms (SNPs) located in the RAI1 5′-upstream region. Using genotype imputation, “R2-Δ2” analysis, and data from the RegulomeDB database, we identified SNPs rs4925102 and rs9907986 as possible regulatory variants, accounting for approximately 30–40% of the variance in RAI1 mRNA expression in both brain regions. Specifically, rs4925102 and rs9907986 are predicted to disrupt the binding of retinoic acid RXR-RAR receptors and the transcription factor DEAF1 (Deformed epidermal autoregulatory factor-1), respectively. Consistent with these predictions, we observed binding of RXRα and RARα to the predicted RAI1 target in chromatin immunoprecipitation assays. Retinoic acid is crucial for early development of the central neural system, and DEAF1 is associated with intellectual disability. The observation that a significant portion of RAI1 mRNA expression is genetically controlled raises the possibility that common RAI1 5′-region regulatory variants contribute more generally to psychiatric disorders.
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48
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Kochinke K, Zweier C, Nijhof B, Fenckova M, Cizek P, Honti F, Keerthikumar S, Oortveld M, Kleefstra T, Kramer J, Webber C, Huynen M, Schenck A. Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. Am J Hum Genet 2016; 98:149-64. [PMID: 26748517 DOI: 10.1016/j.ajhg.2015.11.024] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022] Open
Abstract
Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders.
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49
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Carvill GL, Mefford HC. Next-Generation Sequencing in Intellectual Disability. J Pediatr Genet 2015; 4:128-35. [PMID: 27617123 DOI: 10.1055/s-0035-1564439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 12/19/2022]
Abstract
Next-generation sequencing technologies have revolutionized gene discovery in patients with intellectual disability (ID) and led to an unprecedented expansion in the number of genes implicated in this disorder. We discuss the strategies that have been used to identify these novel genes for both syndromic and nonsyndromic ID and highlight the phenotypic and genetic heterogeneity that underpin this condition. Finally, we discuss the future of defining the genetic etiology of ID, including the role of whole-genome sequencing, mosaicism, and the importance of diagnostic testing in ID.
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Affiliation(s)
- Gemma L Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, United States
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, United States
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50
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Analysis of the effects of depression associated polymorphisms on the activity of the BICC1 promoter in amygdala neurones. THE PHARMACOGENOMICS JOURNAL 2015; 16:366-74. [PMID: 26440730 PMCID: PMC4973013 DOI: 10.1038/tpj.2015.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/01/2015] [Accepted: 07/14/2015] [Indexed: 12/11/2022]
Abstract
The Bicaudal C Homolog 1 (BICC1) gene, which encodes an RNA binding protein, has been identified by genome wide association studies (GWAS) as a candidate gene associated with major depressive disorder (MDD). We explored the hypothesis that MDD associated single-nucleotide polymorphisms (SNPs) affected the ability of cis-regulatory elements within intron 3 of the BICC1 gene to modulate the activity of the BICC1 promoter region. We initially established that the BICC1 promoter drove BICC1 mRNA expression in amygdala, hippocampus and hypothalamus. Intriguingly, we provide evidence that MDD associated polymorphisms alter the ability of the BICC1 promoter to respond to PKA signalling within amygdala neurones. Considering the known role of amygdala PKA pathways in fear learning and mood these observations suggest a possible mechanism through which allelic changes in the regulation of the BICC1 gene in amygdala neurones may contribute to mood disorders. Our findings also suggest a novel direction for the identification of novel drug targets and the design of future personalised therapeutics.
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