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Münzker L, Kimani SW, Fowkes MM, Dong A, Zheng H, Li Y, Dasovich M, Zak KM, Leung AKL, Elkins JM, Kessler D, Arrowsmith CH, Halabelian L, Böttcher J. A ligand discovery toolbox for the WWE domain family of human E3 ligases. Commun Biol 2024; 7:901. [PMID: 39048679 PMCID: PMC11269756 DOI: 10.1038/s42003-024-06584-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/14/2024] [Indexed: 07/27/2024] Open
Abstract
The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15N-NMR-based binding affinity assays and 19F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso-ADP-ribose (iso-ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.
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Affiliation(s)
- Lena Münzker
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Serah W Kimani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Milan M Fowkes
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Hong Zheng
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | | | | | | | - Jonathan M Elkins
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.
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Mattar CN, Chew WL, Lai PS. Embryo and fetal gene editing: Technical challenges and progress toward clinical applications. Mol Ther Methods Clin Dev 2024; 32:101229. [PMID: 38533521 PMCID: PMC10963250 DOI: 10.1016/j.omtm.2024.101229] [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] [Indexed: 03/28/2024]
Abstract
Gene modification therapies (GMTs) are slowly but steadily making progress toward clinical application. As the majority of rare diseases have an identified genetic cause, and as rare diseases collectively affect 5% of the global population, it is increasingly important to devise gene correction strategies to address the root causes of the most devastating of these diseases and to provide access to these novel therapies to the most affected populations. The main barriers to providing greater access to GMTs continue to be the prohibitive cost of developing these novel drugs at clinically relevant doses, subtherapeutic effects, and toxicity related to the specific agents or high doses required. In vivo strategy and treating younger patients at an earlier course of their disease could lower these barriers. Although currently regarded as niche specialties, prenatal and preconception GMTs offer a robust solution to some of these barriers. Indeed, treating either the fetus or embryo benefits from economy of scale, targeting pre-pathological tissues in the fetus prior to full pathogenesis, or increasing the likelihood of complete tissue targeting by correcting pluripotent embryonic cells. Here, we review advances in embryo and fetal GMTs and discuss requirements for clinical application.
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Affiliation(s)
- Citra N.Z. Mattar
- Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
- Department of Obstetrics and Gynaecology, National University Health System, Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, 60 Biopolis St, Singapore, Singapore 138672
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
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Kouhashi M, Yukawa K, Yano N, Hagemeijer MC, Hirata S, Kambe D, Yokoyama A, Yoshida A, Kora K, de Ronde CJ, Vrieswijk S, van der Meijden E, Yoshida T, Yamashita H. A 37-Year-Old Man With Intellectual Disability Discovered to Have Aspartylglucosaminuria: Implications for the Diagnosis of Genetic Causes. Neurol Genet 2024; 10:e200161. [PMID: 38831911 PMCID: PMC11145746 DOI: 10.1212/nxg.0000000000200161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/08/2024] [Indexed: 06/05/2024]
Abstract
Objectives The causes of intellectual disability (ID) are varied, with as many as 1,400 causative genes. We attempted to identify the causative gene in a patient with long-standing undiagnosed ID. Methods Although this was an isolated case with no family history, we searched for the causative gene using trio-based whole-exome sequencing (trio-WES), because severe ID is often caused by genetic variations, and inherited metabolic disorders (IMDs) are assumed to be the cause when regression and epilepsy occur. Results We identified homozygous donor splice-site variants in the AGA gene (aspartylglucosaminidase; NM_000027.4) Chr4(GRCh38):g. 177436275C>A, c.698+1G>T. This gene is implicated in aspartylglucosaminuria (AGU; OMIM #208400) and originated from both of the patient's parents. We confirmed the pathogenicity of the variant by detecting the splicing defect in cDNA from the patient's blood and accumulation of aberrant metabolites in the patient's urine. Discussion We discuss how to more readily achieve an accurate diagnosis for patients with undiagnosed intellectual disabilities. Medical practitioners' awareness of the characteristics of the disease leading to clinical suspicion in patients with matching presentations, and the performance of newborn screening when possible, is important for the diagnosis of ID. In addition, the characteristic symptoms and course of the disease give rise to suspicion of IMDs. Given our results, we consider trio-WES to be a powerful method for identifying the causative genes in cases of ID with genetic causes.
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Affiliation(s)
- Mutsuo Kouhashi
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Kayoko Yukawa
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Naoko Yano
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Marne C Hagemeijer
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Shinya Hirata
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Daisuke Kambe
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Atsushi Yokoyama
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Akira Yoshida
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Kengo Kora
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Corline J de Ronde
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Sandrien Vrieswijk
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Eric van der Meijden
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Takeshi Yoshida
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
| | - Hirofumi Yamashita
- From the Department of Neurology (M.K., K.Y., S.H., D.K., H.Y.), Japanese Red Cross Wakayama Medical Center; Department of Neurology (M.K., S.H.); Department of Pediatrics (N.Y., A. Yokoyama, K.K., T.Y.), Graduate School of Medicine, Kyoto University, Japan; Center for Lysosomal and Metabolic Diseases (M.C.H., C.J.R., S.V., E.M.), Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Neurology (D.K.), Kyoto Kizugawa Hospital; and Department of Pediatrics (A. Yokoyama, A. Yoshida), Japanese Red Cross Wakayama Medical Center, Japan
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Lee IO, Wolstencroft J, Housby H, van den Bree MBM, Chawner SJRA, Hall J, Skuse DH. The inequity of education, health and care plan provision for children and young people with intellectual and developmental disabilities. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2024. [PMID: 38777582 DOI: 10.1111/jir.13139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Children and young people (CYP) with intellectual and developmental disabilities (IDDs) have significant additional educational needs compared with the general population. In England, the government has established a system of education, health and care plans (EHCPs) to support children with special educational needs and disabilities, but disparities exist between the degree of need and the availability of support. We conducted a prospective UK national cohort study (IMAGINE) of children with rare pathogenic genomic variants, all of which are associated with IDD, to investigate associated neuropsychiatric risk. Subsequently, we obtained information from the UK's National Pupil Database on their educational progress through the state school system. We aimed to identify whether they had received EHCP provision and whether that support was associated with their family's socioeconomic status, region of domicile, ethnicity, sex, primary special educational needs (SEN) type, academic performance and mental health well-being. METHODS We recruited 2738 CYP from England into the IMAGINE study between 2014 and 2019. The educational histories of the participants (6-28 years old, mean ± standard deviation = 14 ± 4 years, 56% male) were obtained from the Department for Education's National Pupil Database in 2021. Educational data included attainment scores from the Early Year Foundation Stage (<5 years) to key stage 4 (15-16 years). Each family was assigned an index of multiple deprivation (IMD) score based on their home address postcode. Parents or carers rated their child's emotional and behavioural adjustment on the Strengths and Difficulties Questionnaire (SDQ). The association between receiving an EHCP and the child's IMD score, eligibility for free school meals, English region of domicile, ethnicity, sex, primary SEN type, academic attainment and SDQ score was investigated. RESULTS In this cohort, 78% of participants had received an EHCP. CYP living in the most deprived IMD deciles were substantially less likely to receive EHCP support than those in the least deprived decile, irrespective of their degree of intellectual developmental disability, academic performance or associated mental health problems. There were no sex differences. Children of Asian heritage were more likely to have been granted an EHCP than White children from equivalent IMD deciles. There were striking regional disparities. Participants living in London were significantly more likely to have been awarded an EHCP than participants living anywhere else in England, regardless of their IMD decile; those in the least deprived decile had almost 100% EHCP provision. CONCLUSIONS This study found evidence for nationwide regional inconsistencies in the awarding of EHCP to CYP with significant intellectual impairments of known genetic aetiology. Disparities in funds available to education authorities could be a contributory factor. EHCP support was potentially influenced by how strongly a parent advocates for their child.
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Affiliation(s)
- I O Lee
- Behavioural and Brain Sciences Unit, Population Policy and Practice Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - J Wolstencroft
- Behavioural and Brain Sciences Unit, Population Policy and Practice Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - H Housby
- Behavioural and Brain Sciences Unit, Population Policy and Practice Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - M B M van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - S J R A Chawner
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - J Hall
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - D H Skuse
- Behavioural and Brain Sciences Unit, Population Policy and Practice Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
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Garg P, Jamal F, Srivastava P. RNA-Seq data analysis reveals novel nonsense mutations in the NPR3 gene leading to the progression of intellectual disability disorder. Heliyon 2024; 10:e30755. [PMID: 38765165 PMCID: PMC11101858 DOI: 10.1016/j.heliyon.2024.e30755] [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: 11/07/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Intellectual disability (ID) is a progressive disorder that affects around 1-3% of the world's population. The heterogeneity of intellectual disability makes it difficult to diagnose as a complete disease. Genetic factors and major mutations play a noticeable role in the development and progression of ID. There is a high need to explore novel variants that may lead to new insights into the progressive aspects of ID. In the current course of study, 31 samples of ID from different studies available on GEO (GSE77742, GSE74263, GSE90682, GSE98476, GSE108887, GSE145710, and PRJEB21964) datasets were taken for the study. These datasets were analyzed for differential gene expression and single nucleotide polymorphism (SNPs). The SNPs of high impact were compared with the differentially expressed genes. Comparison leads to the identification of the priority gene ie NPR3 gene. The identified priority gene further was evaluated for the effect of the mutation using a Mutation Taster. Structure comparison analysis of the wild and mutated proteins of the NPR3 gene was further carried out by UCSF Chimera. Structural analysis reveals the anomalies in protein expression affecting the regulations of the NPR3 gene. These findings identified a novel nonsense mutation (E222*) in the downregulated NPR3 gene that leads to anomalies in the regulation of its protein expression. This missense mutation reveals a major role in causing ID. Our study concludes that the decrease in the expression of the NPR3 gene causes delayed sensory, motor, and physiological functions of the human brain leading to neurodevelopmental delay that causes ID.
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Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, UP, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
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Xiao R, Xu P, Liang XL, Zou Z, Zhong JG, Xiang MQ, Hou XH. Effects of the special olympics unified sports soccer training program on executive function in adolescents with intellectual disabilities. J Exerc Sci Fit 2024; 22:103-110. [PMID: 38268818 PMCID: PMC10806089 DOI: 10.1016/j.jesf.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Affiliation(s)
- Rang Xiao
- Guangzhou Sport University, Guangzhou, China
| | - Ping Xu
- Department of Educational Psychology, School of Leisure Sports and Management, Guangzhou Sport University, Guangzhou, China
| | - Xue-Lian Liang
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
| | - Zhi Zou
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
| | - Jiu-Gen Zhong
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
- Shanghai University of Sport, Shanghai, China
| | - Ming-Qiang Xiang
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
| | - Xiao-Hui Hou
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
- Shanghai University of Sport, Shanghai, China
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7
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Wheeler AC. The Multiple Odysseys in Research and Clinical Care for Neurogenetic Conditions. AMERICAN JOURNAL ON INTELLECTUAL AND DEVELOPMENTAL DISABILITIES 2024; 129:110-115. [PMID: 38411239 DOI: 10.1352/1944-7558-129.2.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Neurogenetic conditions (NGC; e.g., fragile X, Angelman, Prader-Willi syndromes) represent the cause for intellectual or developmental disabilities in up to 60% of cases. With expanded diagnostic options and an increasing focus on the development of gene therapies comes the potential of improved quality of life for individuals with NGCs and their families. However, these emerging initiatives also bring new challenges and considerations for NGC researchers and clinicians, including considerations for supporting caregivers and assuring outcome measures for clinical trials adequately reflect the lived experiences of people with NGCs. This paper summarizes the advances and current and future challenges of research and clinical service provision for people with NGCs and their caregivers.
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Affiliation(s)
- Anne C Wheeler
- Anne C. Wheeler, Genomics, Ethics, and Translational Research Program, RTI International
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8
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Martinez D, Jiang E, Zhou Z. Overcoming genetic and cellular complexity to study the pathophysiology of X-linked intellectual disabilities. J Neurodev Disord 2024; 16:5. [PMID: 38424476 PMCID: PMC10902969 DOI: 10.1186/s11689-024-09517-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
X-linked genetic causes of intellectual disability (ID) account for a substantial proportion of cases and remain poorly understood, in part due to the heterogeneous expression of X-linked genes in females. This is because most genes on the X chromosome are subject to random X chromosome inactivation (XCI) during early embryonic development, which results in a mosaic pattern of gene expression for a given X-linked mutant allele. This mosaic expression produces substantial complexity, especially when attempting to study the already complicated neural circuits that underly behavior, thus impeding the understanding of disease-related pathophysiology and the development of therapeutics. Here, we review a few selected X-linked forms of ID that predominantly affect heterozygous females and the current obstacles for developing effective therapies for such disorders. We also propose a genetic strategy to overcome the complexity presented by mosaicism in heterozygous females and highlight specific tools for studying synaptic and circuit mechanisms, many of which could be shared across multiple forms of intellectual disability.
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Affiliation(s)
- Dayne Martinez
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Evan Jiang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Intellectual and Developmental Disabilities Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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Kinoshita S, Kojima K, Ohnishi E, Takayama Y, Kikuchi H, Takada S, Nakabayashi K, Kawai T, Hata K. Loss of NSD2 causes dysregulation of synaptic genes and altered H3K36 dimethylation in mice. Front Genet 2024; 15:1308234. [PMID: 38419783 PMCID: PMC10899350 DOI: 10.3389/fgene.2024.1308234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Background: Epigenetic disruptions have been implicated in neurodevelopmental disorders. NSD2 is associated with developmental delay/intellectual disability; however, its role in brain development and function remains unclear. Methods: We performed transcriptomic and epigenetic analyses using Nsd2 knockout mice to better understand the role of NSD2 in the brain. Results and discussion: Transcriptomic analysis revealed that the loss of NSD2 caused dysregulation of genes related to synaptic transmission and formation. By analyzing changes in H3 lysine 36 dimethylation (H3K36me2), NSD2-mediated H3K36me2 mainly marked quiescent state regions and the redistribution of H3K36me2 occurred at transcribed genes and enhancers. By integrating transcriptomic and epigenetic data, we observed that H3K36me2 changes in a subset of dysregulated genes related to synaptic transmission and formation. These results suggest that NSD2 is involved in the regulation of genes important for neural function through H3K36me2. Our findings provide insights into the role of NSD2 and improve our understanding of epigenetic regulation in the brain.
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Affiliation(s)
- Shiori Kinoshita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of NCCHD Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuaki Kojima
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Eriko Ohnishi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuka Takayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiroki Kikuchi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
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10
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Garg P, Jamal F, Srivastava P. Comparative Transcriptomics Data Profiling Reveals E2F Targets as an Important Biological Pathway Overexpressed in Intellectual Disability Disorder. Bioinform Biol Insights 2024; 18:11779322231224665. [PMID: 38357659 PMCID: PMC10865946 DOI: 10.1177/11779322231224665] [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: 04/04/2023] [Accepted: 12/15/2023] [Indexed: 02/16/2024] Open
Abstract
Intellectual disability (ID) is an early childhood neurodevelopmental disorder that is characterized by impaired intellectual functioning and adaptive behavior. It is one of the major concerns in the field of neurodevelopmental disorders across the globe. Diversified approaches have been put forward to overcome this problem. Among all these approaches, high throughput transcriptomic analysis has taken an important dimension. The identification of genes causing ID rapidly increased over the past 3 to 5 years owing to the use of sophisticated high throughput sequencing platforms. Early monitoring and preventions are much important for such disorder as their progression occurs during fetal development. This study is an attempt to identify differentially expressed genes (DEGs) and upregulated biological processes involved in development of ID patients through comparative analysis of available transcriptomics data. A total of 7 transcriptomic studies were retrieved from National Center for Biotechnology Information (NCBI) and were subjected to quality check and trimming prior to alignment. The normalization and differential expression analysis were carried out using DESeq2 and EdgeR packages of Rstudio to identify DEGs in ID. In progression of the study, functional enrichment analysis of the results obtained from both DESeq2 and EdgeR was done using gene set enrichment analysis (GSEA) tool to identify major upregulated biological processes involved in ID. Our findings concluded that monitoring the level of E2F targets, estrogen, and genes related to oxidative phosphorylation, DNA repair, and glycolysis during the developmental stage of an individual can help in the early detection of ID disorder.
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Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr Rammanohar Lohia Avadh University, Ayodhya, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
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11
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Browne EG, King JR, Surtees ADR. Sleep in people with and without intellectual disabilities: a systematic review and meta-analysis. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2024; 68:1-22. [PMID: 37857569 DOI: 10.1111/jir.13093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Sleep problems are regularly reported in people with intellectual disabilities. Recent years have seen a substantial increase in studies comparing sleep in people with intellectual disabilities to control participants, with an increase in the use of validated, objective measures. Emerging patterns of differences in sleep time and sleep quality warrant pooled investigation. METHODS A systematic search was conducted across three databases (Ovid Embase, PsycInfo and Medline) and returned all papers comparing sleep in people with intellectual disabilities to a control group, published since the last meta-analysis on the topic. A quality framework was employed to rate the risk of bias across studies. Separate meta-analyses of sleep duration and sleep quality were conducted. Subgrouping compared findings for those studies with participants with genetic syndromes or neurodevelopmental conditions and those with heterogeneous intellectual disability. RESULTS Thirteen new papers were identified and combined with those from the previous meta-analysis to provide 34 papers in total. Quality of studies was generally rated highly, though sampling provided risk of bias and adaptive functioning was rarely measured. People with intellectual disability associated with genetic syndromes or neurodevelopmental conditions sleep for shorter time periods (standardised mean difference = .26) and experience worse sleep quality (standardised mean difference = .68) than their peers. People with intellectual disability of heterogeneous origin show no difference in sleep time but have poorer sleep quality. There was some evidence that age moderated these effects. CONCLUSIONS People with intellectual disability have poorer sleep than those without. Subtle patterns suggest that aetiology of intellectual disability moderates the topography of these difficulties, with further work needed to differentiate common and distinct mechanisms across groups.
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Affiliation(s)
- E G Browne
- School of Psychology, University of Birmingham, Birmingham, UK
| | - J R King
- School of Psychology, University of Birmingham, Birmingham, UK
| | - A D R Surtees
- School of Psychology, University of Birmingham, Birmingham, UK
- Division of Mental Health, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
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12
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Racine C, Denommé-Pichon AS, Engel C, Tran Mau-Them F, Bruel AL, Vitobello A, Safraou H, Sorlin A, Nambot S, Delanne J, Garde A, Colin E, Moutton S, Thevenon J, Jean-Marçais N, Willems M, Geneviève D, Pinson L, Perrin L, Laffargue F, Lespinasse J, Lacaze E, Molin A, Gerard M, Lambert L, Benigni C, Patat O, Bourgeois V, Poe C, Chevarin M, Couturier V, Garret P, Philippe C, Duffourd Y, Faivre L, Thauvin-Robinet C. Multiple molecular diagnoses in the field of intellectual disability and congenital anomalies: 3.5% of all positive cases. J Med Genet 2023; 61:36-46. [PMID: 37586840 DOI: 10.1136/jmg-2023-109170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE Wide access to clinical exome/genome sequencing (ES/GS) enables the identification of multiple molecular diagnoses (MMDs), being a long-standing but underestimated concept, defined by two or more causal loci implicated in the phenotype of an individual with a rare disease. Only few series report MMDs rates (1.8% to 7.1%). This study highlights the increasing role of MMDs in a large cohort of individuals addressed for congenital anomalies/intellectual disability (CA/ID). METHODS From 2014 to 2021, our diagnostic laboratory rendered 880/2658 positive ES diagnoses for CA/ID aetiology. Exhaustive search on MMDs from ES data was performed prospectively (January 2019 to December 2021) and retrospectively (March 2014 to December 2018). RESULTS MMDs were identified in 31/880 individuals (3.5%), responsible for distinct (9/31) or overlapping (22/31) phenotypes, and potential MMDs in 39/880 additional individuals (4.4%). CONCLUSION MMDs are frequent in CA/ID and remain a strong challenge. Reanalysis of positive ES data appears essential when phenotypes are partially explained by the initial diagnosis or atypically enriched overtime. Up-to-date clinical data, clinical expertise from the referring physician, strong interactions between clinicians and biologists, and increasing gene discoveries and improved ES bioinformatics tools appear all the more fundamental to enhance chances of identifying MMDs. It is essential to provide appropriate patient care and genetic counselling.
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Affiliation(s)
- Caroline Racine
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Camille Engel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Frederic Tran Mau-Them
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Antonio Vitobello
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Hana Safraou
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Arthur Sorlin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Julian Delanne
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Aurore Garde
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Estelle Colin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sébastien Moutton
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Marjolaine Willems
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - David Geneviève
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
- INSERM U1183, Université de Montpellier, Montpellier, France
| | - Lucile Pinson
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Laurence Perrin
- Genetic Department, Robert-Debré Hospital Department of Genetics, Paris, France
| | - Fanny Laffargue
- Service de Génétique médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - James Lespinasse
- Unité de Génétique médicale, Centre Hospitalier Métropole Savoie, Chambery, France
| | - Elodie Lacaze
- Department of Medical Genetics, Hospital Group Le Havre, Le Havre, France
| | - Arnaud Molin
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | - Marion Gerard
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | | | | | - Olivier Patat
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, France
| | - Valentin Bourgeois
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Charlotte Poe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Martin Chevarin
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Victor Couturier
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Philippine Garret
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christophe Philippe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Yannis Duffourd
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
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Hussain SI, Muhammad N, Shah SUD, Fardous F, Khan SA, Khan N, Rehman AU, Siddique M, Wasan SA, Niaz R, Ullah H, Khan N, Muhammad N, Mirza MU, Wasif N, Khan S. Structural and functional implications of SLC13A3 and SLC9A6 mutations: an in silico approach to understanding intellectual disability. BMC Neurol 2023; 23:353. [PMID: 37794328 PMCID: PMC10548666 DOI: 10.1186/s12883-023-03397-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Intellectual disability (ID) is a condition that varies widely in both its clinical presentation and its genetic underpinnings. It significantly impacts patients' learning capacities and lowers their IQ below 70. The solute carrier (SLC) family is the most abundant class of transmembrane transporters and is responsible for the translocation of various substances across cell membranes, including nutrients, ions, metabolites, and medicines. The SLC13A3 gene encodes a plasma membrane-localized Na+/dicarboxylate cotransporter 3 (NaDC3) primarily expressed in the kidney, astrocytes, and the choroid plexus. In addition to three Na + ions, it brings four to six carbon dicarboxylates into the cytosol. Recently, it was discovered that patients with acute reversible leukoencephalopathy and a-ketoglutarate accumulation (ARLIAK) carry pathogenic mutations in the SLC13A3 gene, and the X-linked neurodevelopmental condition Christianson Syndrome is caused by mutations in the SLC9A6 gene, which encodes the recycling endosomal alkali cation/proton exchanger NHE6, also called sodium-hydrogen exchanger-6. As a result, there are severe impairments in the patient's mental capacity, physical skills, and adaptive behavior. METHODS AND RESULTS Two Pakistani families (A and B) with autosomal recessive and X-linked intellectual disorders were clinically evaluated, and two novel disease-causing variants in the SLC13A3 gene (NM 022829.5) and the SLC9A6 gene (NM 001042537.2) were identified using whole exome sequencing. Family-A segregated a novel homozygous missense variant (c.1478 C > T; p. Pro493Leu) in the exon-11 of the SLC13A3 gene. At the same time, family-B segregated a novel missense variant (c.1342G > A; p.Gly448Arg) in the exon-10 of the SLC9A6 gene. By integrating computational approaches, our findings provided insights into the molecular mechanisms underlying the development of ID in individuals with SLC13A3 and SLC9A6 mutations. CONCLUSION We have utilized in-silico tools in the current study to examine the deleterious effects of the identified variants, which carry the potential to understand the genotype-phenotype relationships in neurodevelopmental disorders.
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Affiliation(s)
- Syeda Iqra Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Salah Ud Din Shah
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Fardous Fardous
- Department of Medical Lab Technology, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Niamatullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Adil U Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Mehwish Siddique
- Department of Zoology, Government Post Graduate College for Women, Satellite Town, Gujranwala, Pakistan
| | - Shoukat Ali Wasan
- Department of Botany, Faculty of Natural Sciences, Shah Abdul Latif University, Khairpur, Sindh, Pakistan
| | - Rooh Niaz
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Hafiz Ullah
- Gomal Center of Biochemistry and Biotechnology (GCBB), Gomal University D. I. Khan, D. I. Khan, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, N9B 1C4, Canada
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan.
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14
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Cuppens T, Kaur M, Kumar AA, Shatto J, Ng ACH, Leclercq M, Reformat MZ, Droit A, Dunham I, Bolduc FV. Developing a cluster-based approach for deciphering complexity in individuals with neurodevelopmental differences. Front Pediatr 2023; 11:1171920. [PMID: 37790694 PMCID: PMC10543689 DOI: 10.3389/fped.2023.1171920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
Objective Individuals with neurodevelopmental disorders such as global developmental delay (GDD) present both genotypic and phenotypic heterogeneity. This diversity has hampered developing of targeted interventions given the relative rarity of each individual genetic etiology. Novel approaches to clinical trials where distinct, but related diseases can be treated by a common drug, known as basket trials, which have shown benefits in oncology but have yet to be used in GDD. Nonetheless, it remains unclear how individuals with GDD could be clustered. Here, we assess two different approaches: agglomerative and divisive clustering. Methods Using the largest cohort of individuals with GDD, which is the Deciphering Developmental Disorders (DDD), characterized using a systematic approach, we extracted genotypic and phenotypic information from 6,588 individuals with GDD. We then used a k-means clustering (divisive) and hierarchical agglomerative clustering (HAC) to identify subgroups of individuals. Next, we extracted gene network and molecular function information with regard to the clusters identified by each approach. Results HAC based on phenotypes identified in individuals with GDD revealed 16 clusters, each presenting with one dominant phenotype displayed by most individuals in the cluster, along with other minor phenotypes. Among the most common phenotypes reported were delayed speech, absent speech, and seizure. Interestingly, each phenotypic cluster molecularly included several (3-12) gene sub-networks of more closely related genes with diverse molecular function. k-means clustering also segregated individuals harboring those phenotypes, but the genetic pathways identified were different from the ones identified from HAC. Conclusion Our study illustrates how divisive (k-means) and agglomerative clustering can be used in order to group individuals with GDD for future basket trials. Moreover, the result of our analysis suggests that phenotypic clusters should be subdivided into molecular sub-networks for an increased likelihood of successful treatment. Finally, a combination of both agglomerative and divisive clustering may be required for developing of a comprehensive treatment.
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Affiliation(s)
- Tania Cuppens
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Manpreet Kaur
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Ajay A. Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julie Shatto
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Andy Cheuk-Him Ng
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Mickael Leclercq
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Marek Z. Reformat
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - François V. Bolduc
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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15
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Curtis D. Social scientists would do well to steer clear of polygenic scores. Behav Brain Sci 2023; 46:e212. [PMID: 37694985 DOI: 10.1017/s0140525x22002448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The problems with polygenic scores (PGSs) have been understated. The fact that they are ancestry-specific means that biases related to sociodemographic factors would be impossible to avoid. Additionally, the requirement to obtain DNA would have profound impacts on study design and required resources, as well as likely introducing recruitment bias. PGSs are unhelpful for social science research.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, University College London, London, UK ; http://www.davecurtis.net/dcurtis.html
- Centre for Psychiatry, Queen Mary University of London, London, UK
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16
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Tan B, Liu S, Feng X, Pan X, Qian G, Liu L, Zhang X, Yao H, Dong X. Expanding the mutational and clinical spectrum of Chinese intellectual disability patients with two novel CTCF variants. Front Pediatr 2023; 11:1195862. [PMID: 37664546 PMCID: PMC10469948 DOI: 10.3389/fped.2023.1195862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
CCCTC-Binding Factor (CTCF) is a protein-coding gene involved in transcriptional regulation, insulator activity, and regulation of chromatin structure, and is closely associated with intellectual developmental disorders. In this study, we report two unrelated Chinese patients with intellectual disability (ID). According to variant interpretation results from exome sequencing data and RNA-seq data, we present two novel heterozygous CTCF variants, NM_006565.3:c.1519_2184del (p. Glu507_Arg727delins47) and NM_006565.3:c.1838_1852del (p.Glu613_Pro617del), found in two distinct unrelated patients, respectively. Moreover, RNA-seq data of patient 1 indicated the absence of the mutant transcript, while in patient 2, the RNA-seq data revealed a CTCF mRNA transcript with a deletion of 15 nucleotides. Notably, the RNA sequencing data revealed 507 differentially expressed genes shared between these two patients. Specifically, among them, 194 were down-regulated, and 313 were up-regulated, primarily involved in gene regulation and cellular response. Our study expands the genetic and clinical spectrum of CTCF and advances our understanding of the pathogenesis of CTCF in vivo.
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Affiliation(s)
- Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guanhua Qian
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Cuppens T, Shatto J, Mangnier L, Kumar AA, Ng ACH, Kaur M, Bui TA, Leclercq M, Droit A, Dunham I, Bolduc FV. Sex difference contributes to phenotypic diversity in individuals with neurodevelopmental disorders. Front Pediatr 2023; 11:1172154. [PMID: 37609366 PMCID: PMC10441218 DOI: 10.3389/fped.2023.1172154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
Objective Gain a better understanding of sex-specific differences in individuals with global developmental delay (GDD), with a focus on phenotypes and genotypes. Methods Using the Deciphering Developmental Disorders (DDD) dataset, we extracted phenotypic information from 6,588 individuals with GDD and then identified statistically significant variations in phenotypes and genotypes based on sex. We compared genes with pathogenic variants between sex and then performed gene network and molecular function enrichment analysis and gene expression profiling between sex. Finally, we contrasted individuals with autism as an associated condition. Results We identified significantly differentially expressed phenotypes in males vs. females individuals with GDD. Autism and macrocephaly were significantly more common in males whereas microcephaly and stereotypies were more common in females. Importantly, 66% of GDD genes with pathogenic variants overlapped between both sexes. In the cohort, males presented with only slightly increased X-linked genes (9% vs. 8%, respectively). Individuals from both sexes harbored a similar number of pathogenic variants overall (3) but females presented with a significantly higher load for GDD genes with high intolerance to loss of function. Sex difference in gene expression correlated with genes identified in a sex specific manner. While we identified sex-specific GDD gene mutations, their pathways overlapped. Interestingly, individuals with GDD but also co-morbid autism phenotypes, we observed distinct mutation load, pathways and phenotypic presentation. Conclusion Our study shows for the first time that males and females with GDD present with significantly different phenotypes. Moreover, while most GDD genes overlapped, some genes were found uniquely in each sex. Surprisingly they shared similar molecular functions. Sorting genes by predicted tolerance to loss of function (pLI) led to identifying an increased mutation load in females with GDD, suggesting potentially a tolerance to GDD genes of higher pLI compared to overall GDD genes. Finally, we show that considering associated conditions (for instance autism) may influence the genomic underpinning found in individuals with GDD and highlight the importance of comprehensive phenotyping.
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Affiliation(s)
- Tania Cuppens
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Julie Shatto
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Loïc Mangnier
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Ajay A. Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Andy Cheuk-Him Ng
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Manpreet Kaur
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Truong An Bui
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Mickael Leclercq
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Francois V. Bolduc
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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Moller-Hansen A, Hejla D, Lee HK, Lyles JB, Yang Y, Chen K, Li WL, Thomas G, Boerkoel CF. Do PACS1 variants impeding adaptor protein binding predispose to syndromic intellectual disability? Am J Med Genet A 2023; 191:2181-2187. [PMID: 37141437 PMCID: PMC10524240 DOI: 10.1002/ajmg.a.63232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
To date, PACS1-neurodevelopmental disorder (PACS1-NDD) has been associated with recurrent variation of Arg203 and is considered diagnostic of PACS1-NDD, an autosomal dominant syndromic intellectual disability disorder. Although incompletely defined, the proposed disease mechanism for this variant is altered PACS1 affinity for its client proteins. Given this proposed mechanism, we hypothesized that PACS1 variants that interfere with binding of adaptor proteins might also give rise to syndromic intellectual disability. Herein, we report a proposita and her mother with phenotypic features overlapping PACS1-NDD and a novel PACS1 variant (NM_018026.3:c.[755C > T];[=], p.(Ser252Phe)) that impedes binding of the adaptor protein GGA3 (Golgi-associated, gamma-adaptin ear-containing, ARF-binding protein 3). We hypothesize that attenuating PACS1 binding of GGA3 also gives rise to a disorder with features overlapping those of PACS1-NDD. This observation better delineates the mechanism by which PACS1 variation predisposes to syndromic intellectual disability.
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Affiliation(s)
- Ashley Moller-Hansen
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Duha Hejla
- Department of Pediatrics, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Hyun Kyung Lee
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Jenea Barbara Lyles
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yunhan Yang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kun Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cornelius F Boerkoel
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
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Brazane M, Dimitrova DG, Pigeon J, Paolantoni C, Ye T, Marchand V, Da Silva B, Schaefer E, Angelova MT, Stark Z, Delatycki M, Dudding-Byth T, Gecz J, Plaçais PY, Teysset L, Préat T, Piton A, Hassan BA, Roignant JY, Motorin Y, Carré C. The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance. Life Sci Alliance 2023; 6:e202201877. [PMID: 36720500 PMCID: PMC9889914 DOI: 10.26508/lsa.202201877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 02/02/2023] Open
Abstract
FTSJ1 is a conserved human 2'-O-methyltransferase (Nm-MTase) that modifies several tRNAs at position 32 and the wobble position 34 in the anticodon loop. Its loss of function has been linked to X-linked intellectual disability (XLID), and more recently to cancers. However, the molecular mechanisms underlying these pathologies are currently unclear. Here, we report a novel FTSJ1 pathogenic variant from an X-linked intellectual disability patient. Using blood cells derived from this patient and other affected individuals carrying FTSJ1 mutations, we performed an unbiased and comprehensive RiboMethSeq analysis to map the ribose methylation on all human tRNAs and identify novel targets. In addition, we performed a transcriptome analysis in these cells and found that several genes previously associated with intellectual disability and cancers were deregulated. We also found changes in the miRNA population that suggest potential cross-regulation of some miRNAs with these key mRNA targets. Finally, we show that differentiation of FTSJ1-depleted human neural progenitor cells into neurons displays long and thin spine neurites compared with control cells. These defects are also observed in Drosophila and are associated with long-term memory deficits. Altogether, our study adds insight into FTSJ1 pathologies in humans and flies by the identification of novel FTSJ1 targets and the defect in neuron morphology.
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Affiliation(s)
- Mira Brazane
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Julien Pigeon
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tao Ye
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, EpiRNASeq Core Facility, UMS2008/US40 IBSLor,Nancy, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Elise Schaefer
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Margarita T Angelova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide; South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Pierre-Yves Plaçais
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Thomas Préat
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Amélie Piton
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Bassem A Hassan
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
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A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy. Genes (Basel) 2023; 14:genes14030707. [PMID: 36980979 PMCID: PMC10048441 DOI: 10.3390/genes14030707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, intellectual disability (ID), and motor dysfunction. Whole exome sequencing of a Pakistani consanguineous family with three brothers affected by ID, cerebral atrophy, mobility, and speech impairment revealed a novel homozygous 3bp-deletion NM_015465.5:c.3162_3164del that leads to the loss of NM_015465.5 (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) amino acid in one of the α-helixes of the tetratricopeptide repeats of GEMIN5. In silico 3D representations of the GEMIN5 dimerization domain show that this variant likely affects the orientation of the downstream sidechains out of the helix axis, which would affect the packing with neighboring helices. The phenotype of all affected siblings overlaps well with previously reported patients, suggesting that NM_015465.5: c.3162_3164del (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) is a novel GEMIN5 pathogenic variant. Overall, our data expands the molecular and clinical phenotype of the recently described neurodevelopmental disorder with cerebellar atrophy and motor dysfunction (NEDCAM) syndrome.
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Al Lihabi A. A literature review of sleep problems and neurodevelopment disorders. Front Psychiatry 2023; 14:1122344. [PMID: 36911135 PMCID: PMC9995546 DOI: 10.3389/fpsyt.2023.1122344] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
INTRODUCTION Sleep is an incredibly complex process that goes beyond relaxing and body resting. Disturbance in sleep leads to several short-term and long-term consequences. Neurodevelopmental diseases such as "autism spectrum disorder" (ASDs), Attention-deficit hyperactivity disorder (ADHD), and intellectual disability commonly experience sleep disorders that affect their clinical presentation, daily function, and quality of life. DISCUSSION The incidence of sleep problems in ASD patients ranges from 32 to 71.5%, especially insomnia, while an estimated 25-50% of people with ADHD report having sleep issues in clinical settings. The incidence of sleep issues is widespread in persons with intellectual disabilities, reaching up to 86%. This article is a literature review covering the neurodevelopmental disorder interaction with sleep disorder and different management. CONCLUSION Disorders of sleep are key concerns in children with neurodevelopmental disorders. In this group of patients, sleep disorders are common and tend to be chronic. Recognizing and diagnosis of sleep disorders will enhance their function, response to treatment, and quality of life.
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Affiliation(s)
- Abeer Al Lihabi
- Taibah University, College of Medicine, psychiatry, Al Madinah AL Munawara, Saudi Arabia
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22
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Streață I, Caramizaru A, Riza AL, Șerban-Sosoi S, Pîrvu A, Cara ML, Cucu MG, Dobrescu AM, Shelby ES, Albeanu A, Burada F, Ioana M. Pathogenic Copy Number Variations Involved in the Genetic Etiology of Syndromic and Non-Syndromic Intellectual Disability-Data from a Romanian Cohort. Diagnostics (Basel) 2022; 12:diagnostics12123137. [PMID: 36553144 PMCID: PMC9777762 DOI: 10.3390/diagnostics12123137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
The investigation of unexplained global developmental delay (GDD)/intellectual disability (ID) is challenging. In low resource settings, patients may not follow a standardized diagnostic process that makes use of the benefits of advanced technologies. Our study aims to explore the contribution of chromosome microarray analysis (CMA) in identifying the genetic etiology of GDD/ID. A total of 371 Romanian patients with syndromic or non-syndromic GDD/ID, without epilepsy, were routinely evaluated in tertiary clinics. A total of 234 males (63.07%) and 137 (36.93%) females, with ages ranging from 6 months to 40 years (median age of 5.5 years), were referred for genetic diagnosis between 2015 and 2022; testing options included CMA and/or karyotyping. Agilent Technologies and Oxford Gene Technology CMA workflows were used. Pathogenic/likely pathogenic copy number variations (pCNVs) were identified in 79 patients (21.29%). Diagnosis yield was comparable between mild ID (17.05%, 22/129) and moderate/severe ID 23.55% (57/242). Higher rates were found in cases where facial dysmorphism (22.97%, 71/309), autism spectrum disorder (ASD) (19.11%, 26/136) and finger anomalies (20%, 27/96) were associated with GDD/ID. GDD/ID plus multiple congenital anomalies (MCA) account for the highest detection rates at 27.42% (17/62). pCNVs represent a significant proportion of the genetic causes of GDD/ID. Our study confirms the utility of CMA in assessing GDD/ID with an uncertain etiology, especially in patients with associated comorbidities.
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Affiliation(s)
- Ioana Streață
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Alexandru Caramizaru
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Anca-Lelia Riza
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Simona Șerban-Sosoi
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Andrei Pîrvu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Monica-Laura Cara
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Department of Public Health, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Mihai-Gabriel Cucu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Amelia Mihaela Dobrescu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Ro-NMCA-ID Group
- The Ro-NMCA-ID (RoNetwork Multiple Congenital Abnormalities with ID) Member of European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA) [EU Framework Partnership Agreement ID: 3HP-HP-FPA ERN-01-2016/739516], 400011 Timisoara, Romania
| | | | | | - Elena-Silvia Shelby
- National University Center for Children’s Neurorehabilitation “Dr. Nicolae Robănescu”, 44 Dumitru Mincă Street, District 4, 041408 Bucharest, Romania
| | - Adriana Albeanu
- Department of Pediatric Neurology, Clinical Emergency Children Hospital Brasov, Nicopole Street No. 45, 500063 Brasov, Romania
| | - Florin Burada
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Mihai Ioana
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
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Meziane H, Birling MC, Wendling O, Leblanc S, Dubos A, Selloum M, Pavlovic G, Sorg T, Kalscheuer VM, Billuart P, Laumonnier F, Chelly J, van Bokhoven H, Herault Y. Large-Scale Functional Assessment of Genes Involved in Rare Diseases with Intellectual Disabilities Unravels Unique Developmental and Behaviour Profiles in Mouse Models. Biomedicines 2022; 10:biomedicines10123148. [PMID: 36551904 PMCID: PMC9775489 DOI: 10.3390/biomedicines10123148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Major progress has been made over the last decade in identifying novel genes involved in neurodevelopmental disorders, although the task of elucidating their corresponding molecular and pathophysiological mechanisms, which are an essential prerequisite for developing therapies, has fallen far behind. We selected 45 genes for intellectual disabilities to generate and characterize mouse models. Thirty-nine of them were based on the frequency of pathogenic variants in patients and literature reports, with several corresponding to de novo variants, and six other candidate genes. We used an extensive screen covering the development and adult stages, focusing specifically on behaviour and cognition to assess a wide range of functions and their pathologies, ranging from basic neurological reflexes to cognitive abilities. A heatmap of behaviour phenotypes was established, together with the results of selected mutants. Overall, three main classes of mutant lines were identified based on activity phenotypes, with which other motor or cognitive deficits were associated. These data showed the heterogeneity of phenotypes between mutation types, recapitulating several human features, and emphasizing the importance of such systematic approaches for both deciphering genetic etiological causes of ID and autism spectrum disorders, and for building appropriate therapeutic strategies.
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Affiliation(s)
- Hamid Meziane
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Olivia Wendling
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Sophie Leblanc
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Aline Dubos
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Vera M. Kalscheuer
- Max Planck Institute for Molecular Genetics, Research Group Development and Disease, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Pierre Billuart
- Institute of Psychiatry and Neuroscience of Paris (IPNP), Université de Paris, INSERM U1266, “Genetic and Development of Cerebral Cortex”, 75014 Paris, France
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, 75014 Paris, France
| | - Frédéric Laumonnier
- UMR1253, iBrain, University of Tours, Inserm, 37032 Tours, France
- Service de Génétique, Centre Hospitalier Régional Universitaire, 37044 Tours, France
| | - Jamel Chelly
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Hans van Bokhoven
- Department of Cognitive Neuroscience, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ Nijmegen, The Netherlands
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch, France
- Correspondence: ; Tel.: +33-388-65-5715
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Geng Y, Zhang T, Alonzo IG, Godar SC, Yates C, Pluimer BR, Harrison DL, Nath AK, Yeh JRJ, Drummond IA, Bortolato M, Peterson RT. Top2a promotes the development of social behavior via PRC2 and H3K27me3. SCIENCE ADVANCES 2022; 8:eabm7069. [PMID: 36417527 PMCID: PMC9683714 DOI: 10.1126/sciadv.abm7069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Little is understood about the embryonic development of sociality. We screened 1120 known drugs and found that embryonic inhibition of topoisomerase IIα (Top2a) resulted in lasting social deficits in zebrafish. In mice, prenatal Top2 inhibition caused defects in social interaction and communication, which are behaviors that relate to core symptoms of autism. Mutation of Top2a in zebrafish caused down-regulation of a set of genes highly enriched for genes associated with autism in humans. Both the Top2a-regulated and autism-associated gene sets have binding sites for polycomb repressive complex 2 (PRC2), a regulatory complex responsible for H3K27 trimethylation (H3K27me3). Moreover, both gene sets are highly enriched for H3K27me3. Inhibition of the PRC2 component Ezh2 rescued social deficits caused by Top2 inhibition. Therefore, Top2a is a key component of an evolutionarily conserved pathway that promotes the development of social behavior through PRC2 and H3K27me3.
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Affiliation(s)
- Yijie Geng
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Tejia Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Ivy G. Alonzo
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Sean C. Godar
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Christopher Yates
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Brock R. Pluimer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Devin L. Harrison
- The Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Anjali K. Nath
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
- Metabolism Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Iain A. Drummond
- Davis Center for Aging and Regeneration, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Marco Bortolato
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Randall T. Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
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van der Laan L, Rooney K, Alders M, Relator R, McConkey H, Kerkhof J, Levy MA, Lauffer P, Aerden M, Theunis M, Legius E, Tedder ML, Vissers LELM, Koene S, Ruivenkamp C, Hoffer MJV, Wieczorek D, Bramswig NC, Herget T, González VL, Santos-Simarro F, Tørring PM, Denomme-Pichon AS, Isidor B, Keren B, Julia S, Schaefer E, Francannet C, Maillard PY, Misra-Isrie M, Van Esch H, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. Episignature Mapping of TRIP12 Provides Functional Insight into Clark-Baraitser Syndrome. Int J Mol Sci 2022; 23:ijms232213664. [PMID: 36430143 PMCID: PMC9690904 DOI: 10.3390/ijms232213664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Clark-Baraitser syndrome is a rare autosomal dominant intellectual disability syndrome caused by pathogenic variants in the TRIP12 (Thyroid Hormone Receptor Interactor 12) gene. TRIP12 encodes an E3 ligase in the ubiquitin pathway. The ubiquitin pathway includes activating E1, conjugating E2 and ligating E3 enzymes which regulate the breakdown and sorting of proteins. This enzymatic pathway is crucial for physiological processes. A significant proportion of TRIP12 variants are currently classified as variants of unknown significance (VUS). Episignatures have been shown to represent a powerful diagnostic tool to resolve inconclusive genetic findings for Mendelian disorders and to re-classify VUSs. Here, we show the results of DNA methylation episignature analysis in 32 individuals with pathogenic, likely pathogenic and VUS variants in TRIP12. We identified a specific and sensitive DNA methylation (DNAm) episignature associated with pathogenic TRIP12 variants, establishing its utility as a clinical biomarker for Clark-Baraitser syndrome. In addition, we performed analysis of differentially methylated regions as well as functional correlation of the TRIP12 genome-wide methylation profile with the profiles of 56 additional neurodevelopmental disorders.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Peter Lauffer
- Department of Pediatric Endocrinology, Emma Children’s Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Mio Aerden
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Miel Theunis
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | | | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Mariette J. V. Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Nuria C. Bramswig
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Vanesa López González
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, CIBERER, 30120 Murcia, Spain
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, 28029 Madrid, Spain
| | - Pernille M. Tørring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Anne-Sophie Denomme-Pichon
- UF6254 Innovation en Diagnostic Genomique des Maladies Rares, 21070 Dijon, France
- Équipe Génétique des Anomalies du Développement (GAD), CHU Dijon-Bourgogne, 21000 Dijon, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | - Boris Keren
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, 75013 Paris, France
| | - Sophie Julia
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Elise Schaefer
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Christine Francannet
- Service de Genetique Medicale, CHU de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | | | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Hilde Van Esch
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
- Correspondence: (B.S.); (P.H.)
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (B.S.); (P.H.)
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Yi S, Chen F, Qin Z, Yi S, Huang L, Huang L, Feng Y, Wei H, Yang Q, Zhang Q, Luo J. Novel Synonymous and Frameshift Variants in the TRIP12 Gene Identified in 2 Chinese Patients With Intellectual Disability. NEUROLOGY GENETICS 2022; 8:e200025. [PMID: 36275919 PMCID: PMC9585485 DOI: 10.1212/nxg.0000000000200025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/20/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives Clark-Baraitser syndrome is characterized by intellectual disability with or without autism spectrum disorders, speech delay, motor delay, behavioral abnormalities, and facial dysmorphism. It is caused by a heterozygous pathogenic variant in the thyroid hormone receptor interactor 12 (TRIP12) gene. However, loss of function and haploinsufficiency are the pathogenic mechanisms behind the TRIP12-related disorder. Methods We conducted an exome sequencing analysis for 2 unrelated patients with moderate intellectual disability, speech delay, and motor delay. Results We identified 2 de novo TRIP12 mutations in these 2 patients. One patient had a frameshift duplication, whereas the other had a synonymous variant. Both patients presented with common features of the syndrome, but clinical heterogeneity has been also observed between them. For the synonymous variant, reverse transcription PCR in RNA extracted from leukocytes demonstrated the presence of a truncated messenger RNA (mRNA) transcript that skipped exon 12. This transcript escapes degradation at the mRNA level. To assess the effect of the synonymous substitute on TRIP12 proteolytic activity, the expression of 9 known responsive genes at the mRNA level was measured, of which 3 genes were upregulated at least 2-fold in the patient. Discussion We reported 2 patients with Clark-Baraitser syndrome caused by novel synonymous and frameshift variants in the TRIP12 gene, and our study expands the mutation spectrum of the TRIP12 gene. This study will help to improve our understanding of variable phenotypic presentations in TRIP12-related disorders.
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Chen Y, Fan J, Xiao D, Li X. The role of SCAMP5 in central nervous system diseases. Neurol Res 2022; 44:1024-1037. [PMID: 36217917 DOI: 10.1080/01616412.2022.2107754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
OBJECTIVE Secretory carrier membrane proteins (SCAMPs) constitute a group of membrane transport proteins in plants, insects and mammals. The mammalian genome contains five types of SCAMP genes, namely, SCAMP1-SCAMP5. SCAMPs participate in the vesicle cycling fusion of vesicles and cell membranes and play roles in regulating exocytosis and endocytosis, activating synaptic function and transmitting nerve signals. Among these proteins, SCAMP5 is highly expressed in the brain and has direct or indirect effects on the function of the central nervous system. This paper may allow us to better understand the role of SCAMP5 in the central nervous system diseases. SCAMP5 regulates membrane transport, controls the exocytosis of SVs and is related to secretion carrier and membrane function. In addition, SCAMP5 plays a major role in the normal maintenance of the physiological functions of nerve cells. This article summarizes the effects of SCAMP5 on nerve cell exocytosis, endocytosis and synaptic function, as well as the relationship between SCAMP5 and various neurological diseases, to better understand the role of SCAMP5 in the pathogenesis of neurological diseases. METHODS Through PubMed, this paper examined and analyzed the role of SCAMP5 in the central nervous system, as well as the relationship between SCAMP5 and various neurological diseases using the key terms "secretory carrier membrane proteins"," SCAMP5"," exocytosis"," endocytosis", "synaptic function", "central nervous system diseases" up to 01 March 2022. RESULTS SCAMP5 regulates membrane transport, controls the exocytosis of SVs and is related to secretion carrier and membrane function. In addition, SCAMP5 plays a major role in the normal maintenance of the physiological functions of nerve cells. CONCLUSION This article summarizes the effects of SCAMP5 on nerve cell exocytosis, endocytosis and synaptic function, as well as the relationship between SCAMP5 and various neurological diseases, to better understand the role of SCAMP5 in the pathogenesis of neurological diseases.
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Affiliation(s)
- Ye Chen
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Jiali Fan
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Dongqiong Xiao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Xihong Li
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
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28
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de Toledo VHC, Feltrin AS, Barbosa AR, Tahira AC, Brentani H. Sex differences in gene regulatory networks during mid-gestational brain development. Front Hum Neurosci 2022; 16:955607. [PMID: 36061507 PMCID: PMC9428411 DOI: 10.3389/fnhum.2022.955607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Neurodevelopmental disorders differ considerably between males and females, and fetal brain development is one of the most critical periods to determine risk for these disorders. Transcriptomic studies comparing male and female fetal brain have demonstrated that the highest difference in gene expression occurs in sex chromosomes, but several autossomal genes also demonstrate a slight difference that has not been yet explored. In order to investigate biological pathways underlying fetal brain sex differences, we applied medicine network principles using integrative methods such as co-expression networks (CEMiTool) and regulatory networks (netZoo). The pattern of gene expression from genes in the same pathway tend to reflect biologically relevant phenomena. In this study, network analysis of fetal brain expression reveals regulatory differences between males and females. Integrating two different bioinformatics tools, our results suggest that biological processes such as cell cycle, cell differentiation, energy metabolism and extracellular matrix organization are consistently sex-biased. MSET analysis demonstrates that these differences are relevant to neurodevelopmental disorders, including autism.
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Affiliation(s)
- Victor Hugo Calegari de Toledo
- Departamento e Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Ana Carolina Tahira
- Laboratório de Expressão Gênica, Departamento de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | - Helena Brentani
- Departamento e Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Helena Brentani
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29
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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Human Brain Models of Intellectual Disability: Experimental Advances and Novelties. Int J Mol Sci 2022; 23:ijms23126476. [PMID: 35742919 PMCID: PMC9224308 DOI: 10.3390/ijms23126476] [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: 04/28/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Intellectual disability (ID) is characterized by deficits in conceptual, social and practical domains. ID can be caused by both genetic defects and environmental factors and is extremely heterogeneous, which complicates the diagnosis as well as the deciphering of the underlying pathways. Multiple scientific breakthroughs during the past decades have enabled the development of novel ID models. The advent of induced pluripotent stem cells (iPSCs) enables the study of patient-derived human neurons in 2D or in 3D organoids during development. Gene-editing tools, such as CRISPR/Cas9, provide isogenic controls and opportunities to design personalized gene therapies. In practice this has contributed significantly to the understanding of ID and opened doors to identify novel therapeutic targets. Despite these advances, a number of areas of improvement remain for which novel technologies might entail a solution in the near future. The purpose of this review is to provide an overview of the existing literature on scientific breakthroughs that have been advancing the way ID can be studied in the human brain. The here described human brain models for ID have the potential to accelerate the identification of underlying pathophysiological mechanisms and the development of therapies.
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Saghi M, InanlooRahatloo K, Alavi A, Kahrizi K, Najmabadi H. Intellectual disability associated with craniofacial dysmorphism due to POLR3B mutation and defect in spliceosomal machinery. BMC Med Genomics 2022; 15:89. [PMID: 35436926 PMCID: PMC9014605 DOI: 10.1186/s12920-022-01237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Intellectual disability (ID) is a clinically important disease and a most prevalent neurodevelopmental disorder. The etiology and pathogenesis of ID are poorly recognized. Exome sequencing revealed a homozygous missense mutation in the POLR3B gene in a consanguineous family with three Intellectual disability with craniofacial anomalies patients. POLR3B gene encoding the second largest subunit of RNA polymerase III. Methods We performed RNA sequencing on blood samples to obtain insights into the biological pathways influenced by POLR3B mutation. We applied the results of our RNA-Seq analysis to several gene ontology programs such as ToppGene, Enrichr, KEGG. Results A significant decrease in expression of several spliceosomal RNAs, ribosomal proteins, and transcription factors was detected in the affected, compared to unaffected, family members. Conclusions We hypothesize that POLR3B mutation dysregulates the expression of some important transcription factors, ribosomal and spliceosomal genes, and impairments in protein synthesis and splicing mediated in part by transcription factors such as FOXC2 and GATA1 contribute to impaired neuronal function and concurrence of intellectual disability and craniofacial anomalies in our patients. Our study highlights the emerging role of the spliceosome and ribosomal proteins in intellectual disability. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01237-5.
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Affiliation(s)
- Mostafa Saghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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32
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Moudi M, Vahidi Mehrjardi MY, Kalantar SM, Taheri M, Metanat Z, Ghasemi N, Dehghani M. Co-segregation of variant NSUN2 Lue198Arg among Iranian family with intellectual disability: a case report. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Intellectual disability is characterized by impairments in adaptive behavior and cognitive functioning manifested during the developmental period. Since disabilities are heterogeneous, variant analysis can help us confirm and accurately diagnose children with intellectual disabilities. Some papers reported that bi-allelic variants of the NSUN2 gene caused a group of neurological disorders, including non-syndromic autosomal recessive intellectual disability (NS-ARID), Dubowitz syndrome, and familial restrictive cardiomyopathy 1 (RCM1). We report on a consanguineous family with three siblings diagnosed with intellectual disability.
Case presentation
The 7-year-old female was referred to Ali-Asghar hospital, Zahedan, Iran, with clinical manifestations comprising moderate intellectual disability, ptosis, long face, and short stature. Chromosome banding, metabolic testing, and magnetic resonance imaging examinations revealed no abnormalities. Accordingly, other affected siblings born of the same parents were considered. Whole-exome sequencing (WES) was conducted on the sufferer to consider NS-ARID variants. Findings identified a variant with uncertain significance (NM_017755.6: c.593 T > G) in the NSUN2 gene in the proband. This variant was confirmed through Sanger sequencing of the affected and unaffected family members. Besides, the computational results showed that the L198R exchange could change the interaction between wild-type and other residues in the protein. The affected patients with NS-ARID had similar clinical characteristics and genetic abnormalities.
Conclusion
Taken together, we described the variant in three Iranian siblings; further expanding of the other variants involved in the disease will be evident by using high-throughput sequencing technologies.
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Brea-Fernández AJ, Álvarez-Barona M, Amigo J, Tubío-Fungueiriño M, Caamaño P, Fernández-Prieto M, Barros F, De Rubeis S, Buxbaum J, Carracedo Á. Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability. Eur J Hum Genet 2022; 30:938-945. [PMID: 35322241 PMCID: PMC9349217 DOI: 10.1038/s41431-022-01087-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
Intellectual disability (ID), a neurodevelopmental disorder affecting 1-3% of the general population, is characterized by limitations in both intellectual function and adaptive skills. The high number of conditions associated with ID underlines its heterogeneous origin and reveals the difficulty of obtaining a rapid and accurate genetic diagnosis. However, the Next Generation Sequencing, and the whole exome sequencing (WES) in particular, has boosted the diagnosis rate associated with ID. In this study, WES performed on 244 trios of patients clinically diagnosed with isolated or syndromic ID and their respective unaffected parents has allowed the identification of the underlying genetic basis of ID in 64 patients, yielding a diagnosis rate of 25.2%. Our results suggest that trio-based WES facilitates ID's genetic diagnosis, particularly in patients who have been extensively waiting for a definitive molecular diagnosis. Moreover, genotypic information from parents provided by trio-based WES enabled the detection of a high percentage (61.5%) of de novo variants inside our cohort. Establishing a quick genetic diagnosis of ID would allow early intervention and better clinical management, thus improving the quality of life of these patients and their families.
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Affiliation(s)
- Alejandro J Brea-Fernández
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.
| | - Miriam Álvarez-Barona
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jorge Amigo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | - María Tubío-Fungueiriño
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Caamaño
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | - Montserrat Fernández-Prieto
- Genetics Group, GC05, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | | | - Joseph Buxbaum
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain.,Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Leung AWS, Leung HCM, Wong CL, Zheng ZX, Lui WW, Luk HM, Lo IFM, Luo R, Lam TW. ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell. BMC Med Genomics 2022; 15:43. [PMID: 35246132 PMCID: PMC8895767 DOI: 10.1186/s12920-022-01190-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 02/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field. Having a high sequencing error of ONT and limited throughput from a single MinION flowcell, however, limits its applicability for accurate variant detection. Medical exome sequencing (MES) targets clinically significant exon regions, allowing rapid and comprehensive screening of pathogenic variants. By applying MES with MinION sequencing, the technology can achieve a more uniform capture of the target regions, shorter turnaround time, and lower sequencing cost per sample. METHOD We introduced a cost-effective optimized workflow, ECNano, comprising a wet-lab protocol and bioinformatics analysis, for accurate variant detection at 4800 clinically important genes and regions using a single MinION flowcell. The ECNano wet-lab protocol was optimized to perform long-read target enrichment and ONT library preparation to stably generate high-quality MES data with adequate coverage. The subsequent variant-calling workflow, Clair-ensemble, adopted a fast RNN-based variant caller, Clair, and was optimized for target enrichment data. To evaluate its performance and practicality, ECNano was tested on both reference DNA samples and patient samples. RESULTS ECNano achieved deep on-target depth of coverage (DoC) at average > 100× and > 98% uniformity using one MinION flowcell. For accurate ONT variant calling, the generated reads sufficiently covered 98.9% of pathogenic positions listed in ClinVar, with 98.96% having at least 30× DoC. ECNano obtained an average read length of 1000 bp. The long reads of ECNano also covered the adjacent splice sites well, with 98.5% of positions having ≥ 30× DoC. Clair-ensemble achieved > 99% recall and accuracy for SNV calling. The whole workflow from wet-lab protocol to variant detection was completed within three days. CONCLUSION We presented ECNano, an out-of-the-box workflow comprising (1) a wet-lab protocol for ONT target enrichment sequencing and (2) a downstream variant detection workflow, Clair-ensemble. The workflow is cost-effective, with a short turnaround time for high accuracy variant calling in 4800 clinically significant genes and regions using a single MinION flowcell. The long-read exon captured data has potential for further development, promoting the application of long-read sequencing in personalized disease treatment and risk prediction.
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Affiliation(s)
- Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | | | - Chak-Lim Wong
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Zhen-Xian Zheng
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Wui-Wang Lui
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Ho-Ming Luk
- Department of Health, Clinical Genetic Service, Hong Kong, SAR, China
| | - Ivan Fai-Man Lo
- Department of Health, Clinical Genetic Service, Hong Kong, SAR, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.
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Riet F, Mittelhaeuser C, Lux A, Bour R, Selloum M, Sorg T, Herault Y, Meziane H. Behavioral Testing Design for Evaluation of Cognitive Disabilities. Curr Protoc 2022; 2:e382. [PMID: 35195951 DOI: 10.1002/cpz1.382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Intellectual disabilities (ID) constitute a class of human neurodevelopmental diseases and are a major medical and socioeconomic problem owing to their high incidence and enormous burden to the families of those affected. In the past three decades, mutant mouse technologies have provided powerful tools for elucidating the pathophysiological mechanisms underlying behavioral and developmental alterations related to IDs and for addressing new therapeutic strategies, and major progress has been made revealing previously unidentified genes involved in ID. However, the pathological hallmarks of IDs are very heterogeneous in regard to both the functional deficits observed and the severity of the phenotype, even within the same mutation types. For this reason, an appropriate experimental design is required to reduce the risk of false negatives and positives in animal functional genomic studies. This experimental design should address functions important to evaluate, tests, and the appropriate workflow. Here, we propose an extensive behavioral screen with detailed protocols, which was successfully used in a systematic mouse functional genomic approach to gain pathway-based insights into mechanisms leading to cognitive dysfunction in humans. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Assessment of circadian activity and ingestive behavior Basic Protocol 2: Assessment of neurological reflexes and motor abilities using the grip and rotarod tests Basic Protocol 3: Evaluation of anxiety-related behavior using the elevated plus maze Basic Protocol 4: Evaluation of recognition memory using the object recognition task Basic Protocol 5: Evaluation of social behavior using the social recognition test Basic Protocol 6: Evaluation of working memory using the Y-maze spontaneous alternation test Basic Protocol 7: Evaluation of emotional learning and memory using the fear conditioning test.
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Affiliation(s)
- Fabrice Riet
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Christophe Mittelhaeuser
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Aline Lux
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Raphael Bour
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France.,Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
| | - Hamid Meziane
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
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36
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Moudi M, Vahidi Mehrjardi MY, Hozhabri H, Metanat Z, Kalantar SM, Taheri M, Ghasemi N, Dehghani M. Novel variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability in Iranian consanguineous families. J Clin Lab Anal 2022; 36:e24241. [PMID: 35019165 PMCID: PMC8842163 DOI: 10.1002/jcla.24241] [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: 09/20/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 11/17/2022] Open
Abstract
Background Intellectual disability (ID) is a heterogeneous group of neurodevelopmental disorders that is characterized by significant impairment in intellectual and adaptive functioning with onset during the developmental period. Whole‐exome sequencing (WES)‐based studies in the consanguineous families with individuals affected with ID have shown a high burden of relevant variants. So far, over 700 genes have been reported in syndromic and non‐syndromic ID. However, genetic causes in more than 50% of ID patients still remain unclear. Methods Whole‐exome sequencing was applied for investigation of various variants of ID, then Sanger sequencing and in silico analysis in ten patients from five Iranian consanguineous families diagnosed with autosomal recessive neurodevelopmental disorders, intellectual disability, performed for confirming the causative mutation within the probands. The most patients presented moderate‐to‐severe intellectual disability, developmental delay, seizure, speech problem, high level of lactate, and onset before 10 years. Results Filtering the data identified by WES, two novel homozygous missense variants in FBXO31 and TIMM50 genes and one previously reported mutation in the CEP290 gene in the probands were found. Sanger sequencing confirmed the homozygote variant's presence of TIMM50 and FBXO31 genes in six patients and two affected siblings in their respective families. Our computational results predicted that the variants are located in the conserved regions across different species and have the impacts on the protein stability. Conclusion Hence, we provide evidence for the pathogenicity of two novel variants in the patients which will expand our knowledge about potential mutation involved in the heterogeneous disease.
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Affiliation(s)
- Mahdiyeh Moudi
- Department of Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | | | - Zahra Metanat
- Department of Genetics, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed Mehdi Kalantar
- Department of Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohsen Taheri
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Genetics, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Nasrin Ghasemi
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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37
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Neurogenetic disorders across the lifespan: from aberrant development to degeneration. Nat Rev Neurol 2022; 18:117-124. [PMID: 34987232 PMCID: PMC10132523 DOI: 10.1038/s41582-021-00595-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 02/08/2023]
Abstract
Intellectual disability and autism spectrum disorder (ASD) are common, and genetic testing is increasingly performed in individuals with these diagnoses to inform prognosis, refine management and provide information about recurrence risk in the family. For neurogenetic conditions associated with intellectual disability and ASD, data on natural history in adults are scarce; however, as older adults with these disorders are identified, it is becoming clear that some conditions are associated with both neurodevelopmental problems and neurodegeneration. Moreover, emerging evidence indicates that some neurogenetic conditions associated primarily with neurodegeneration also affect neurodevelopment. In this Perspective, we discuss examples of diseases that have developmental and degenerative overlap. We propose that neurogenetic disorders should be studied continually across the lifespan to understand the roles of the affected genes in brain development and maintenance, and to inform strategies for treatment.
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38
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Korb L, O'Regan D, Conley J, Dillon E, Briggs R, Courtenay K, Perera B. Sleep: the neglected life factor in adults with intellectual disabilities. BJPsych Bull 2021; 47:139-145. [PMID: 34937594 DOI: 10.1192/bjb.2021.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Sleep is vital for our physical and mental health. Studies have shown that there is a high prevalence of sleep disorders and sleep difficulties amongst adults with intellectual disabilities. Despite this, sleep is often overlooked or its disorders are considered to be difficult to treat in adults with intellectual disabilities. There is a significant amount of research and guidance on management of sleep disorders in the general population. However, the evidence base for sleep disorders in adults with intellectual disabilities is limited. In this review paper, we look at the current evidence base for sleep disorders in adults with an intellectual disability, discuss collaborative working between intellectual disabilities psychiatrists and sleep medicine specialists to manage sleep disorders, and provide recommendations for future directions.
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Affiliation(s)
- Laura Korb
- Barnet, Enfield and Haringey Mental Health NHS Trust, UK
| | | | - Jane Conley
- Barnet, Enfield and Haringey Mental Health NHS Trust, UK
| | | | | | - Ken Courtenay
- Barnet, Enfield and Haringey Mental Health NHS Trust, UK
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39
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Bui TA, Shatto J, Cuppens T, Droit A, Bolduc FV. Phenotypic Trade-Offs: Deciphering the Impact of Neurodiversity on Drug Development in Fragile X Syndrome. Front Psychiatry 2021; 12:730987. [PMID: 34733188 PMCID: PMC8558248 DOI: 10.3389/fpsyt.2021.730987] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common single-gene cause of intellectual disability and autism spectrum disorder. Individuals with FXS present with a wide range of severity in multiple phenotypes including cognitive delay, behavioral challenges, sleep issues, epilepsy, and anxiety. These symptoms are also shared by many individuals with other neurodevelopmental disorders (NDDs). Since the discovery of the FXS gene, FMR1, FXS has been the focus of intense preclinical investigation and is placed at the forefront of clinical trials in the field of NDDs. So far, most studies have aimed to translate the rescue of specific phenotypes in animal models, for example, learning, or improving general cognitive or behavioral functioning in individuals with FXS. Trial design, selection of outcome measures, and interpretation of results of recent trials have shown limitations in this type of approach. We propose a new paradigm in which all phenotypes involved in individuals with FXS would be considered and, more importantly, the possible interactions between these phenotypes. This approach would be implemented both at the baseline, meaning when entering a trial or when studying a patient population, and also after the intervention when the study subjects have been exposed to the investigational product. This approach would allow us to further understand potential trade-offs underlying the varying effects of the treatment on different individuals in clinical trials, and to connect the results to individual genetic differences. To better understand the interplay between different phenotypes, we emphasize the need for preclinical studies to investigate various interrelated biological and behavioral outcomes when assessing a specific treatment. In this paper, we present how such a conceptual shift in preclinical design could shed new light on clinical trial results. Future clinical studies should take into account the rich neurodiversity of individuals with FXS specifically and NDDs in general, and incorporate the idea of trade-offs in their designs.
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Affiliation(s)
- Truong An Bui
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Julie Shatto
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Tania Cuppens
- Centre de Recherche du CHU de Québec-Université Laval et Département de Médecine Moléculaire de l'Université Laval, Laval, QC, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec-Université Laval et Département de Médecine Moléculaire de l'Université Laval, Laval, QC, Canada
| | - François V. Bolduc
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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40
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Xian W, Cao J, Yuan X, Wang G, Jin Q, Zhang H, Zhou G, You L. Deficiency of Intellectual Disability-Related Gene Brpf1 Attenuated Hippocampal Excitatory Synaptic Transmission and Impaired Spatial Learning and Memory Ability. Front Cell Dev Biol 2021; 9:711792. [PMID: 34485298 PMCID: PMC8415984 DOI: 10.3389/fcell.2021.711792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Patients with monoallelic bromodomain and PHD finger-containing protein 1 (BRPF1) mutations showed intellectual disability. The hippocampus has essential roles in learning and memory. Our previous work indicated that Brpf1 was specifically and strongly expressed in the hippocampus from the perinatal period to adulthood. We hypothesized that mouse Brpf1 plays critical roles in the morphology and function of hippocampal neurons, and its deficiency leads to learning and memory deficits. To test this, we performed immunofluorescence, whole-cell patch clamp, and mRNA-Seq on shBrpf1-infected primary cultured hippocampal neurons to study the effect of Brpf1 knockdown on neuronal morphology, electrophysiological characteristics, and gene regulation. In addition, we performed stereotactic injection into adult mouse hippocampus to knock down Brpf1 in vivo and examined the learning and memory ability by Morris water maze. We found that mild knockdown of Brpf1 reduced mEPSC frequency of cultured hippocampal neurons, before any significant changes of dendritic morphology showed. We also found that Brpf1 mild knockdown in the hippocampus showed a decreasing trend on the spatial learning and memory ability of mice. Finally, mRNA-Seq analyses showed that genes related to learning, memory, and synaptic transmission (such as C1ql1, Gpr17, Htr1d, Glra1, Cxcl10, and Grin2a) were dysregulated upon Brpf1 knockdown. Our results showed that Brpf1 mild knockdown attenuated hippocampal excitatory synaptic transmission and reduced spatial learning and memory ability, which helps explain the symptoms of patients with BRPF1 mutations.
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Affiliation(s)
- Weiwei Xian
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jingli Cao
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiangshan Yuan
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guoxiang Wang
- Institutes of Brain Sciences, Fudan University, Shanghai, China
| | - Qiuyan Jin
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hang Zhang
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guomin Zhou
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai, China
| | - Linya You
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai, China
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41
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Trakadis Y, Accogli A, Qi B, Bloom D, Joober R, Levy E, Tabbane K. Next-generation gene panel testing in adolescents and adults in a medical neuropsychiatric genetics clinic. Neurogenetics 2021; 22:313-322. [PMID: 34363551 DOI: 10.1007/s10048-021-00664-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/21/2021] [Indexed: 01/04/2023]
Abstract
Intellectual disability (ID) encompasses a clinically and genetically heterogeneous group of neurodevelopmental disorders that may present with psychiatric illness in up to 40% of cases. Despite the evidence for clinical utility of genetic panels in pediatrics, there are no published studies in adolescents/adults with ID or autism spectrum disorder (ASD). This study was approved by our institutional research ethics board. We retrospectively reviewed the medical charts of all patients evaluated between January 2017 and December 2019 in our adult neuropsychiatric genetics clinic at the McGill University Health Centre (MUHC), who had undergone a comprehensive ID/ASD gene panel. Thirty-four patients aged > 16 years, affected by ID/ASD and/or other neuropsychiatric/behavioral disorders, were identified. Pathogenic or likely pathogenic variants were identified in one-third of our cohort (32%): 8 single-nucleotide variants in 8 genes (CASK, SHANK3, IQSEC2, CHD2, ZBTB20, TREX1, SON, and TUBB2A) and 3 copy number variants (17p13.3, 16p13.12p13.11, and 9p24.3p24.1). The presence of psychiatric/behavioral disorders, regardless of the co-occurrence of ID, and, at a borderline level, the presence of ID alone were associated with positive genetic findings (p = 0.024 and p = 0.054, respectively). Moreover, seizures were associated with positive genetic results (p = 0.024). One-third of individuals presenting with psychiatric illness who met our red flags for Mendelian diseases have pathogenic or likely pathogenic variants which can be identified using a comprehensive ID/ASD gene panel (~ 2500 genes) performed on an exome backbone.
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Affiliation(s)
- Y Trakadis
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Room A04.3140, 1001 Boul. Décarie, Montreal, QC, H4A 3J1, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada. .,Douglas Mental Health Institute/Hospital, Montreal, Canada. .,Department of Psychiatry, McGill University, Montreal, Canada.
| | - A Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Room A04.3140, 1001 Boul. Décarie, Montreal, QC, H4A 3J1, Canada
| | - B Qi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - D Bloom
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - R Joober
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - E Levy
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - K Tabbane
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
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42
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Rojano E, Córdoba-Caballero J, Jabato FM, Gallego D, Serrano M, Pérez B, Parés-Aguilar Á, Perkins JR, Ranea JAG, Seoane-Zonjic P. Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer. J Pers Med 2021; 11:730. [PMID: 34442375 PMCID: PMC8398478 DOI: 10.3390/jpm11080730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 12/21/2022] Open
Abstract
Exhaustive and comprehensive analysis of pathological traits is essential to understanding genetic diseases, performing precise diagnosis and prescribing personalized treatments. It is particularly important for disease cohorts, as thoroughly detailed phenotypic profiles allow patients to be compared and contrasted. However, many disease cohorts contain patients that have been ascribed low numbers of very general and relatively uninformative phenotypes. We present Cohort Analyzer, a tool that measures the phenotyping quality of patient cohorts. It calculates multiple statistics to give a general overview of the cohort status in terms of the depth and breadth of phenotyping, allowing us to detect less well-phenotyped patients for re-examining or excluding from further analyses. In addition, it performs clustering analysis to find subgroups of patients that share similar phenotypic profiles. We used it to analyse three cohorts of genetic diseases patients with very different properties. We found that cohorts with the most specific and complete phenotypic characterization give more potential insights into the disease than those that were less deeply characterised by forming more informative clusters. For two of the cohorts, we also analysed genomic data related to the patients, and linked the genomic data to the patient-subgroups by mapping shared variants to genes and functions. The work highlights the need for improved phenotyping in this era of personalized medicine. The tool itself is freely available alongside a workflow to allow the analyses shown in this work to be applied to other datasets.
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Affiliation(s)
- Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
| | - José Córdoba-Caballero
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
| | - Fernando M. Jabato
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Supercomputation and Bioinformatics (SCBI), University of Malaga, 29071 Malaga, Spain
- LifeWatch-ERIC, 41071 Seville, Spain
| | - Diana Gallego
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria idiPAZ, 28049 Madrid, Spain
| | - Mercedes Serrano
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
- Neuropediatric Department, Institut de Recerca Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Belén Pérez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria idiPAZ, 28049 Madrid, Spain
| | - Álvaro Parés-Aguilar
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
| | - James R. Perkins
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
| | - Juan A. G. Ranea
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
| | - Pedro Seoane-Zonjic
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
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Mattie LJ. Translational Research and Clinical Implications Regarding Communication Outcomes in Neurogenetic Disorders. Semin Speech Lang 2021; 42:275-276. [PMID: 34311479 DOI: 10.1055/s-0041-1730986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Laura J Mattie
- Department of Speech and Hearing Science, University of Illinois at Urbana-Champaign, Champaign, Illinois
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Dong Y, Shi X, Du K, Xu R, Jia T, Wang J, Wang L, Han R. First Chinese patient with mental retardation-40 due to a de novo CHAMP1 frameshift mutation: Case report and literature review. Exp Ther Med 2021; 22:907. [PMID: 34257719 PMCID: PMC8243316 DOI: 10.3892/etm.2021.10339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/28/2021] [Indexed: 12/16/2022] Open
Abstract
Mental retardation-40 (MRD40) is a rare autosomal dominant neurodevelopmental disorder with a poor prognosis that is caused by a heterozygous mutation in chromosome alignment maintaining phosphoprotein 1 (CHAMP1). It was previously considered a non-syndromic disease due to the lack of specific external features. Only limited international reports describing CHAMP1 mutations are currently available. The present case study was the first to report on a Chinese patient with MRD40. The patient presented with severe global development delay with significant craniofacial dysmorphia. Using trio whole-exome sequencing, a novel de novo frameshift mutation in CHAMP1, NM_032436.2: c.530delCinsTTT, was identified, which expands the spectrum of the known pathogenic variants. The present case report helps to improve the syndromic profile of the rare MRD40 disorder and provides an example for the clinical diagnosis of MRD40.
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Affiliation(s)
- Yan Dong
- Neurology Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Xiaoyi Shi
- Development and Behavior Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Kaixian Du
- Neurology Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Ruijuan Xu
- Neurology Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Tianming Jia
- Neurology Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Jun Wang
- Department of Children's Rehabilitation, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Lijun Wang
- Neurology Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Rui Han
- Neurology Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
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The effect of functioning on Quality of Life Inventory-Disability measured quality of life is not mediated or moderated by parental psychological distress. Qual Life Res 2021; 30:2875-2885. [PMID: 33939076 DOI: 10.1007/s11136-021-02855-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE The measurement of quality of life (QOL) in children with intellectual disability often relies upon proxy report via caregivers. The current study investigated whether caregiver psychological distress mediates or moderates the effects of impairment on their ratings of QOL in children with intellectual disability. METHODS Caregivers of 447 children with an intellectual disability reported their child's day-to-day functioning, their own psychological distress using the Kessler Psychological Distress Scale, and the Quality of Life Inventory-Disability (QI-Disability), a measure of QOL for proxy report of a child's observable behaviours that indicate quality of life. Linear regression was used to assess the effects of the child's functional abilities on their QI-Disability score and causal mediation analysis to estimate the extent to which these effects were mediated by caregivers' psychological distress. RESULTS A minority of caregivers (n = 121, 27.1%) reported no psychological distress. Lower day-to-day functional abilities, such as being fully dependent on others to manage their personal needs were associated with lower total QOL scores. There was no significant mediation effect of caregiver psychological distress on the association between child functioning and total QOL scores. Moderation analyses revealed small and largely nonsignificant interaction coefficients, indicating that caregiver psychological distress did not influence the strength of the relationship between child functioning and total QOL scores. CONCLUSION Caregiver psychological distress did not mediate or moderate the relationship between the level of functional abilities and QOL in children with intellectual disability. QI-Disability measured observable child behaviours which may reduce the influence of caregiver factors on the accurate measure of QOL for children with intellectual disability.
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46
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Milone R, Scalise R, Pasquariello R, Berloffa S, Ricca I, Battini R. De Novo 1q21.3q22 Duplication Revaluation in a "Cold" Complex Neuropsychiatric Case with Syndromic Intellectual Disability. Genes (Basel) 2021; 12:genes12040511. [PMID: 33807234 PMCID: PMC8066010 DOI: 10.3390/genes12040511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 11/26/2022] Open
Abstract
Syndromic intellectual disability often obtains a genetic diagnosis due to the combination of first and next generation sequencing techniques, although their interpretation may require revaluation over the years. Here we report on a composite neuropsychiatric case whose phenotype includes moderate intellectual disability, spastic paraparesis, movement disorder, and bipolar disorder, harboring a 1.802 Mb de novo 1q21.3q22 duplication. The role of this duplication has been reconsidered in the light of negativity of many other genetic exams, and of the possible pathogenic role of many genes included in this duplication, potentially configuring a contiguous gene-duplication syndrome.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Roberta Scalise
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Tuscan PhD Program of Neuroscience, University of Florence, Pisa and Siena, 50139 Florence, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Stefano Berloffa
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Ivana Ricca
- Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56125 Pisa, Italy
- Correspondence: ; Tel.: +39-050886229; Fax: +39-050886247
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Cao J, Xian W, Palihati M, Zhu Y, Wang G, Xie Y, Zhou G, You L. Deficiency of intellectual disability-related gene Brpf1 reduced inhibitory neurotransmission in MGE-derived GABAergic interneurons. G3-GENES GENOMES GENETICS 2021; 11:6179329. [PMID: 33744924 PMCID: PMC8496217 DOI: 10.1093/g3journal/jkab090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022]
Abstract
Intellectual disability is closely related to impaired GABA neurotransmission. Brpf1 was specifically expressed in medial ganglionic eminence (MGE), a developmental niche of GABAergic interneurons, and patients with BRPF1 mutations showed intellectual disability. To test its role in the development and function of MGE-derived GABAergic interneurons, we performed immunofluorescence staining, whole-cell patch-clamp, MGE transplantation, and mRNA-Seq to understand its effect on neuronal differentiation, dendritic morphology, electrophysiology, migration, and gene regulation, using mouse MGE-derived GABAergic interneurons infected with AAV-shBrpf1. The results showed that Brpf1 knockdown had a decreasing trend, although not significant, on the differentiation of GABAergic interneurons into parvalbumin+ interneurons. Moreover, increased firing threshold, decreased number of evoked action potentials, and a reduced amplitude of miniature inhibitory postsynaptic currents were observed before any significant change of MAP2+ dendritic morphology and in vivo migration ability appeared. Finally, mRNA-Seq analysis revealed that genes related to neurodevelopment and synaptic transmission such as Map2k7 were dysregulated. Our results demonstrated a key role of Brpf1 in inhibitory neurotransmission and related gene expression of GABAergic interneurons.
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Affiliation(s)
- Jingli Cao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Weiwei Xian
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Maierdan Palihati
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yu Zhu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Guoxiang Wang
- Institutes of Brain Sciences, Fudan University, Shanghai 200032, China
| | - Yunli Xie
- Institutes of Brain Sciences, Fudan University, Shanghai 200032, China
| | - Guomin Zhou
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.,Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai 200032, China
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.,Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai 200032, China
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48
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Yamada M, Ono M, Ishii T, Suzuki H, Uehara T, Takenouchi T, Kosaki K. Establishing intellectual disability as the key feature of patients with biallelic RNPC3 variants. Am J Med Genet A 2021; 185:1836-1840. [PMID: 33650182 DOI: 10.1002/ajmg.a.62152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 01/14/2023]
Abstract
Some mammalian genes contain both major and minor introns, the splicing of which require distinctive major and minor spliceosomes, respectively; these genes are referred to as minor intron containing-genes. RNPC3 (RNA-binding domain-containing protein 3) is one of the proteins that are unique to the minor spliceosome U11/U12 di-snRNP. Only two families with biallelic pathogenic variants in the RNPC3 gene encoding the protein have been reported so far, and the affected members in both families had proportional short stature. While the affected members of the originally identified family did not have intellectual disability, the patients from the other family exhibited intellectual disability. Here, we report on a patient with severe primordial microcephalic dwarfism and intellectual disability who carried compound heterozygous variants in RNPC3 (NM_017619.3): c.261dup, p.Leu88Thrfs*11 and c.1228T>G, p.Phe410Val. The single nucleotide substitution c.1228T>G had a very high predictive score for pathogenicity: the p.Phe410 residue is highly conserved down to fish. Based on ACMG (American College of Medical Genetics and Genomics) guideline, this non-synonymous variant was scored as likely pathogenic. This documentation of yet another patient with biallelic RNPC3 variants exhibiting intellectual disability lends further support to the notion that intellectual disability is a key feature of the spectrum of RNPC3-related disorders.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Masae Ono
- Department of Pediatrics, Tokyo Teishin Hospital, Tokyo, Japan
| | - Tomohiro Ishii
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.,Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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Cristancho AG, Marsh ED. Epigenetics modifiers: potential hub for understanding and treating neurodevelopmental disorders from hypoxic injury. J Neurodev Disord 2020; 12:37. [PMID: 33327934 PMCID: PMC7745506 DOI: 10.1186/s11689-020-09344-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The fetal brain is adapted to the hypoxic conditions present during normal in utero development. Relatively more hypoxic states, either chronic or acute, are pathologic and can lead to significant long-term neurodevelopmental sequelae. In utero hypoxic injury is associated with neonatal mortality and millions of lives lived with varying degrees of disability. MAIN BODY Genetic studies of children with neurodevelopmental disease indicate that epigenetic modifiers regulating DNA methylation and histone remodeling are critical for normal brain development. Epigenetic modifiers are also regulated by environmental stimuli, such as hypoxia. Indeed, epigenetic modifiers that are mutated in children with genetic neurodevelopmental diseases are regulated by hypoxia in a number of preclinical models and may be part of the mechanism for the long-term neurodevelopmental sequelae seem in children with hypoxic brain injury. Thus, a comprehensive understanding the role of DNA methylation and histone modifications in hypoxic injury is critical for developing novel strategies to treat children with hypoxic injury. CONCLUSIONS This review focuses on our current understanding of the intersection between epigenetics, brain development, and hypoxia. Opportunities for the use of epigenetics as biomarkers of neurodevelopmental disease after hypoxic injury and potential clinical epigenetics targets to improve outcomes after injury are also discussed. While there have been many published studies on the epigenetics of hypoxia, more are needed in the developing brain in order to determine which epigenetic pathways may be most important for mitigating the long-term consequences of hypoxic brain injury.
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Affiliation(s)
- Ana G Cristancho
- Departments of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
- Division of Child Neurology, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Eric D Marsh
- Departments of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA.
- Division of Child Neurology, Children's Hospital of Philadelphia, Philadelphia, USA.
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50
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Brunet M, Vargas C, Larrieu D, Torrisani J, Dufresne M. E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions. Int J Mol Sci 2020; 21:ijms21228515. [PMID: 33198194 PMCID: PMC7697007 DOI: 10.3390/ijms21228515] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
The Thyroid hormone Receptor Interacting Protein 12 (TRIP12) protein belongs to the 28-member Homologous to the E6-AP C-Terminus (HECT) E3 ubiquitin ligase family. First described as an interactor of the thyroid hormone receptor, TRIP12’s biological importance was revealed by the embryonic lethality of a murine model bearing an inactivating mutation in the TRIP12 gene. Further studies showed the participation of TRIP12 in the regulation of major biological processes such as cell cycle progression, DNA damage repair, chromatin remodeling, and cell differentiation by an ubiquitination-mediated degradation of key protein substrates. Moreover, alterations of TRIP12 expression have been reported in cancers that can serve as predictive markers of therapeutic response. The TRIP12 gene is also referenced as a causative gene associated to intellectual disorders such as Clark–Baraitser syndrome and is clearly implicated in Autism Spectrum Disorder. The aim of the review is to provide an exhaustive and integrated overview of the different aspects of TRIP12 ranging from its regulation, molecular functions and physio-pathological implications.
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Affiliation(s)
- Manon Brunet
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Claire Vargas
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Dorian Larrieu
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Jérôme Torrisani
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
| | - Marlène Dufresne
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
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