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Cheng SS, Mody AC, Woo CM. Opportunities for Therapeutic Modulation of O-GlcNAc. Chem Rev 2024; 124:12918-13019. [PMID: 39509538 DOI: 10.1021/acs.chemrev.4c00417] [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: 11/15/2024]
Abstract
O-Linked β-N-acetylglucosamine (O-GlcNAc) is an essential, dynamic monosaccharide post-translational modification (PTM) found on serine and threonine residues of thousands of nucleocytoplasmic proteins. The installation and removal of O-GlcNAc is controlled by a single pair of enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), respectively. Since its discovery four decades ago, O-GlcNAc has been found on diverse classes of proteins, playing important functional roles in many cellular processes. Dysregulation of O-GlcNAc homeostasis has been implicated in the pathogenesis of disease, including neurodegeneration, X-linked intellectual disability (XLID), cancer, diabetes, and immunological disorders. These foundational studies of O-GlcNAc in disease biology have motivated efforts to target O-GlcNAc therapeutically, with multiple clinical candidates under evaluation. In this review, we describe the characterization and biochemistry of OGT and OGA, cellular O-GlcNAc regulation, development of OGT and OGA inhibitors, O-GlcNAc in pathophysiology, clinical progress of O-GlcNAc modulators, and emerging opportunities for targeting O-GlcNAc. This comprehensive resource should motivate further study into O-GlcNAc function and inspire strategies for therapeutic modulation of O-GlcNAc.
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Affiliation(s)
- Steven S Cheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Alison C Mody
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Affiliate member of the Broad Institute, Cambridge, Massachusetts 02142, United States
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2
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Qin S, Zeng J, Wang J, Ye M, Deng Q, Wang X, Zhang Z, Yi D, Wu Y, Li-Ling J. Delineation of an inverted tandem Xq23-26.3 duplication in a female featuring extremely short stature and mild mental deficiency. Mol Cytogenet 2023; 16:33. [PMID: 38031145 PMCID: PMC10685508 DOI: 10.1186/s13039-023-00663-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Partial duplications involving the long arm of the X chromosome are associated with mental retardation, short stature, microcephaly, and a wide range of physical findings. Female carriers usually have no clinical phenotype. Occasionally, they may also have heterogeneous features due to non-random inactivation of the X chromosome. METHODS The peripheral blood sample was collected from the patient and subjected to a few genetic testing, including chromosomal karyotyping, Chromosomal microarray analysis (CMA), Optical genome mapping, short tandem repeat (STR) analysis for Determination of parental origin, and X chromosome inactivation (XCI) analysis. RESULTS We have identified a de novo Xq23-Xq26.3 duplication in an adult female featuring extremely short stature and mild mental deficiency. Chromosome analysis detected a duplication on Xq23-q26.3 with a size of approximately 20 Mb. The duplication region has encompassed a number of genes, among which ARHGEF6, PHF6, HPRT1 and SLC9A6 are associated with X-linked mental retardation. Further analysis suggested that the duplication has derived from her father, was of the inversion duplication type and involved various degrees of skewed X chromosome inactivation. CONCLUSION Correlation with her phenotypes might indicate new mechanisms by which the X chromosome may lead to short stature and mental retardation. Our findings thereby may shed more light on the phenotypic implication of functional disomy of X-chromosome genes.
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Affiliation(s)
- Shengfang Qin
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China.
| | - Jiuzhi Zeng
- West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Reproductive Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Jin Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Mengling Ye
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Qin Deng
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Xueyan Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Zhuo Zhang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Dangying Yi
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Yang Wu
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Jesse Li-Ling
- West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Department of Reproductive Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China.
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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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Santoso AD, De Ridder D. Fatty Acid Amide Hydrolase: An Integrative Clinical Perspective. Cannabis Cannabinoid Res 2023; 8:56-76. [PMID: 35900294 DOI: 10.1089/can.2021.0237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introduction: Fatty acid amide hydrolase (FAAH) is one of the main terminating enzymes of the endocannabinoid system (ECS). Since being discovered in 1996, the modulation of FAAH has been viewed as a compelling alternative strategy to obtain the beneficial effect of the ECS. With a considerable amount of FAAH-related publication over time, the next step would be to comprehend the proximity of this evidence for clinical application. Objective: This review intends to highlight the rationale of FAAH modulation and provide the latest evidence from clinical studies. Methods: Publication searches were conducted to gather information focused on FAAH-related clinical evidence with an extension to the experimental research to understand the biological plausibility. The subtopics were selected to be multidisciplinary to offer more perspective on the current state of the arts. Discussion: Experimental and clinical studies have demonstrated that FAAH was highly expressed not only in the central nervous system but also in the peripheral tissues. As the key regulator of endocannabinoid signaling, it would appear that FAAH plays a role in the modulation of mood and emotional response, reward system, pain perception, energy metabolism and appetite regulation, inflammation, and other biological processes. Genetic variants may be associated with some conditions such as substance/alcohol use disorders, obesity, and eating disorder. The advancement of functional neuroimaging has enabled the evaluation of the neurochemistry of FAAH in brain tissues and this can be incorporated into clinical trials. Intriguingly, the application of FAAH inhibitors in clinical trials seems to provide less striking results in comparison with the animal models, although some potential still can be seen. Conclusion: Modulation of FAAH has an immense potential to be a new therapeutic candidate for several disorders. Further exploration, however, is still needed to ensure who is the best candidate for the treatment strategy.
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Affiliation(s)
- Anugrah D Santoso
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Department of Urology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Dirk De Ridder
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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Azzarà A, Rumore R, Brugnoletti F, Tabolacci E, Bottillo I, Sangiorgi E, Gurrieri F. RADX Gene Variant May Predispose to Familial Asperger Syndrome. Genes (Basel) 2023; 14:301. [PMID: 36833228 PMCID: PMC9957148 DOI: 10.3390/genes14020301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/04/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Asperger syndrome (AS) is a pervasive developmental disorder characterized by general impairment in socialization, stereotypical behavior, defective adaptation to the social context usually without intellectual disability, and some high functioning areas related to memory and mathematics. Clinical criteria are not well defined and the etiology is heterogeneous and mostly unknown. Like in typical autism spectrum disorders (ASD), the genetic background plays a crucial role in AS, and often an almost mendelian segregation can be observed in some families. We performed a whole exome sequencing (WES) in three relatives of a family with vertical transmission of AS-ASD to identify variants in candidate genes segregating with the phenotype. Variant p.(Cys834Ser) in the RADX gene was the only one segregating among all the affected family members. This gene encodes a single-strand DNA binding factor, which mediates the recruitment of genome maintenance proteins to sites of replication stress. Replication stress and genome instability have been reported recently in neural progenitor cells derived from ASD patients, leading to a disruption of long neural genes involved in cell-cell adhesion and migration. We propose RADX as a new gene that when mutated could represent a predisposing factor to AS-ASD.
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Affiliation(s)
- Alessia Azzarà
- Research Unit of Medical Genetics, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Roberto Rumore
- Istituto di Medicina Genomica, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Fulvia Brugnoletti
- Oncogenetics Unit, Service of Oncology, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Elisabetta Tabolacci
- Istituto di Medicina Genomica, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Irene Bottillo
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, 00152 Rome, Italy
| | - Eugenio Sangiorgi
- Istituto di Medicina Genomica, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Fiorella Gurrieri
- Research Unit of Medical Genetics, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
- Operative Research Unit of Medical Genetics, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
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6
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Dobrigna M, Poëa-Guyon S, Rousseau V, Vincent A, Toutain A, Barnier JV. The molecular basis of p21-activated kinase-associated neurodevelopmental disorders: From genotype to phenotype. Front Neurosci 2023; 17:1123784. [PMID: 36937657 PMCID: PMC10017488 DOI: 10.3389/fnins.2023.1123784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Although the identification of numerous genes involved in neurodevelopmental disorders (NDDs) has reshaped our understanding of their etiology, there are still major obstacles in the way of developing therapeutic solutions for intellectual disability (ID) and other NDDs. These include extensive clinical and genetic heterogeneity, rarity of recurrent pathogenic variants, and comorbidity with other psychiatric traits. Moreover, a large intragenic mutational landscape is at play in some NDDs, leading to a broad range of clinical symptoms. Such diversity of symptoms is due to the different effects DNA variations have on protein functions and their impacts on downstream biological processes. The type of functional alterations, such as loss or gain of function, and interference with signaling pathways, has yet to be correlated with clinical symptoms for most genes. This review aims at discussing our current understanding of how the molecular changes of group I p21-activated kinases (PAK1, 2 and 3), which are essential actors of brain development and function; contribute to a broad clinical spectrum of NDDs. Identifying differences in PAK structure, regulation and spatio-temporal expression may help understanding the specific functions of each group I PAK. Deciphering how each variation type affects these parameters will help uncover the mechanisms underlying mutation pathogenicity. This is a prerequisite for the development of personalized therapeutic approaches.
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Affiliation(s)
- Manon Dobrigna
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Sandrine Poëa-Guyon
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Véronique Rousseau
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Aline Vincent
- Department of Genetics, EA7450 BioTARGen, University Hospital of Caen, Caen, France
| | - Annick Toutain
- Department of Genetics, University Hospital of Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Jean-Vianney Barnier
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
- *Correspondence: Jean-Vianney Barnier,
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Characterization of a mGluR5 Knockout Rat Model with Hallmarks of Fragile X Syndrome. Life (Basel) 2022; 12:life12091308. [PMID: 36143345 PMCID: PMC9504063 DOI: 10.3390/life12091308] [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: 06/30/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The number of reported cases of neurodevelopmental disorders has increased significantly in the last few decades, but the etiology of these diseases remains poorly understood. There is evidence of a fundamental link between genetic abnormalities and symptoms of autism spectrum disorders (ASDs), and the most common monogenetic inheritable form of ASDs is Fragile X Syndrome (FXS). Previous studies indicate that FXS is linked to glutamate signaling regulation by the G-protein-coupled metabotropic glutamate receptor 5 (mGluR5), which has been shown to have a regulatory role in neuroinflammation. We characterized the effect of knocking out mGluR5 in an organism known to have complex cognitive functions—the rat. The heterozygous phenotype is the most clinically relevant; therefore, we performed analysis in heterozygous pups. We showed developmental abnormalities in heterozygous mGluR5 knockout rats, as well as a significant increase in chemokine (C-X-C motif) ligand 1 (CXCL) expression, a hallmark indicator of early onset inflammation. We quantified an increase in microglial density in the knockout pups and quantified morphological phenotypes representative of greater reactivity in the male vs. female and postnatal day 28 heterozygous pups compared to postnatal day 14 heterozygous pups. In response to injury, reactive microglia release matrix metalloproteases, contribute to extracellular matrix (ECM) breakdown, and are responsible for eradicating cellular and molecular debris. In our study, the changes in microglial density and reactivity correlated with abnormalities in the mRNA expression levels of ECM proteins and with the density of perineuronal nets. We saw atypical neuropsychiatric behavior in open field and elevated plus tests in heterozygous pups compared to wild-type litter and age-matched controls. These results demonstrate the pathological potential of the mGluR5 knockout in rats and further support the presence of neuroinflammatory roots in ASDs.
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SLITRK2 variants associated with neurodevelopmental disorders impair excitatory synaptic function and cognition in mice. Nat Commun 2022; 13:4112. [PMID: 35840571 PMCID: PMC9287327 DOI: 10.1038/s41467-022-31566-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
SLITRK2 is a single-pass transmembrane protein expressed at postsynaptic neurons that regulates neurite outgrowth and excitatory synapse maintenance. In the present study, we report on rare variants (one nonsense and six missense variants) in SLITRK2 on the X chromosome identified by exome sequencing in individuals with neurodevelopmental disorders. Functional studies showed that some variants displayed impaired membrane transport and impaired excitatory synapse-promoting effects. Strikingly, these variations abolished the ability of SLITRK2 wild-type to reduce the levels of the receptor tyrosine kinase TrkB in neurons. Moreover, Slitrk2 conditional knockout mice exhibited impaired long-term memory and abnormal gait, recapitulating a subset of clinical features of patients with SLITRK2 variants. Furthermore, impaired excitatory synapse maintenance induced by hippocampal CA1-specific cKO of Slitrk2 caused abnormalities in spatial reference memory. Collectively, these data suggest that SLITRK2 is involved in X-linked neurodevelopmental disorders that are caused by perturbation of diverse facets of SLITRK2 function.
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Functional validation of variants of unknown significance using CRISPR gene editing and transcriptomics: A Kleefstra syndrome case study. Gene X 2022; 821:146287. [PMID: 35176430 DOI: 10.1016/j.gene.2022.146287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
There are an estimated > 400 million people living with a rare disease globally, with genetic variants the cause of approximately 80% of cases. Next Generation Sequencing (NGS) rapidly identifies genetic variants however they are often of unknown significance. Low throughput functional validation in specialist laboratories is the current ad hoc approach for functional validation of genetic variants, which creating major bottlenecks in patient diagnosis. This study investigates the application of CRISPR gene editing followed by genome wide transcriptomic profiling to facilitate patient diagnosis. As proof-of-concept, we introduced a variant in the Euchromatin histone methyl transferase (EHMT1) gene into HEK293T cells. We identified changes in the regulation of the cell cycle, neural gene expression and suppression of gene expression changes on chromosome 19 and chromosome X, that are in keeping with Kleefstra syndrome clinical phenotype and/or provide insight into disease mechanism. This study demonstrates the utility of genome editing followed by functional readouts to rapidly and systematically validating the function of variants of unknown significance in patients suffering from rare diseases.
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Cokyaman T, Silan F. Diagnostic Utility of Array Comparative Genomic Hybridization in Children with Neurological Diseases. Fetal Pediatr Pathol 2022; 41:68-76. [PMID: 32401632 DOI: 10.1080/15513815.2020.1764683] [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] [Indexed: 10/24/2022]
Abstract
INTRODUCTION We evaluated the contribution of array comparative genomic hybridization (aCGH) to the final diagnosis in children with neurocognitive disturbances or dysmorphic findings, but lacked a specific diagnosis. MATERIALS AND METHODS Medical files of pediatric patients with neurocognitive disturbances who underwent aCGH analysis were reviewed retrospectively. RESULTS Of 155 patients, 77 copy number variations were detected and 50% (39/77) were considered causative. The aCGH's final diagnostic rate was 25.1% (39/155). CONCLUSION With aCGH analysis, the diagnosis rate for patients with undiagnosed neurocognitive disturbances or dysmorphic syndrome may increase by 25-30%. If the phenotypic findings of the widely known neurocognitive disturbances cannot be identified during the initial clinical assessment, aCGH analysis may be beneficial.
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Affiliation(s)
- Turgay Cokyaman
- Pediatric Neurology, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Fatma Silan
- Medical Genetics, Faculty of Medicine, Çanakkale Onsekiz Mart University, Canakkale, Turkey
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11
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Qiu T, Dai Q, Wang Q. A novel de novo hemizygous ARHGEF9 mutation associated with severe intellectual disability and epilepsy: a case report. J Int Med Res 2021; 49:3000605211058372. [PMID: 34851771 PMCID: PMC8647271 DOI: 10.1177/03000605211058372] [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: 12/05/2022] Open
Abstract
ARHGEF9 encodes collybistin, a brain-specific guanosine diphosphate-guanosine-5′-triphosphate exchange factor that plays an important role in clustering of gephyrin and γ-aminobutyric acid type A receptors in the postsynaptic membrane. Overwhelming evidence suggests that defects in this protein can cause X-linked intellectual disability, which comprises a series of clinical phenotypes, including autism spectrum disorder, behavior disorder, intellectual disability, and febrile seizures. Here, we report a boy with clinical symptoms of severe intellectual disability, epilepsy, and developmental delay and regression. Trio exome sequencing (trio-clinical exome sequencing) identified a novel hemizygous deletion, c.656_c.669delACTTCTTTGAGGCC (p. His219Leu fs*9), in exon 5 of ARHGEF9. This variant was not reported in either the Genome Aggregation Database or our database of 309 patients with neurodevelopmental disorders. Oxcarbazepine and levetiracetam reduced the frequency of the patient’s epileptic seizures to a certain extent, but psychomotor developmental delay and developmental regression became more obvious with age. This case study seeks to report a de novo loss-of-function mutation of ARHGEF9, aiming to emphasize the genetic diagnosis of X-linked intellectual disability and further improve knowledge of the ethnic distribution of ARHGEF9 mutations.
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Affiliation(s)
- Tong Qiu
- Division of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Qian Dai
- Division of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Qiu Wang
- Division of Rehabilitation Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
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Biesecker LG, Green ED, Manolio T, Solomon BD, Curtis D. Should all babies have their genome sequenced at birth? BMJ 2021; 375:n2679. [PMID: 34789511 DOI: 10.1136/bmj.n2679] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Eric D Green
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Teri Manolio
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | - David Curtis
- UCL Genetics Institute, University College London, UK
- Centre for Psychiatry, Queen Mary University of London, UK
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Simonetti L, Ferreira LGA, Vidi AC, de Souza JS, Kunii IS, Melaragno MI, de Mello CB, Carvalheira G, Dias da Silva MR. Intelligence Quotient Variability in Klinefelter Syndrome Is Associated With GTPBP6 Expression Under Regulation of X-Chromosome Inactivation Pattern. Front Genet 2021; 12:724625. [PMID: 34616429 PMCID: PMC8488338 DOI: 10.3389/fgene.2021.724625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022] Open
Abstract
Klinefelter syndrome (KS) displays a broad dysmorphological, endocrinological, and neuropsychological clinical spectrum. We hypothesized that the neurocognitive dysfunction present in KS relies on an imbalance in X-chromosome gene expression. Thus, the X-chromosome inactivation (XCI) pattern and neurocognitive X-linked gene expression were tested and correlated with intelligence quotient (IQ) scores. We evaluated 11 KS patients by (a) IQ assessment, (b) analyzing the XCI patterns using both HUMARA and ZDHHC15 gene assays, and (c) blood RT-qPCR to investigate seven X-linked genes related to neurocognitive development (GTPBP6, EIF2S3, ITM2A, HUWE1, KDM5C, GDI1, and VAMP7) and XIST in comparison with 14 (male and female) controls. Considering IQ 80 as the standard minimum reference, we verified that the variability in IQ scores in KS patients seemed to be associated with the XCI pattern. Seven individuals in the KS group presented a random X-inactivation (RXI) and lower average IQ than the four individuals who presented a skewed X-inactivation (SXI) pattern. The evaluation of gene expression showed higher GTPBP6 expression in KS patients with RXI than in controls (p = 0.0059). Interestingly, the expression of GTPBP6 in KS patients with SXI did not differ from that observed in controls. Therefore, our data suggest for the first time that GTPBP6 expression is negatively associated with full-scale IQ under the regulation of the type of XCI pattern. The SXI pattern may regulate GTPBP6 expression, thereby dampening the impairment in cognitive performance and playing a role in intelligence variability in individuals with KS, which warrants further mechanistic investigations.
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Affiliation(s)
- Luciane Simonetti
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Lucas G A Ferreira
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Angela Cristina Vidi
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Janaina Sena de Souza
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ilda S Kunii
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Claudia Berlim de Mello
- Department of Psychobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gianna Carvalheira
- Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Magnus R Dias da Silva
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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14
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Tegtmeyer M, Nehme R. Leveraging the Genetic Diversity of Human Stem Cells in Therapeutic Approaches. J Mol Biol 2021; 434:167221. [PMID: 34474087 DOI: 10.1016/j.jmb.2021.167221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 01/14/2023]
Abstract
Since their discovery 15 years ago, human pluripotent stem cell (hPSC) technologies have begun to revolutionize science and medicine, rapidly expanding beyond investigative research to drug discovery and development. Efforts to leverage hPSCs over the last decade have focused on increasing both the complexity and in vivo fidelity of human cellular models through enhanced differentiation methods. While these evolutions have fostered novel insights into disease mechanisms and influenced clinical drug discovery and development, there are still several considerations that limit the utility of hPSC models. In this review, we highlight important, yet underexplored avenues to broaden their reach. We focus on (i) the importance of diversifying existing hPSC collections, and their utilization to investigate therapeutic strategies in individuals from different genetic backgrounds, ancestry and sex; (ii) considerations for the selection of therapeutically relevant hPSC-based models; (iii) strategies to adequately increase the scale of cell-based studies; and (iv) the advances and constraints of clinical trials in a dish. Moreover, we advocate for harnessing the translational capabilities of hPSC models along with the use of innovative, scalable approaches for understanding genetic biases and the impact of sex and ancestry on disease mechanisms and drug efficacy and response. The next decade of hPSC innovation is poised to provide vast insights into the genetic basis of human disease and enable rapid advances to develop, repurpose, and ensure the safety of the next generation of disease therapies across diverse human populations.
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Affiliation(s)
- Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Centre for Stem Cells and Regenerative Medicine, King's College London, London, UK
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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15
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de Castro Fonseca M, de Oliveira JF, Araujo BHS, Canateli C, do Prado PFV, Amorim Neto DP, Bosque BP, Rodrigues PV, de Godoy JVP, Tostes K, Filho HVR, Nascimento AFZ, Saito A, Tonoli CCC, Batista FAH, de Oliveira PSL, Figueira AC, Souza da Costa S, Krepischi ACV, Rosenberg C, Westfahl H, da Silva AJR, Franchini KG. Molecular and cellular basis of hyperassembly and protein aggregation driven by a rare pathogenic mutation in DDX3X. iScience 2021; 24:102841. [PMID: 34381968 PMCID: PMC8335631 DOI: 10.1016/j.isci.2021.102841] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 12/30/2022] Open
Abstract
Current studies estimate that 1–3% of females with unexplained intellectual disability (ID) present de novo splice site, nonsense, frameshift, or missense mutations in the DDX3X protein (DEAD-Box Helicase 3 X-Linked). However, the cellular and molecular mechanisms by which DDX3X mutations impair brain development are not fully comprehended. Here, we show that the ID-linked missense mutation L556S renders DDX3X prone to aggregation. By using a combination of biophysical assays and imaging approaches, we demonstrate that this mutant assembles solid-like condensates and amyloid-like fibrils. Although we observed greatly reduced expression of the mutant allele in a patient who exhibits skewed X inactivation, this appears to be enough to sequestrate healthy proteins into solid-like ectopic granules, compromising cell function. Therefore, our data suggest ID-linked DDX3X L556S mutation as a disorder arising from protein misfolding and aggregation. DDX3X mutations skew X-inactivation and are found in 1-3% of unexplained ID in females DDX3X mutant proteins assemble solid-like condensates and amyloid-like fibrils Aberrant granules formed by DDX3X mutants sequestrate healthy DDX3X protein ID-linked DDX3X L556S mutation decreases cell viability and induces apoptosis
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Affiliation(s)
- Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Juliana Ferreira de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Bruno Henrique Silva Araujo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Camila Canateli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paula Favoretti Vital do Prado
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Dionísio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Andrey Fabricio Ziem Nascimento
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Angela Saito
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Fernanda Aparecida Heleno Batista
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Ana Carolina Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Harry Westfahl
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antônio José Roque da Silva
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil
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16
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Piergiorge RM, de Vasconcelos ATR, Gonçalves Pimentel MM, Santos-Rebouças CB. Strict network analysis of evolutionary conserved and brain-expressed genes reveals new putative candidates implicated in Intellectual Disability and in Global Development Delay. World J Biol Psychiatry 2021; 22:435-445. [PMID: 32914658 DOI: 10.1080/15622975.2020.1821916] [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: 01/14/2023]
Abstract
OBJECTIVES Intellectual Disability (ID) and Global Development Delay (GDD) are frequent reasons for referral to genetic services and although they present overlapping phenotypes concerning cognitive, motor, language, or social skills, they are not exactly synonymous. Aiming to better understand independent or shared mechanisms related to these conditions and to identify new candidate genes, we performed a highly stringent protein-protein interaction network based on genes previously related to ID/GDD in the Human Phenotype Ontology portal. METHODS ID/GDD genes were searched for reliable interactions through STRING and clustering analysis was applied to detect biological complexes through the MCL algorithm. Six coding hub genes (TP53, CDC42, RAC1, GNB1, APP, and EP300) were recognised by the Cytoscape NetworkAnalyzer plugin, interacting with 1625 proteins not yet associated with ID or GDD. Genes encoding these proteins were explored by gene ontology, associated diseases, evolutionary conservation, and brain expression. RESULTS One hundred and seventy-two new putative genes playing a role in enriched processes/pathways previously related to ID and GDD were revealed, some of which were already postulated to be linked to ID/GDD in additional databases. CONCLUSIONS Our findings expanded the aetiological genetic landscape of ID/GDD and showed evidence that both conditions are closely related at the molecular and functional levels.
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Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Márcia Mattos Gonçalves Pimentel
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
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17
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Pan X, Zhao J, Zhou Z, Chen J, Yang Z, Wu Y, Bai M, Jiao Y, Yang Y, Hu X, Cheng T, Lu Q, Wang B, Li CL, Lu YJ, Diao L, Zhong YQ, Pan J, Zhu J, Xiao HS, Qiu ZL, Li J, Wang Z, Hui J, Bao L, Zhang X. 5'-UTR SNP of FGF13 causes translational defect and intellectual disability. eLife 2021; 10:63021. [PMID: 34184986 PMCID: PMC8241442 DOI: 10.7554/elife.63021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 06/17/2021] [Indexed: 12/15/2022] Open
Abstract
The congenital intellectual disability (ID)-causing gene mutations remain largely unclear, although many genetic variations might relate to ID. We screened gene mutations in Chinese Han children suffering from severe ID and found a single-nucleotide polymorphism (SNP) in the 5′-untranslated region (5′-UTR) of fibroblast growth factor 13 (FGF13) mRNA (NM_001139500.1:c.-32c>G) shared by three male children. In both HEK293 cells and patient-derived induced pluripotent stem cells, this SNP reduced the translation of FGF13, which stabilizes microtubules in developing neurons. Mice carrying the homologous point mutation in 5′-UTR of Fgf13 showed delayed neuronal migration during cortical development, and weakened learning and memory. Furthermore, this SNP reduced the interaction between FGF13 5′-UTR and polypyrimidine-tract-binding protein 2 (PTBP2), which was required for FGF13 translation in cortical neurons. Thus, this 5′-UTR SNP of FGF13 interferes with the translational process of FGF13 and causes deficits in brain development and cognitive functions.
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Affiliation(s)
- Xingyu Pan
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Brain-Intelligence Project Center, Shanghai, China
| | - Jingrong Zhao
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhiying Zhou
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Jijun Chen
- Shanghai Brain-Intelligence Project Center, Shanghai, China
| | - Zhenxing Yang
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Yuxuan Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Meizhu Bai
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yang Jiao
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Yun Yang
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xuye Hu
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Tianling Cheng
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qianyun Lu
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Bin Wang
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Chang-Lin Li
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Ying-Jin Lu
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Lei Diao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Qing Zhong
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Pan
- Shanghai Brain-Intelligence Project Center, Shanghai, China
| | - Jianmin Zhu
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Hua-Sheng Xiao
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Zi-Long Qiu
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zefeng Wang
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Xu Zhang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
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18
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Wilson HA, Creighton C, Scharfman H, Choleris E, MacLusky NJ. Endocrine Insights into the Pathophysiology of Autism Spectrum Disorder. Neuroscientist 2020; 27:650-667. [PMID: 32912048 DOI: 10.1177/1073858420952046] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Autism spectrum disorder (ASD) is a class of neurodevelopmental disorders that affects males more frequently than females. Numerous genetic and environmental risk factors have been suggested to contribute to the development of ASD. However, no one factor can adequately explain either the frequency of the disorder or the male bias in its prevalence. Gonadal, thyroid, and glucocorticoid hormones all contribute to normal development of the brain, hence perturbations in either their patterns of secretion or their actions may constitute risk factors for ASD. Environmental factors may contribute to ASD etiology by influencing the development of neuroendocrine and neuroimmune systems during early life. Emerging evidence suggests that the placenta may be particularly important as a mediator of the actions of environmental and endocrine risk factors on the developing brain, with the male being particularly sensitive to these effects. Understanding how various risk factors integrate to influence neural development may facilitate a clearer understanding of the etiology of ASD.
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Affiliation(s)
- Hayley A Wilson
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Carolyn Creighton
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Helen Scharfman
- Departments of Child & Adolescent Psychiatry, Neuroscience & Physiology, and Psychiatry, New York University Langone Health, New York, NY, USA.,Center for Dementia Research, The Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - Elena Choleris
- Department of Psychology, University of Guelph, Guelph, Ontario, Canada
| | - Neil J MacLusky
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
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19
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Glasson EJ, Buckley N, Chen W, Leonard H, Epstein A, Skoss R, Jacoby P, Blackmore AM, Bourke J, Downs J. Systematic Review and Meta-analysis: Mental Health in Children With Neurogenetic Disorders Associated With Intellectual Disability. J Am Acad Child Adolesc Psychiatry 2020; 59:1036-1048. [PMID: 31945412 DOI: 10.1016/j.jaac.2020.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/11/2019] [Accepted: 01/08/2020] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The behavioral phenotype of neurogenetic disorders associated with intellectual disability often includes psychiatric comorbidity. The objectives of this systematic review and meta-analysis were to systematically review the prevalence of psychiatric disorders and symptoms in children and adolescents with these disorders and compare phenotypic signatures between syndromes. METHOD MEDLINE and PsycINFO databases were searched for articles from study inception to December 2018. Eligible articles were peer reviewed, were published in English, and reported prevalence data for psychiatric disorders and symptoms in children and adolescents aged 4 to 21 years using a formal psychiatric assessment or a standardized assessment of mental health symptoms. Pooled prevalence was determined using a random-effects meta-analysis in studies with sufficient data. Prevalence estimates were compared with general population data using a test of binomial proportions. RESULTS Of 2,301 studies identified for review, 39 articles were included in the final pool, which provided data on 4,039 children and adolescents. Ten syndromes were represented, and five were predominant: Down syndrome, 22q11.2 deletion syndrome, fragile X syndrome, Williams syndrome, and Prader-Willi syndrome. The Child Behavior Checklist was the most commonly used assessment tool for psychiatric symptoms. The pooled prevalence with total scores above the clinical threshold was lowest for Down syndrome (32% [95% confidence interval, 19%-44%]) and highest for Prader-Willi syndrome (74% [95% CI, 65%-82%]) with each syndrome associated with significantly higher prevalence than in the general population. Parallel trends were observed for the internalizing and externalizing domains and social subscale scores. CONCLUSION Differential vulnerability for psychiatric phenotype expression across the disorders was observed. Syndromes with higher levels of social ability or competence appear to offer relative protection against developing psychopathology. This preliminary finding merits further exploration.
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Affiliation(s)
- Emma J Glasson
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Nicholas Buckley
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Wai Chen
- Complex Attention and Hyperactivity Disorders Service, Perth, Australia; and the Centre and Discipline of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, The University of Western Australia, Perth, Australia
| | - Helen Leonard
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Amy Epstein
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Rachel Skoss
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Peter Jacoby
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | | | - Jenny Bourke
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Jenny Downs
- Telethon Kids Institute, The University of Western Australia, Perth, Australia; School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia.
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20
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Turkmen AS, Lin S. Detecting X-linked common and rare variant effects in family-based sequencing studies. Genet Epidemiol 2020; 45:36-45. [PMID: 32864779 DOI: 10.1002/gepi.22352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/26/2020] [Accepted: 08/03/2020] [Indexed: 11/08/2022]
Abstract
The breakthroughs in next generation sequencing have allowed us to access data consisting of both common and rare variants, and in particular to investigate the impact of rare genetic variation on complex diseases. Although rare genetic variants are thought to be important components in explaining genetic mechanisms of many diseases, discovering these variants remains challenging, and most studies are restricted to population-based designs. Further, despite the shift in the field of genome-wide association studies (GWAS) towards studying rare variants due to the "missing heritability" phenomenon, little is known about rare X-linked variants associated with complex diseases. For instance, there is evidence that X-linked genes are highly involved in brain development and cognition when compared with autosomal genes; however, like most GWAS for other complex traits, previous GWAS for mental diseases have provided poor resources to deal with identification of rare variant associations on X-chromosome. In this paper, we address the two issues described above by proposing a method that can be used to test X-linked variants using sequencing data on families. Our method is much more general than existing methods, as it can be applied to detect both common and rare variants, and is applicable to autosomes as well. Our simulation study shows that the method is efficient, and exhibits good operational characteristics. An application to the University of Miami Study on Genetics of Autism and Related Disorders also yielded encouraging results.
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Affiliation(s)
- Asuman S Turkmen
- Statistics Department, The Ohio State University, Columbus, Ohio.,Statistics Department, The Ohio State University, Newark, Ohio
| | - Shili Lin
- Statistics Department, The Ohio State University, Columbus, Ohio
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21
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Mehvari S, Larti F, Hu H, Fattahi Z, Beheshtian M, Abedini SS, Arzhangi S, Ropers HH, Kalscheuer VM, Auld D, Kahrizi K, Riazalhosseini Y, Najmabadi H. Whole genome sequencing identifies a duplicated region encompassing Xq13.2q13.3 in a large Iranian family with intellectual disability. Mol Genet Genomic Med 2020; 8:e1418. [PMID: 32715656 PMCID: PMC7549592 DOI: 10.1002/mgg3.1418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/16/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
Background The X chromosome has historically been one of the most thoroughly investigated chromosomes regarding intellectual disability (ID), whose etiology is attributed to many factors including copy number variations (CNVs). Duplications of the long arm of the X chromosome have been reported in patients with ID, short stature, facial anomalies, and in many cases hypoplastic genitalia and/or behavioral abnormalities. Methods Here, we report on a large Iranian family with X‐linked ID caused by a duplication on the X chromosome identified by whole genome sequencing in combination with linkage analysis. Results Seven affected males in different branches of the family presented with ID, short stature, seizures, facial anomalies, behavioral abnormalities (aggressiveness, self‐injury, anxiety, impaired social interactions, and shyness), speech impairment, and micropenis. The duplication of the region Xq13.2q13.3, which is ~1.8 Mb in size, includes seven protein‐coding OMIM genes. Three of these genes, namely SLC16A2, RLIM, and NEXMIF, if impaired, can lead to syndromes presenting with ID. Of note, this duplicated region was located within a linkage interval with a LOD score >3. Conclusion Our report indicates that CNVs should be considered in multi‐affected families where no candidate gene defect has been identified in sequencing data analysis.
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Affiliation(s)
- Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hao Hu
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Islamic Republic of Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Islamic Republic of Iran
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hans-Hilger Ropers
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University Medicine, Mainz, Germany
| | | | - Daniel Auld
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, Montreal, Quebec, Canada
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, Montreal, Quebec, Canada
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Islamic Republic of Iran
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22
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Van Dijck A, Barbosa S, Bermudez-Martin P, Khalfallah O, Gilet C, Martinuzzi E, Elinck E, Kooy RF, Glaichenhaus N, Davidovic L. Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome. BMC Neurol 2020; 20:138. [PMID: 32295518 PMCID: PMC7161166 DOI: 10.1186/s12883-020-01715-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/01/2020] [Indexed: 12/20/2022] Open
Abstract
Background Fragile X syndrome (FXS) is the most frequent cause of inherited intellectual disability and the most commonly identified monogenic cause of autism. Recent studies have shown that long-term pathological consequences of FXS are not solely confined to the central nervous system (CNS) but rather extend to other physiological dysfunctions in peripheral organs. To gain insights into possible immune dysfunctions in FXS, we profiled a large panel of immune-related biomarkers in the serum of FXS patients and healthy controls. Methods We have used a sensitive and robust Electro Chemi Luminescence (ECL)-based immunoassay to measure the levels of 52 cytokines in the serum of n = 25 FXS patients and n = 29 healthy controls. We then used univariate statistics and multivariate analysis, as well as an advanced unsupervised clustering method, to identify combinations of immune-related biomarkers that could discriminate FXS patients from healthy individuals. Results While the majority of the tested cytokines were present at similar levels in FXS patients and healthy individuals, nine chemokines, CCL2, CCL3, CCL4, CCL11, CCL13, CCL17, CCL22, CCL26 and CXCL10, were present at much lower levels in FXS patients. Using robust regression, we show that six of these biomarkers (CCL2, CCL3, CCL11, CCL22, CCL26 and CXCL10) were negatively associated with FXS diagnosis. Finally, applying the K-sparse unsupervised clustering method to the biomarker dataset allowed for the identification of two subsets of individuals, which essentially matched the FXS and healthy control categories. Conclusions Our data show that FXS patients exhibit reduced serum levels of several chemokines and may therefore exhibit impaired immune responses. The present study also highlights the power of unsupervised clustering methods to identify combinations of biomarkers for diagnosis and prognosis in medicine.
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Affiliation(s)
- Anke Van Dijck
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
| | - Susana Barbosa
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Patricia Bermudez-Martin
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Olfa Khalfallah
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Cyprien Gilet
- Université Côte d'Azur, CNRS, Laboratoire Informatique Signaux et Systèmes de Sophia Antipolis, Valbonne, France
| | - Emanuela Martinuzzi
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Ellen Elinck
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
| | - Nicolas Glaichenhaus
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Laetitia Davidovic
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.
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23
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Wang Y, Zhu LN, Ma XW, Yang F, Xu XL, Yang Y, Yang X, Peng W, Zhang WQ, Liang JY, Zhu WD, Jiang TJ, Zhang XL, Feng ZC. Gene-Focused Networks Underlying Phenotypic Convergence in a Systematically Phenotyped Cohort With Heterogeneous Intellectual Disability. Front Bioeng Biotechnol 2020; 8:45. [PMID: 32117926 PMCID: PMC7019181 DOI: 10.3389/fbioe.2020.00045] [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: 11/18/2019] [Accepted: 01/21/2020] [Indexed: 11/13/2022] Open
Abstract
The broad spectrum of intellectual disability (ID) patients' clinical manifestations, the heterogeneity of ID genetic variation, and the diversity of the phenotypic variation represent major challenges for ID diagnosis. By exploiting a manually curated systematic phenotyping cohort of 3803 patients harboring ID, we identified 704 pathogenic genes, 3848 pathogenic sites, and 2075 standard phenotypes for underlying molecular perturbations and their phenotypic impact. We found the positive correlation between the number of phenotypes and that of patients that revealed their extreme heterogeneities, and the relative contribution of multiple determinants to the heterogeneity of ID phenotypes. Nevertheless, despite the extreme heterogeneity in phenotypes, the ID genes had a specific bias of mutation types, and the top 44 genes that ranked by the number of patients accounted for 39.9% of total patients. More interesting, enriched co-occurrent phenotypes and co-occurrent phenotype networks for each gene had the potential for prioritizing ID genes, further exhibited the convergences of ID phenotypes. Then we established a predictor called IDpred using machine learning methods for ID pathogenic genes prediction. Using10-fold cross-validation, our evaluation shows remarkable AUC values for IDpred (auc = 0.978), demonstrating the robustness and reliability of our tool. Besides, we built the most comprehensive database of ID phenotyped cohort to date: IDminer http://218.4.234.74:3100/IDminer/, which included the curated ID data and integrated IDpred tool for both clinical and experimental researchers. The IDminer serves as an important resource and user-friendly interface to help researchers investigate ID data, and provide important implications for the diagnosis and pathogenesis of developmental disorders of cognition.
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Affiliation(s)
- Yan Wang
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Li-Na Zhu
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Xiu-Wei Ma
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Fang Yang
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
| | - Xi-Lin Xu
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
| | - Yao Yang
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Xiao Yang
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Wei Peng
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Wan-Qiao Zhang
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Jin-Yu Liang
- The Second People’s Hospital of Aohanqi, Inner Mongolia, China
| | - Wei-Dong Zhu
- The Second People’s Hospital of Aohanqi, Inner Mongolia, China
| | - Tai-Jiao Jiang
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xin-Lei Zhang
- Suzhou Geneworks Technology Co., Ltd., Suzhou, China
| | - Zhi-Chun Feng
- BaYi Children’s Hospital, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
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24
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Abstract
Sex differences in the incidence or severity of disease characterize many autoimmune and neurodegenerative diseases. Multiple sclerosis is a complex disease with both autoimmune and neurodegenerative aspects and is characterized by sex differences in susceptibility and progression. Research in the study sex differences is a way to capitalize on a known clinical observation, mechanistically disentangle it at the laboratory bench, then translate basic research findings back to the clinic as a novel treatment trial tailored to optimally benefit each sex. This "Bedside to Bench to Bedside" approach based on sex differences in MS will be reviewed here, first for disease susceptibility then for disability progression.
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Affiliation(s)
- Rhonda R Voskuhl
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
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25
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Tejada MI, Ibarluzea N. Non-syndromic X linked intellectual disability: Current knowledge in light of the recent advances in molecular and functional studies. Clin Genet 2020; 97:677-687. [PMID: 31898314 DOI: 10.1111/cge.13698] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/09/2019] [Accepted: 12/24/2019] [Indexed: 12/23/2022]
Abstract
Since the discovery of the FMR1 gene and the clinical and molecular characterization of Fragile X Syndrome in 1991, more than 141 genes have been identified in the X-chromosome in these 28 years thanks to applying continuously evolving molecular techniques to X-linked intellectual disability (XLID) families. In the past decade, array comparative genomic hybridization and next generation sequencing technologies have accelerated gene discovery exponentially. Classically, XLID has been subdivided in syndromic intellectual disability (S-XLID)-where intellectual disability (ID) is always associated with other recognizable physical and/or neurological features-and non-specific or non-syndromic intellectual disability (NS-XLID) where the only common feature is ID. Nevertheless, new advances on the study of these entities have showed that this classification is not always clear-cut because distinct variants in several of these XLID genes can result in S-XLID as well as in NS-XLID. This review focuses on the current knowledge on the XLID genes involved in non-syndromic forms, with the emphasis on their pathogenic mechanism, thus allowing the possibility to elucidate why some of them can give both syndromic and non-syndromic phenotypes.
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Affiliation(s)
- María Isabel Tejada
- Genetics Service, Cruces University Hospital, Osakidetza Basque Health Service, Barakaldo, Spain.,Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Nekane Ibarluzea
- Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
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26
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Jackson MR, Loring KE, Homan CC, Thai MH, Määttänen L, Arvio M, Jarvela I, Shaw M, Gardner A, Gecz J, Shoubridge C. Heterozygous loss of function of IQSEC2/ Iqsec2 leads to increased activated Arf6 and severe neurocognitive seizure phenotype in females. Life Sci Alliance 2019; 2:2/4/e201900386. [PMID: 31439632 PMCID: PMC6706959 DOI: 10.26508/lsa.201900386] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/25/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
Clinical presentations of mutations in the IQSEC2 gene on the X-chromosome initially implicated to cause non-syndromic intellectual disability (ID) in males have expanded to include early onset seizures in males as well as in females. The molecular pathogenesis is not well understood, nor the mechanisms driving disease expression in heterozygous females. Using a CRISPR/Cas9-edited Iqsec2 KO mouse model, we confirm the loss of Iqsec2 mRNA expression and lack of Iqsec2 protein within the brain of both founder and progeny mice. Both male (52%) and female (46%) Iqsec2 KO mice present with frequent and recurrent seizures. Focusing on Iqsec2 KO heterozygous female mice, we demonstrate increased hyperactivity, altered anxiety and fear responses, decreased social interactions, delayed learning capacity and decreased memory retention/novel recognition, recapitulating psychiatric issues, autistic-like features, and cognitive deficits present in female patients with loss-of-function IQSEC2 variants. Despite Iqsec2 normally acting to activate Arf6 substrate, we demonstrate that mice modelling the loss of Iqsec2 function present with increased levels of activated Arf6. We contend that loss of Iqsec2 function leads to altered regulation of activated Arf6-mediated responses to synaptic signalling and immature synaptic networks. We highlight the importance of IQSEC2 function for females by reporting a novel nonsense variant c.566C > A, p.(S189*) in an elderly female patient with profound intellectual disability, generalised seizures, and behavioural disturbances. Our human and mouse data reaffirm IQSEC2 as another disease gene with an unexpected X-chromosome heterozygous female phenotype. Our Iqsec2 mouse model recapitulates the phenotypes observed in human patients despite the differences in the IQSEC2/Iqsec2 gene X-chromosome inactivation between the species.
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Affiliation(s)
- Matilda R Jackson
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Karagh E Loring
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Claire C Homan
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Monica Hn Thai
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Laura Määttänen
- Department of Child Neurology, Turku University Hospital, Turku, Finland
| | - Maria Arvio
- Department of Child Neurology, Turku University Hospital, Turku, Finland.,Joint Authority for Päijät-Häme Social and Health Care, Lahti, Finland.,PEDEGO, Oulu University Hospital, Oulu, Finland
| | - Irma Jarvela
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Marie Shaw
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Alison Gardner
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Jozef Gecz
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Cheryl Shoubridge
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia .,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
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27
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Khayat W, Hackett A, Shaw M, Ilie A, Dudding-Byth T, Kalscheuer VM, Christie L, Corbett MA, Juusola J, Friend KL, Kirmse BM, Gecz J, Field M, Orlowski J. A recurrent missense variant in SLC9A7 causes nonsyndromic X-linked intellectual disability with alteration of Golgi acidification and aberrant glycosylation. Hum Mol Genet 2019; 28:598-614. [PMID: 30335141 DOI: 10.1093/hmg/ddy371] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
We report two unrelated families with multigenerational nonsyndromic intellectual disability (ID) segregating with a recurrent de novo missense variant (c.1543C>T:p.Leu515Phe) in the alkali cation/proton exchanger gene SLC9A7 (also commonly referred to as NHE7). SLC9A7 is located on human X chromosome at Xp11.3 and has not yet been associated with a human phenotype. The gene is widely transcribed, but especially abundant in brain, skeletal muscle and various secretory tissues. Within cells, SLC9A7 resides in the Golgi apparatus, with prominent enrichment in the trans-Golgi network (TGN) and post-Golgi vesicles. In transfected Chinese hamster ovary AP-1 cells, the Leu515Phe mutant protein was correctly targeted to the TGN/post-Golgi vesicles, but its N-linked oligosaccharide maturation as well as that of a co-transfected secretory membrane glycoprotein, vesicular stomatitis virus G (VSVG) glycoprotein, was reduced compared to cells co-expressing SLC9A7 wild-type and VSVG. This correlated with alkalinization of the TGN/post-Golgi compartments, suggestive of a gain-of-function. Membrane trafficking of glycosylation-deficient Leu515Phe and co-transfected VSVG to the cell surface, however, was relatively unaffected. Mass spectrometry analysis of patient sera also revealed an abnormal N-glycosylation profile for transferrin, a clinical diagnostic marker for congenital disorders of glycosylation. These data implicate a crucial role for SLC9A7 in the regulation of TGN/post-Golgi pH homeostasis and glycosylation of exported cargo, which may underlie the cellular pathophysiology and neurodevelopmental deficits associated with this particular nonsyndromic form of X-linked ID.
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Affiliation(s)
- Wujood Khayat
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Anna Hackett
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Alina Ilie
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Tracy Dudding-Byth
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Louise Christie
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Kathryn L Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Brian M Kirmse
- Department of Pediatrics, Division of Medical Genetics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - John Orlowski
- Department of Physiology, McGill University, Montreal, Quebec, Canada
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28
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Van Esch H, Colnaghi R, Freson K, Starokadomskyy P, Zankl A, Backx L, Abramowicz I, Outwin E, Rohena L, Faulkner C, Leong GM, Newbury-Ecob RA, Challis RC, Õunap K, Jaeken J, Seuntjens E, Devriendt K, Burstein E, Low KJ, O'Driscoll M. Defective DNA Polymerase α-Primase Leads to X-Linked Intellectual Disability Associated with Severe Growth Retardation, Microcephaly, and Hypogonadism. Am J Hum Genet 2019; 104:957-967. [PMID: 31006512 PMCID: PMC6506757 DOI: 10.1016/j.ajhg.2019.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/04/2019] [Indexed: 12/26/2022] Open
Abstract
Replicating the human genome efficiently and accurately is a daunting challenge involving the duplication of upward of three billion base pairs. At the core of the complex machinery that achieves this task are three members of the B family of DNA polymerases: DNA polymerases α, δ, and ε. Collectively these multimeric polymerases ensure DNA replication proceeds at optimal rates approaching 2 × 103 nucleotides/min with an error rate of less than one per million nucleotides polymerized. The majority of DNA replication of undamaged DNA is conducted by DNA polymerases δ and ε. The DNA polymerase α-primase complex performs limited synthesis to initiate the replication process, along with Okazaki-fragment synthesis on the discontinuous lagging strand. An increasing number of human disorders caused by defects in different components of the DNA-replication apparatus have been described to date. These are clinically diverse and involve a wide range of features, including variable combinations of growth delay, immunodeficiency, endocrine insufficiencies, lipodystrophy, and cancer predisposition. Here, by using various complementary approaches, including classical linkage analysis, targeted next-generation sequencing, and whole-exome sequencing, we describe distinct missense and splice-impacting mutations in POLA1 in five unrelated families presenting with an X-linked syndrome involving intellectual disability, proportionate short stature, microcephaly, and hypogonadism. POLA1 encodes the p180 catalytic subunit of DNA polymerase α-primase. A range of replicative impairments could be demonstrated in lymphoblastoid cell lines derived from affected individuals. Our findings describe the presentation of pathogenic mutations in a catalytic component of a B family DNA polymerase member, DNA polymerase α.
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Affiliation(s)
- Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium; Laboratory for the Genetics of Cognition, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
| | - Rita Colnaghi
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andreas Zankl
- Department of Clinical Genetics, the Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Hospital Westmead Clinical School, Sydney Medical School, the University of Sydney, Westmead, NSW 2145, Australia; Bone Biology Division and Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Liesbeth Backx
- Laboratory for the Genetics of Cognition, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Iga Abramowicz
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Emily Outwin
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Luis Rohena
- Division of Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, TX 78234, USA
| | - Claire Faulkner
- Bristol Genetics Laboratory, Southmead Hospital, BS10 5NB Bristol, UK
| | - Gary M Leong
- Department of Paediatrics, Nepean Hospital, Nepean Clinical School, the University of Sydney, Kingswood, NSW 2747, Australia
| | - Ruth A Newbury-Ecob
- Clinical Genetics, St. Michael's Hospital, University Hospitals NHS Trust, BS2 8HW Bristol, UK
| | - Rachel C Challis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Jacques Jaeken
- Center for Metabolic Diseases, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Eve Seuntjens
- Developmental Neurobiology, Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390 Texas, USA
| | - Karen J Low
- Clinical Genetics, St. Michael's Hospital, University Hospitals NHS Trust, BS2 8HW Bristol, UK
| | - Mark O'Driscoll
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK.
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29
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Huo L, Teng Z, Wang H, Liu X. A novel splice site mutation in AP1S2 gene for X-linked mental retardation in a Chinese pedigree and literature review. Brain Behav 2019; 9:e01221. [PMID: 30714330 PMCID: PMC6422709 DOI: 10.1002/brb3.1221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Pettigrew syndrome (PGS) is a rare X-linked mental retardation that caused by AP1S2 mutation. The pathogenesis of AP1S2 deficiency has remained elusive. The purpose of this study is to give a comprehensive overview of the phenotypic and genetic spectrum of AP1S2 mutations. METHODS This study systematically analyzed clinical features and genetic information of a Chinese family with AP1S2 variation, and reviewed previously reported literatures with the same gene variation. RESULTS We identified a new c.1-1 G>C mutation in AP1S2 gene from a four generation family with seven affected individuals and found the elevated neuron-specific enolase (NSE) in a patient. We summarized the clinical manifestation of 59 patients with AP1S2 mutation. We found that pathogenic point mutations affecting AP1S2 are associated with dysmorphic features and neurodevelopmental problems, which included highly variable mental retardation (MR), delayed in walking, abnormal speech, hypotonia, abnormal brain, abnormal behavior including aggressive behavior, ASD, self-abusive, and abnormal gait. Patients with splice site mutation were more likely to lead to seizures. By contrast, patients with nonsense mutations are more susceptible to microcephaly. CONCLUSION Our findings suggest AP1S2 mutations contribute to a broad spectrum of neurodevelopmental disorders and are important in the etiological spectrum of PGS.
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Affiliation(s)
- Liang Huo
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ziteng Teng
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hua Wang
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xueyan Liu
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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Wong K, Leonard H, Pearson G, Glasson EJ, Forbes D, Ravikumara M, Jacoby P, Bourke J, Srasuebkul P, Trollor J, Wilson A, Nagarajan L, Downs J. Epidemiology of gastrostomy insertion for children and adolescents with intellectual disability. Eur J Pediatr 2019; 178:351-361. [PMID: 30554367 DOI: 10.1007/s00431-018-3304-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 12/12/2022]
Abstract
The largest group of recipients of pediatric gastrostomy have neurological impairment with intellectual disability (ID). This study investigated trends in first gastrostomy insertion according to markers of disadvantage and ID etiology. Linked administrative and health data collected over a 32-year study period (1983-2014) for children with ID born between 1983 and 2009 in Western Australia were examined. The annual incidence rate change over calendar year was calculated for all children and according to socioeconomic status, geographical remoteness, and Aboriginality. The most likely causes of ID were identified using available diagnosis codes in the linked data set. Of 11,729 children with ID, 325 (2.8%) received a first gastrostomy within the study period. The incidence rate was highest in the 0-2 age group and there was an increasing incidence trend with calendar time for each age group under 6 years of age. This rate change was greatest in children from the lowest socioeconomic status quintile, who lived in regional/remote areas or who were Aboriginal. The two largest identified groups of ID were genetically caused syndromes (15.1%) and neonatal encephalopathy (14.8%).Conclusion: Gastrostomy is increasingly used in multiple neurological conditions associated with ID, with no apparent accessibility barriers in terms of socioeconomic status, remoteness, or Aboriginality. What is Known: • The use of gastrostomy insertion in pediatrics is increasing and the most common recipients during childhood have neurological impairment, most of whom also have intellectual disability (ID). What is New: • Nearly 3% of children with ID had gastrostomy insertion performed, with the highest incidence in children under 3 years of age. • Gastrostomy use across different social groups was equitable in the Australian setting.
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Affiliation(s)
- Kingsley Wong
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia
| | - Helen Leonard
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia
| | - Glenn Pearson
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia
| | - Emma J Glasson
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia
| | - David Forbes
- Medical School, The University of Western Australia, Perth, Australia
- Department of Health, Government of Western Australia, Perth, Australia
| | - Madhur Ravikumara
- Department of Gastroenterology, Perth Children's Hospital, Perth, Australia
| | - Peter Jacoby
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia
| | - Jenny Bourke
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia
| | - Preeyaporn Srasuebkul
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, UNSW Sydney, Sydney, Australia
| | - Julian Trollor
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, UNSW Sydney, Sydney, Australia
| | - Andrew Wilson
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia
- Department of Respiratory Medicine, Perth Children's Hospital, Perth, Australia
- School of Paediatrics, The University of Western Australia, Perth, Australia
- School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia
| | - Lakshmi Nagarajan
- Children's Neuroscience Service, Department of Neurology, Perth Children's Hospital, Perth, Australia
| | - Jenny Downs
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia.
- School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia.
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Sex Differences in the Effects of Prenatal Bisphenol A Exposure on Genes Associated with Autism Spectrum Disorder in the Hippocampus. Sci Rep 2019; 9:3038. [PMID: 30816183 PMCID: PMC6395584 DOI: 10.1038/s41598-019-39386-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/21/2019] [Indexed: 11/30/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder inexplicably biased towards males. Although prenatal exposure to bisphenol A (BPA) has recently been associated with the ASD risk, whether BPA dysregulates ASD-related genes in the developing brain remains unclear. In this study, transcriptome profiling by RNA-seq analysis of hippocampi isolated from neonatal pups prenatally exposed to BPA was conducted and revealed a list of differentially expressed genes (DEGs) associated with ASD. Among the DEGs, several ASD candidate genes, including Auts2 and Foxp2, were dysregulated and showed sex differences in response to BPA exposure. The interactome and pathway analyses of DEGs using Ingenuity Pathway Analysis software revealed significant associations between the DEGs in males and neurological functions/disorders associated with ASD. Moreover, the reanalysis of transcriptome profiling data from previously published BPA studies consistently showed that BPA-responsive genes were significantly associated with ASD-related genes. The findings from this study indicate that prenatal BPA exposure alters the expression of ASD-linked genes in the hippocampus and suggest that maternal BPA exposure may increase ASD susceptibility by dysregulating genes associated with neurological functions known to be negatively impacted in ASD, which deserves further investigations.
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Uliana V, Bonatti F, Zanatta V, Mozzoni P, Martorana D, Percesepe A. Spectrum of X-linked intellectual disabilities and psychiatric symptoms in a family harbouring a Xp22.12 microduplication encompassing the RPS6KA3 gene. J Genet 2019. [DOI: 10.1007/s12041-019-1055-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Leboucher A, Bermudez-Martin P, Mouska X, Amri EZ, Pisani DF, Davidovic L. Fmr1-Deficiency Impacts Body Composition, Skeleton, and Bone Microstructure in a Mouse Model of Fragile X Syndrome. Front Endocrinol (Lausanne) 2019; 10:678. [PMID: 31632352 PMCID: PMC6783488 DOI: 10.3389/fendo.2019.00678] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/18/2019] [Indexed: 11/13/2022] Open
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder associated with intellectual disability, hyperactivity, and autism. FXS is due to the silencing of the X-linked FMR1 gene. Murine models of FXS, knock-out (KO) for the murine homolog Fmr1, have been generated, exhibiting CNS-related behavioral, and neuronal anomalies reminiscent of the human phenotypes. As a reflection of the almost ubiquitous expression of the FMR1 gene, FXS is also accompanied by physical abnormalities. This suggests that the FMR1-deficiency could impact skeletal ontogenesis. In the present study, we highlight that Fmr1-KO mice display changes in body composition with an increase in body weight, likely due to both increase of skeleton length and muscular mass along with reduced visceral adiposity. We also show that, while Fmr1-deficiency has no overt impact on cortical bone mineral density (BMD), cortical thickness was increased, and cortical eccentricity was decreased in the femurs from Fmr1-KO mice as compared to controls. Also, trabecular pore volume was reduced and trabecular thickness distribution was shifted toward higher ranges in Fmr1-KO femurs. Finally, we show that Fmr1-KO mice display increased physical activity. Although the precise molecular signaling mechanism that produces these skeletal and bone microstructure changes remains to be determined, our study warrants further investigation on the impact of FMR1-deficiency on whole-body composition, as well as skeletal and bone architecture.
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Affiliation(s)
| | | | - Xavier Mouska
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | | | - Laetitia Davidovic
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
- *Correspondence: Laetitia Davidovic
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34
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Zablotskaya A, Van Esch H, Verstrepen KJ, Froyen G, Vermeesch JR. Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability. BMC Med Genomics 2018; 11:123. [PMID: 30567555 PMCID: PMC6299999 DOI: 10.1186/s12920-018-0446-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/06/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The etiology of more than half of all patients with X-linked intellectual disability remains elusive, despite array-based comparative genomic hybridization, whole exome or genome sequencing. Since short read massive parallel sequencing approaches do not allow the detection of larger tandem repeat expansions, we hypothesized that such expansions could be a hidden cause of X-linked intellectual disability. METHODS We selectively captured over 1800 tandem repeats on the X chromosome and characterized them by long read single molecule sequencing in 3 families with idiopathic X-linked intellectual disability. RESULTS In male DNA samples, full tandem repeat length sequences were obtained for 88-93% of the targets and up to 99.6% of the repeats with a moderate guanine-cytosine content. Read length and analysis pipeline allow to detect cases of > 900 bp tandem repeat expansion. In one family, one repeat expansion co-occurs with down-regulation of the neighboring MIR222 gene. This gene has previously been implicated in intellectual disability and is apparently linked to FMR1 and NEFH overexpression associated with neurological disorders. CONCLUSIONS This study demonstrates the power of single molecule sequencing to measure tandem repeat lengths and detect expansions, and suggests that tandem repeat mutations may be a hidden cause of X-linked intellectual disability.
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Affiliation(s)
- Alena Zablotskaya
- Department of Human Genetics and Center for Human Genetics, Laboratory for Cytogenetics and Genome Research, University Hospitals Leuven, KU Leuven, O&N I Herestraat 49 - box 606, 3000, Leuven, Belgium
| | - Hilde Van Esch
- Department of Human Genetics and Center for Human Genetics, Laboratory for Genetics of Cognition, University Hospitals Leuven, KU Leuven, O&N I Herestraat 49 - box 606, 3000, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB Center for Microbiology and CMPG Lab for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1 - box 2471, 3001, Leuven, Belgium
| | - Guy Froyen
- Clinical Biology, Laboratory for Molecular Diagnostics, Jessa Hospital, Stadsomvaart 11, 3500, Hasselt, Belgium
| | - Joris R Vermeesch
- Department of Human Genetics and Center for Human Genetics, Laboratory for Cytogenetics and Genome Research, University Hospitals Leuven, KU Leuven, O&N I Herestraat 49 - box 606, 3000, Leuven, Belgium.
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Polygenic risk score for schizophrenia is not strongly associated with the expression of specific genes or gene sets. Psychiatr Genet 2018; 28:59-65. [PMID: 29672343 DOI: 10.1097/ypg.0000000000000197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The polygenic risk score (PRS) is derived from single nucleotide polymorphisms (SNPs) including those that are genome-wide significant and also including a large number of others more weakly associated with schizophrenia. Such variants are widely dispersed, though concentrated near genes expressed in the brain, and it has been proposed that these SNP associations result from impacts on cell regulatory networks that ultimately affect the expression or function of a modest number of 'core' genes. A previous study showed association of some genome-wide association study-significant variants with expression of a number of genes, by examining pairwise correlations of gene expression with SNP genotypes. METHODS The present study used data downloaded from the CommonMind Consortium site, consisting of SNP genotypes and RNAseq expression data from the dorsolateral prefrontal cortex, to examine whether the expression of individual genes or sets of genes correlated with PRS in 207 controls and 209 schizophrenia cases. RESULTS Although the PRS was significantly associated with phenotype, the correlations with genes and gene sets followed distributions expected by chance. Thus, this analysis failed to show that the PRS captures a cumulative effect of multiple variants impacting the expression of a small number of genes and it failed to focus attention on a small number of genes of biological relevance. CONCLUSION The multiple SNP associations observed in schizophrenia may result from other mechanisms, including effects mediated indirectly through environmental risk factors.
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36
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Tzschach A. X-chromosomale Intelligenzminderung. MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Zusammenfassung
X-chromosomale Intelligenzminderung („X-linked intellectual disability“, XLID) ist eine heterogene Krankheitsgruppe; inzwischen sind mehr als 100 XLID-Gene identifiziert worden. Das Fragile-X-Syndrom mit CGG-Repeatexpansion in der 5’-UTR des FMR1-Gens ist die häufigste monogene Ursache für Intelligenzminderung. Weitere X‑chromosomale Gene mit vergleichsweise hohen Mutationsprävalenzen sind ATRX, RPS6KA3, GPC3, SLC16A2, SLC6A8 und ARX. Die Ursachen für XLID verteilen sich zu ca. 90 % auf molekulargenetisch nachweisbare Mutationen und zu ca. 10 % auf chromosomale Kopienzahlvarianten („copy-number variants“, CNVs). Häufige CNVs sind Duplikationen in Xq28 unter Einschluss von MECP2 sowie das Xp11.22-Duplikations-Syndrom mit Überexpression von HUWE1. Mit den aktuellen Untersuchungsmethoden kann bei ca. 10 % der männlichen Patienten mit Intelligenzminderung eine X‑chromosomale Ursache nachgewiesen werden. Neue Erkenntnisse zu XLID sind für die nächsten Jahre am ehesten in den nicht kodierenden Regionen zu erwarten, wo wahrscheinlich ein weiterer Teil der Ursachen für das bislang nicht vollständig erklärte Überwiegen männlicher Patienten zu suchen ist.
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Affiliation(s)
- Andreas Tzschach
- Aff1 0000 0001 2111 7257 grid.4488.0 Institut für Klinische Genetik Technische Universität Dresden Fetscherstr. 74 01307 Dresden Deutschland
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37
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A weighted burden test using logistic regression for integrated analysis of sequence variants, copy number variants and polygenic risk score. Eur J Hum Genet 2018; 27:114-124. [PMID: 30258123 DOI: 10.1038/s41431-018-0272-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/15/2018] [Accepted: 08/30/2018] [Indexed: 12/16/2022] Open
Abstract
Previously described methods of analysis allow variants in a gene to be weighted more highly according to rarity and/or predicted function and then for the variant contributions to be summed into a gene-wise risk score, which can be compared between cases and controls using a t-test. However, this does not allow incorporating covariates into the analysis. Schizophrenia is an example of an illness where there is evidence that different kinds of genetic variation can contribute to risk, including common variants contributing to a polygenic risk score (PRS), very rare copy number variants (CNVs) and sequence variants. A logistic regression approach has been implemented to compare the gene-wise risk scores between cases and controls, while incorporating as covariates population principal components, the PRS and the presence of pathogenic CNVs and sequence variants. A likelihood ratio test is performed, comparing the likelihoods of logistic regression models with and without this score. The method was applied to an ethnically heterogeneous exome-sequenced sample of 6000 controls and 5000 schizophrenia cases. In the raw analysis, the test statistic is inflated but inclusion of principal components satisfactorily controls for this. In this dataset, the inclusion of the PRS and effect from CNVs and sequence variants had only small effects. The set of genes which are FMRP targets showed some evidence for enrichment of rare, functional variants among cases (p = 0.0005). This approach can be applied to any disease in which different kinds of genetic and non-genetic risk factors make contributions to risk.
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Weighted Burden Analysis of Exome-Sequenced Case-Control Sample Implicates Synaptic Genes in Schizophrenia Aetiology. Behav Genet 2018; 48:198-208. [PMID: 29564678 PMCID: PMC5934462 DOI: 10.1007/s10519-018-9893-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/13/2018] [Indexed: 11/04/2022]
Abstract
A previous study of exome-sequenced schizophrenia cases and controls reported an excess of singleton, gene-disruptive variants among cases, concentrated in particular gene sets. The dataset included a number of subjects with a substantial Finnish contribution to ancestry. We have reanalysed the same dataset after removal of these subjects and we have also included non-singleton variants of all types using a weighted burden test which assigns higher weights to variants predicted to have a greater effect on protein function. We investigated the same 31 gene sets as previously and also 1454 GO gene sets. The reduced dataset consisted of 4225 cases and 5834 controls. No individual variants or genes were significantly enriched in cases but 13 out of the 31 gene sets were significant after Bonferroni correction and the “FMRP targets” set produced a signed log p value (SLP) of 7.1. The gene within this set with the highest SLP, equal to 3.4, was FYN, which codes for a tyrosine kinase which phosphorylates glutamate metabotropic receptors and ionotropic NMDA receptors, thus modulating their trafficking, subcellular distribution and function. In the most recent GWAS of schizophrenia it was identified as a “prioritized candidate gene”. Two of the subunits of the NMDA receptor which are substrates of FYN are coded for by GRIN1 (SLP = 1.7) and GRIN2B (SLP = 2.1). Of note, for some sets there was a substantial enrichment of non-singleton variants. Of 1454 GO gene sets, three were significant after Bonferroni correction. Identifying specific genes and variants will depend on genotyping them in larger samples and/or demonstrating that they cosegregate with illness within pedigrees.
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Delaye JB, Patin F, Lagrue E, Le Tilly O, Bruno C, Vuillaume ML, Raynaud M, Benz-De Bretagne I, Laumonnier F, Vourc'h P, Andres C, Blasco H. Post hoc analysis of plasma amino acid profiles: towards a specific pattern in autism spectrum disorder and intellectual disability. Ann Clin Biochem 2018; 55:543-552. [PMID: 29388433 DOI: 10.1177/0004563218760351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Objectives Autism spectrum disorders and intellectual disability present a challenge for therapeutic and dietary management. We performed a re-analysis of plasma amino acid chromatography of children with autism spectrum disorders ( n = 22) or intellectual disability ( n = 29) to search for a metabolic signature that can distinguish individuals with these disorders from controls ( n = 30). Methods We performed univariate and multivariate analyses using different machine learning strategies, from the raw data of the amino acid chromatography. Finally, we analysed the metabolic pathways associated with discriminant biomarkers. Results Multivariate analysis revealed models to discriminate patients with autism spectrum disorders or intellectual disability and controls from plasma amino acid profiles ( P < 0.0003). Univariate analysis showed that autism spectrum disorder and intellectual disability patients shared similar differences relative to controls, including lower glutamate ( P < 0.0001 and P = 0.0002, respectively) and serine ( P = 0.002 for both) concentrations. The multivariate model ( P < 6.12.10-7) to discriminate between autism spectrum disorders and intellectual disability revealed the involvement of urea, 3-methyl-histidine and histidine metabolism. Biosigner analysis and univariate analysis confirmed the role of 3-methylhistidine ( P = 0.004), histidine ( P = 0.003), urea ( P = 0.0006) and lysine ( P = 0.002). Conclusions We revealed discriminant metabolic patterns between autism spectrum disorders, intellectual disability and controls. Amino acids known to play a role in neurotransmission were discriminant in the models comparing autism spectrum disorders or intellectual disability to controls, and histidine and b-alanine metabolism was specifically highlighted in the model.
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Affiliation(s)
- Jean-Baptiste Delaye
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France
| | - Franck Patin
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France.,2 UMR 1253, Université de Tours, Tours, France
| | - Emmanuelle Lagrue
- 2 UMR 1253, Université de Tours, Tours, France.,3 CHRU de Tours, Service de Neuropédiatrie, Tours, France
| | - Olivier Le Tilly
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France
| | - Clement Bruno
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France.,2 UMR 1253, Université de Tours, Tours, France
| | - Marie-Laure Vuillaume
- 2 UMR 1253, Université de Tours, Tours, France.,4 CHRU de Tours, Service de Génétique, Tours, France
| | - Martine Raynaud
- 2 UMR 1253, Université de Tours, Tours, France.,4 CHRU de Tours, Service de Génétique, Tours, France
| | - Isabelle Benz-De Bretagne
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France.,2 UMR 1253, Université de Tours, Tours, France
| | - Frederic Laumonnier
- 2 UMR 1253, Université de Tours, Tours, France.,4 CHRU de Tours, Service de Génétique, Tours, France
| | - Patrick Vourc'h
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France.,2 UMR 1253, Université de Tours, Tours, France
| | - Christian Andres
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France.,2 UMR 1253, Université de Tours, Tours, France
| | - Helene Blasco
- 1 CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France.,2 UMR 1253, Université de Tours, Tours, France
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Verkerk AJMH, Zeidler S, Breedveld G, Overbeek L, Huigh D, Koster L, van der Linde H, de Esch C, Severijnen LA, de Vries BBA, Swagemakers SMA, Willemsen R, Hoogeboom AJM, van der Spek PJ, Oostra BA. CXorf56, a dendritic neuronal protein, identified as a new candidate gene for X-linked intellectual disability. Eur J Hum Genet 2018; 26:552-560. [PMID: 29374277 DOI: 10.1038/s41431-017-0051-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Intellectual disability (ID) comprises a large group of heterogeneous disorders, often without a known molecular cause. X-linked ID accounts for 5-10% of male ID cases. We investigated a large, three-generation family with mild ID and behavior problems in five males and one female, with a segregation suggestive for X-linked inheritance. Linkage analysis mapped a disease locus to a 7.6 Mb candidate region on the X-chromosome (LOD score 3.3). Whole-genome sequencing identified a 2 bp insertion in exon 2 of the chromosome X open reading frame 56 gene (CXorf56), resulting in a premature stop codon. This insertion was present in all intellectually impaired individuals and carrier females. Additionally, X-inactivation status showed skewed methylation patterns favoring the inactivation of the mutated allele in the unaffected carrier females. We demonstrate that the insertion leads to nonsense-mediated decay and that CXorf56 mRNA expression is reduced in the impaired males and female. In murine brain slices and primary hippocampal neuronal cultures, CXorf56 protein was present and localized in the nucleus, cell soma, dendrites, and dendritic spines. Although no other families have been identified with pathogenic variants in CXorf56, these results suggest that CXorf56 is the causative gene in this family, and thus a novel candidate gene for X-linked ID with behavior problems.
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Affiliation(s)
- Annemieke J M H Verkerk
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands. .,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guido Breedveld
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lydia Overbeek
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daphne Huigh
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Linda Koster
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Herma van der Linde
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Celine de Esch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lies-Anne Severijnen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter J van der Spek
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Li J, Wang Q, Wang H, Wu Y, Yin J, Chen J, Zheng Z, Jiang T, Xie L, Wu F, Zhang H, Li X, Xu H, Xiao J. Lentivirus Mediating FGF13 Enhances Axon Regeneration after Spinal Cord Injury by Stabilizing Microtubule and Improving Mitochondrial Function. J Neurotrauma 2017; 35:548-559. [PMID: 28922963 DOI: 10.1089/neu.2017.5205] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fibroblast growth factor 13 (FGF13), a nonsecretory protein of the FGF family, plays a crucial role in developing cortical neurons by stabilizing the microtubule. In previous studies, we showed that regulation of microtubule dynamics was instrumental for both growth cone initiation and for promoting regrowth of injured axon. However, the expression and effect of FGF13 in spinal cord or after spinal cord injury (SCI) remains undefined. Here, we demonstrated a role of FGF13 in regulating microtubule dynamics and in enhancing axon regeneration after SCI. Administration of FGF13 not only promoted neuronal polarization, axon formation, and growth cone initiation in vitro, but it also facilitated functional recovery following SCI. In addition, we found that upregulation of FGF13 in primary cortical neurons was accompanied by enhanced mitochondrial function, which is essential for axon regeneration. Our study has defined a novel mechanism underlying the beneficial effect of FGF13 on axon regeneration, pointing out that FGF13 may serve as a potential candidate for treating SCI or other central nervous system (CNS) injury.
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Affiliation(s)
- Jiawei Li
- 1 Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University , Wenzhou, Zhejiang, China .,2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Qingqing Wang
- 1 Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University , Wenzhou, Zhejiang, China .,2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Haoli Wang
- 1 Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University , Wenzhou, Zhejiang, China .,2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Yanqing Wu
- 3 The Institute of Life Sciences, Wenzhou University , Wenzhou, Zhejiang, China
| | - Jiayu Yin
- 2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Jian Chen
- 1 Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University , Wenzhou, Zhejiang, China .,2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Zengming Zheng
- 1 Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University , Wenzhou, Zhejiang, China .,2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Ting Jiang
- 2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Ling Xie
- 2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Fenzan Wu
- 4 Department of Neurosurgery, Cixi People's Hospital, Wenzhou Medical University , Ningbo, Zhejiang, China
| | - Hongyu Zhang
- 2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Xiaokun Li
- 3 The Institute of Life Sciences, Wenzhou University , Wenzhou, Zhejiang, China
| | - Huazi Xu
- 1 Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University , Wenzhou, Zhejiang, China
| | - Jian Xiao
- 1 Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University , Wenzhou, Zhejiang, China .,2 Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University , Wenzhou, Zhejiang, China
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Li X, Xie H, Chen Q, Yu X, Yi Z, Li E, Zhang T, Wang J, Zhong J, Chen X. Clinical and molecular genetic characterization of familial MECP2 duplication syndrome in a Chinese family. BMC MEDICAL GENETICS 2017; 18:131. [PMID: 29141583 PMCID: PMC5688748 DOI: 10.1186/s12881-017-0486-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/24/2017] [Indexed: 01/09/2023]
Abstract
Background Chromosomal duplication at the Xq28 region including the MECP2 gene, share consistent clinical phenotypes and a distinct facial phenotype known as MECP2 duplication syndrome. The typical clinical features include infantile hypotonia, mild dysmorphic features, a broad range of neurodevelopmental disorders, recurrent infections, and progressive spasticity. Methods This Chinese MECP2 duplication syndrome family includes six patients (five males and one female), and four asymptomatic female carriers. Two kinds of chips including 4x180K CNV + SNP chip and custom 8x60K CNV chip were used to detect MECP2 duplication, and then fluorescent in situ hybridization (FISH) analysis was performed to identify the exact copy number of MECP2. X-chromosome inactivation (XCI) analysis on AR gene was detected for all female family members, and the microsatellite analysis on MECP2 was used to validate the recombination event on MECP2 region. Results The affected male subjects presented with a broad range of neurodevelopmental symptoms (severe intellectual disability, developmental delay, seizure, language deficit, and autism spectrum disorder) as well as facial dysmorphism and other symptoms which were consistent with that of Western patients previous reported. Seizure is reported in Chinese patients for the first time. In addition, we validated three recombination events for the MECP2-duplication allele during maternal transmission due to X homologous recombination. Conclusions We provided the largest known Chinese pedigree with MECP2 duplication syndrome. The detailed clinical description and molecular genetic characterization in all affected family members further delineate the typical phenotype of this genomic disorder in Chinese population. Electronic supplementary material The online version of this article (10.1186/s12881-017-0486-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyan Li
- Department of Neurology, Jiangxi Children's Hospital, Yangming Road, Donghu District, Nanchang, 330006, China.,Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Room 616, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Hua Xie
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Room 616, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China.,Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Qian Chen
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Xiongying Yu
- Department of Neurology, Jiangxi Children's Hospital, Yangming Road, Donghu District, Nanchang, 330006, China
| | - Zhaoshi Yi
- Department of Neurology, Jiangxi Children's Hospital, Yangming Road, Donghu District, Nanchang, 330006, China
| | - Erzhen Li
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Room 616, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Jian Wang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jianmin Zhong
- Department of Neurology, Jiangxi Children's Hospital, Yangming Road, Donghu District, Nanchang, 330006, China.
| | - Xiaoli Chen
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Room 616, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China. .,Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China.
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43
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Han JY, Lee IG, Shin S, Kim M, Jang JH, Park J. The first patient with sporadic X-linked intellectual disability with de novo ZDHHC9 mutation identified by targeted next-generation sequencing. Eur J Med Genet 2017; 60:499-503. [DOI: 10.1016/j.ejmg.2017.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/27/2017] [Accepted: 07/03/2017] [Indexed: 11/27/2022]
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Curtis D. Construction of an Exome-Wide Risk Score for Schizophrenia Based on a Weighted Burden Test. Ann Hum Genet 2017; 82:11-22. [PMID: 28895126 DOI: 10.1111/ahg.12212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/06/2017] [Accepted: 08/01/2017] [Indexed: 02/05/2023]
Abstract
Polygenic risk scores obtained as a weighted sum of associated variants can be used to explore association in additional data sets and to assign risk scores to individuals. The methods used to derive polygenic risk scores from common SNPs are not suitable for variants detected in whole exome sequencing studies. Rare variants, which may have major effects, are seen too infrequently to judge whether they are associated and may not be shared between training and test subjects. A method is proposed whereby variants are weighted according to their frequency, their annotations and the genes they affect. A weighted sum across all variants provides an individual risk score. Scores constructed in this way are used in a weighted burden test and are shown to be significantly different between schizophrenia cases and controls using a five-way cross-validation procedure. This approach represents a first attempt to summarise exome sequence variation into a summary risk score, which could be combined with risk scores from common variants and from environmental factors. It is hoped that the method could be developed further.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, UCL, Darwin Building, Gower Street, London, WC1E 6BT.,Centre for Psychiatry, Barts and the London School of Medicine and Dentistry
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45
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Chatron N, Thibault L, Lespinasse J, Labalme A, Schluth-Bolard C, Till M, Edery P, Touraine R, des Portes V, Lesca G, Sanlaville D. Genetic Counselling Pitfall: Co-Occurrence of an 11.8-Mb Xp22 Duplication and an Xp21.2 Duplication Disrupting IL1RAPL1. Mol Syndromol 2017; 8:325-330. [PMID: 29230163 DOI: 10.1159/000479455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2017] [Indexed: 01/19/2023] Open
Abstract
We report a 3-generation family in which 2 Xp copy number variations (CNVs) co-segregate. The proband presented with syndromic intellectual disability. The CNV had been revealed by conventional karyotyping, identifying a large Xp22 duplication causing an Xp functional disomy. Family studies found that this duplication was inherited from the proband's mother and was also present in one of his sisters. This sister had conventional karyotyping performed during pregnancy with a normal result. Postnatally, her child, the proband's nephew, presented with autism spectrum disorders. aCGH revealed a 339-kb IL1RAPL1 duplication. Overall, the proband, his mother, and one of his sisters all harboured both CNVs, while his other sister and the 2 sons of each sister only carried the IL1RAPL1 intragenic duplication. As seen in this family, we emphasise the importance of small CNV detection, the pathogenicity of IL1RAPL1 exonic duplications in male carriers, and the difficulties for genetic counselling with the risk of double diagnosis in a single patient.
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Affiliation(s)
- Nicolas Chatron
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France.,Equipe GENDEV INSERM U1028, CNRS, UMR5292, Lyon, France.,Université de Lyon, Lyon, France
| | - Lucie Thibault
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France
| | | | - Audrey Labalme
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France
| | - Caroline Schluth-Bolard
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France.,Equipe GENDEV INSERM U1028, CNRS, UMR5292, Lyon, France.,Université de Lyon, Lyon, France
| | - Marianne Till
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France
| | - Patrick Edery
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France.,Equipe GENDEV INSERM U1028, CNRS, UMR5292, Lyon, France.,Université de Lyon, Lyon, France
| | - Renaud Touraine
- Service de Génétique, CHU de Saint Etienne, Saint Etienne, HFME, Bron, France
| | - Vincent des Portes
- Université de Lyon, Lyon, France.,Hospices Civils de Lyon, Centre de Référence National "Déficiences Intellectuelles de Causes Rares", HFME, Bron, France.,CNRS UMR 5304, ISC, Bron, France
| | - Gaetan Lesca
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France.,Equipe GENDEV INSERM U1028, CNRS, UMR5292, Lyon, France.,Université de Lyon, Lyon, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France.,Equipe GENDEV INSERM U1028, CNRS, UMR5292, Lyon, France.,Université de Lyon, Lyon, France
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Genetic Defects Underlie the Non-syndromic Autosomal Recessive Intellectual Disability (NS-ARID). Open Life Sci 2017. [DOI: 10.1515/biol-2017-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractIntellectual disability (ID) is a neurodevelopmental disorder which appears frequently as the result of genetic mutations and may be syndromic (S-ID) or non-syndromic (NS-ID). ID causes an important economic burden, for patient's family, health systems, and society. Identifying genes that cause S-ID can easily be evaluated due to the clinical symptoms or physical anomalies. However, in the case of NS-ID due to the absence of co-morbid features, the latest molecular genetic techniques can be used to understand the genetic defects that underlie it. Recent studies have shown that non-syndromic autosomal recessive (NS-ARID) is extremely heterogeneous and contributes much more than X-linked ID. However, very little is known about the genes and loci involved in NS-ARID relative to X-linked ID, and whose complete genetic etiology remains obscure. In this review article, the known genetic etiology of NS-ARID and possible relationships between genes and the associated molecular pathways of their encoded proteins has been reviewed which will enhance our understanding about the underlying genes and mechanisms in NS-ARID.
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47
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Incorrect dosage of IQSEC2, a known intellectual disability and epilepsy gene, disrupts dendritic spine morphogenesis. Transl Psychiatry 2017; 7:e1110. [PMID: 28463240 PMCID: PMC5534949 DOI: 10.1038/tp.2017.81] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 02/23/2017] [Indexed: 12/18/2022] Open
Abstract
There is considerable genetic and phenotypic heterogeneity associated with intellectual disability (ID), specific learning disabilities, attention-deficit hyperactivity disorder, autism and epilepsy. The intelligence quotient (IQ) motif and SEC7 domain containing protein 2 gene (IQSEC2) is located on the X-chromosome and harbors mutations that contribute to non-syndromic ID with and without early-onset seizure phenotypes in both sexes. Although IQ and Sec7 domain mutations lead to partial loss of IQSEC2 enzymatic activity, the in vivo pathogenesis resulting from these mutations is not known. Here we reveal that IQSEC2 has a key role in dendritic spine morphology. Partial loss-of-function mutations were modeled using a lentiviral short hairpin RNA (shRNA) approach, which achieved a 57% knockdown of Iqsec2 expression in primary hippocampal cell cultures from mice. Investigating gross morphological parameters after 8 days of in vitro culture (8DIV) identified a 32% reduction in primary axon length, in contrast to a 27% and 31% increase in the number and complexity of dendrites protruding from the cell body, respectively. This increase in dendritic complexity and spread was carried through dendritic spine development, with a 34% increase in the number of protrusions per dendritic segment compared with controls at 15DIV. Although the number of dendritic spines had normalized by 21DIV, a reduction was noted in the number of immature spines. In contrast, when modeling increased dosage, overexpression of wild-type IQSEC2 led to neurons with shorter axons that were more compact and displayed simpler dendritic branching. Disturbances to dendritic morphology due to knockdown of Iqsec2 were recapitulated in neurons from Iqsec2 knockout mice generated in our laboratory using CRISPR/Cas9 technology. These observations provide evidence of dosage sensitivity for IQSEC2, which normally escapes X-inactivation in females, and links these disturbances in expression to alterations in the morphology of developing neurons.
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Cantone I, Dharmalingam G, Chan YW, Kohler AC, Lenhard B, Merkenschlager M, Fisher AG. Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation. Genome Biol 2017; 18:2. [PMID: 28118853 PMCID: PMC5264468 DOI: 10.1186/s13059-016-1136-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/14/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the inactive X chromosome (Xi) and the determinants of locus susceptibility are, however, poorly understood. Here we use cell fusion-mediated pluripotent reprograming to study human Xi reactivation and allele-specific single nucleotide polymorphisms (SNPs) to identify reactivated loci. RESULTS We show that a subset of human Xi genes is rapidly reactivated upon re-expression of the pluripotency network. These genes lie within the most evolutionary recent segments of the human X chromosome that are depleted of LINE1 and enriched for SINE elements, predicted to impair XIST spreading. Interestingly, this cadre of genes displays stochastic Xi expression in human fibroblasts ahead of reprograming. This stochastic variability is evident between clones, by RNA-sequencing, and at the single-cell level, by RNA-FISH, and is not attributable to differences in repressive histone H3K9me3 or H3K27me3 levels. Treatment with the DNA demethylating agent 5-deoxy-azacytidine does not increase Xi expression ahead of reprograming, but instead reveals a second cadre of genes that only become susceptible to reactivation upon induction of pluripotency. CONCLUSIONS Collectively, these data not only underscore the multiple pathways that contribute to maintaining silencing along the human Xi chromosome but also suggest that transcriptional stochasticity among human cells could be useful for predicting and engineering epigenetic strategies to achieve locus-specific or domain-specific human Xi gene reactivation.
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Affiliation(s)
- Irene Cantone
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Gopuraja Dharmalingam
- Bioinformatics and Computing facility, MRC London Institute of Medical Sciences, Imperial College, London, UK
| | - Yi-Wah Chan
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Anne-Celine Kohler
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Imperial College, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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Laino L, Bottillo I, Piedimonte C, Bernardini L, Torres B, Grammatico B, Bargiacchi S, Mulargia C, Calvani M, Cardona F, Castori M, Grammatico P. Clinical and molecular characterization of a boy with intellectual disability, facial dysmorphism, minor digital anomalies and a complex IL1RAPL1 intragenic rearrangement. Eur J Paediatr Neurol 2016; 20:971-976. [PMID: 27470653 DOI: 10.1016/j.ejpn.2016.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/22/2016] [Accepted: 07/02/2016] [Indexed: 01/16/2023]
Abstract
X-linked intellectual disability accounts for 10-12% of cases of cognitive impairment in males. Mutations in IL1RAPL1 are an emerging form of apparently non-syndromic X-linked intellectual disability. We report a 8-year-old intellectually disabled boy with speech delay, and unusual facial and digital anomalies who showed a novel and complex IL1RAPL1 rearrangement. It was defined by two intragenic non-contiguous duplications inherited from the unaffected mother. Chromosome X inactivation study on the mother's blood leukocytes, urinary sediment and buccal swab did not show a significant skewed inactivation. Comparison with previously described patients with IL1RAPL1 disruption was carried. Although data on craniofacial features were scanty in many papers, subtle facial dysmorphism with a thin upper lip seemed a quietly represented picture without any other genotype-phenotype correlations. Our study expands the molecular repertoire of IL1RAPL1 mutations in intellectual disability and points out the need of more accurate clinical descriptions to better define the related phenotype.
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Affiliation(s)
- Luigi Laino
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy.
| | - Irene Bottillo
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Caterina Piedimonte
- Department of Pediatrics and Child Neuropsychiatry, Sapienza University, Policlinico Umberto I University Hospital, Rome, Italy
| | - Laura Bernardini
- Unit of Cytogenetics, Mendel Laboratory, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, FG, Italy
| | - Barbara Torres
- Unit of Cytogenetics, Mendel Laboratory, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, FG, Italy
| | - Barbara Grammatico
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Simone Bargiacchi
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Claudia Mulargia
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Mauro Calvani
- Division of Pediatrics, San Camillo-Forlanini Hospital, Rome, Italy
| | - Francesco Cardona
- Department of Pediatrics and Child Neuropsychiatry, Sapienza University, Policlinico Umberto I University Hospital, Rome, Italy
| | - Marco Castori
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Paola Grammatico
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
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50
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Genovese G, Fromer M, Stahl EA, Ruderfer DM, Chambert K, Landén M, Moran JL, Purcell SM, Sklar P, Sullivan PF, Hultman CM, McCarroll SA. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. Nat Neurosci 2016; 19:1433-1441. [PMID: 27694994 PMCID: PMC5104192 DOI: 10.1038/nn.4402] [Citation(s) in RCA: 327] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Abstract
By analyzing the exomes of 12,332 unrelated Swedish individuals – including 4,877 affected with schizophrenia – in ways informed by exome sequences from 45,376 other individuals, we identified 244,246 coding-sequence and splice-site ultra-rare variants (URVs) that were unique to individual Swedes. We found that gene-disruptive and putatively protein-damaging URVs (but not synonymous URVs) were more abundant in schizophrenia cases than controls (P = 1.3 × 10−10). This elevation of protein-compromising URVs was several times larger than an analogously elevated rate for de novo mutations, suggesting that most rare-variant effects on schizophrenia risk are inherited. Among individuals with schizophrenia, the elevated frequency of protein-compromising URVs was concentrated in brain-expressed genes, particularly in neuronally expressed genes; most of this genetic signal arose from large sets of genes whose RNAs have been found to interact with synaptically localized proteins. Our results suggest that synaptic dysfunction may mediate a large fraction of strong, individually rare genetic influences on schizophrenia risk.
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Affiliation(s)
- Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Menachem Fromer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mikael Landén
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience a Physiology at Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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