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Lin JR, Zhao Y, Jabalameli MR, Nguyen N, Mitra J, Swillen A, Vorstman JAS, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, Owen MJ, Williams NM, Bassett AS, McDonald-McGinn DM, Gur RE, Bearden CE, Morrow BE, Lachman HM, Zhang ZD. Rare coding variants as risk modifiers of the 22q11.2 deletion implicate postnatal cortical development in syndromic schizophrenia. Mol Psychiatry 2023; 28:2071-2080. [PMID: 36869225 DOI: 10.1038/s41380-023-02009-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023]
Abstract
22q11.2 deletion is one of the strongest known genetic risk factors for schizophrenia. Recent whole-genome sequencing of schizophrenia cases and controls with this deletion provided an unprecedented opportunity to identify risk modifying genetic variants and investigate their contribution to the pathogenesis of schizophrenia in 22q11.2 deletion syndrome. Here, we apply a novel analytic framework that integrates gene network and phenotype data to investigate the aggregate effects of rare coding variants and identified modifier genes in this etiologically homogenous cohort (223 schizophrenia cases and 233 controls of European descent). Our analyses revealed significant additive genetic components of rare nonsynonymous variants in 110 modifier genes (adjusted P = 9.4E-04) that overall accounted for 4.6% of the variance in schizophrenia status in this cohort, of which 4.0% was independent of the common polygenic risk for schizophrenia. The modifier genes affected by rare coding variants were enriched with genes involved in synaptic function and developmental disorders. Spatiotemporal transcriptomic analyses identified an enrichment of coexpression between modifier and 22q11.2 genes in cortical brain regions from late infancy to young adulthood. Corresponding gene coexpression modules are enriched with brain-specific protein-protein interactions of SLC25A1, COMT, and PI4KA in the 22q11.2 deletion region. Overall, our study highlights the contribution of rare coding variants to the SCZ risk. They not only complement common variants in disease genetics but also pinpoint brain regions and developmental stages critical to the etiology of syndromic schizophrenia.
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Affiliation(s)
- Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Nha Nguyen
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Eva W C Chow
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Marianne van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Beverly S Emanuel
- Division of Human Genetics and 22q and You Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Nigel M Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Anne S Bassett
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Donna M McDonald-McGinn
- Division of Human Genetics and 22q and You Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Carrie E Bearden
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA.
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Jabalameli MR, Zhang ZD. Substance abuse and the risk of severe COVID-19: Mendelian randomization confirms the causal role of opioids but hints a negative causal effect for cannabinoids. Front Genet 2022; 13:1070428. [PMID: 36583016 PMCID: PMC9792508 DOI: 10.3389/fgene.2022.1070428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/11/2022] [Indexed: 12/15/2022] Open
Abstract
Since the start of the COVID-19 global pandemic, our understanding of the underlying disease mechanism and factors associated with the disease severity has dramatically increased. A recent study investigated the relationship between substance use disorders (SUD) and the risk of severe COVID-19 in the United States and concluded that the risk of hospitalization and death due to COVID-19 is directly correlated with substance abuse, including opioid use disorder (OUD) and cannabis use disorder (CUD). While we found this analysis fascinating, we believe this observation may be biased due to comorbidities (such as hypertension, diabetes, and cardiovascular disease) confounding the direct effect of SUD on severe COVID-19 illness. To answer this question, we sought to investigate the causal relationship between substance abuse and medication-taking history (as a proxy trait for comorbidities) with the risk of COVID-19 adverse outcomes. Our Mendelian randomization analysis confirms the causal relationship between OUD and severe COVID-19 illness but suggests an inverse causal effect for cannabinoids. Considering that COVID-19 mortality is largely attributed to disturbed immune regulation, the possible modulatory impact of cannabinoids in alleviating cytokine storms merits further investigation.
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Affiliation(s)
- M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA.
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Zhang Q, Tombline G, Ablaeva J, Zhang L, Zhou X, Smith Z, Zhao Y, Xiaoli AM, Wang Z, Lin JR, Jabalameli MR, Mitra J, Nguyen N, Vijg J, Seluanov A, Gladyshev VN, Gorbunova V, Zhang ZD. Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation. Cell Rep 2021; 37:109965. [PMID: 34758328 PMCID: PMC8656434 DOI: 10.1016/j.celrep.2021.109965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 06/07/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
The North American beaver is an exceptionally long-lived and cancer-resistant rodent species. Here, we report the evolutionary changes in its gene coding sequences, copy numbers, and expression. We identify changes that likely increase its ability to detoxify aldehydes, enhance tumor suppression and DNA repair, and alter lipid metabolism, potentially contributing to its longevity and cancer resistance. Hpgd, a tumor suppressor gene, is uniquely duplicated in beavers among rodents, and several genes associated with tumor suppression and longevity are under positive selection in beavers. Lipid metabolism genes show positive selection signals, changes in copy numbers, or altered gene expression in beavers. Aldh1a1, encoding an enzyme for aldehydes detoxification, is particularly notable due to its massive expansion in beavers, which enhances their cellular resistance to ethanol and capacity to metabolize diverse aldehyde substrates from lipid oxidation and their woody diet. We hypothesize that the amplification of Aldh1a1 may contribute to the longevity of beavers. Zhang et al. examine the genome of North American beavers and find evolutionary changes that could contribute to beavers’ longevity. In particular, Aldh1a1, encoding an enzyme for aldehyde detoxification, is massively expanded in the beaver genome, protecting them against exposure to aldehydes from lipid oxidation and their woody diet.
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Affiliation(s)
- Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary Smith
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alus M Xiaoli
- Departments of Medicine and Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhen Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nha Nguyen
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
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Lin JR, Sin-Chan P, Napolioni V, Torres GG, Mitra J, Zhang Q, Jabalameli MR, Wang Z, Nguyen N, Gao T, Laudes M, Görg S, Franke A, Nebel A, Greicius MD, Atzmon G, Ye K, Gorbunova V, Ladiges WC, Shuldiner AR, Niedernhofer LJ, Robbins PD, Milman S, Suh Y, Vijg J, Barzilai N, Zhang ZD. Rare genetic coding variants associated with human longevity and protection against age-related diseases. Nat Aging 2021; 1:783-794. [PMID: 37117627 DOI: 10.1038/s43587-021-00108-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/05/2021] [Indexed: 12/18/2022]
Abstract
Extreme longevity in humans has a strong genetic component, but whether this involves genetic variation in the same longevity pathways as found in model organisms is unclear. Using whole-exome sequences of a large cohort of Ashkenazi Jewish centenarians to examine enrichment for rare coding variants, we found most longevity-associated rare coding variants converge upon conserved insulin/insulin-like growth factor 1 signaling and AMP-activating protein kinase signaling pathways. Centenarians have a number of pathogenic rare coding variants similar to control individuals, suggesting that rare variants detected in the conserved longevity pathways are protective against age-related pathology. Indeed, we detected a pro-longevity effect of rare coding variants in the Wnt signaling pathway on individuals harboring the known common risk allele APOE4. The genetic component of extreme human longevity constitutes, at least in part, rare coding variants in pathways that protect against aging, including those that control longevity in model organisms.
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Jabalameli MR, Fitzpatrick FM, Colombo R, Howles SA, Leggatt G, Walker V, Wiberg A, Kunji ERS, Ennis S. Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones. Mol Genet Genomic Med 2021; 9:e1749. [PMID: 34346195 PMCID: PMC8683635 DOI: 10.1002/mgg3.1749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 05/13/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Calcium kidney stones are common and recurrences are often not preventable by available empiric remedies. Their etiology is multifactorial and polygenic, and an increasing number of genes are implicated. Their identification will enable improved management. METHODS DNA from three stone-formers in a Southampton family (UK) and two from an Italian family were analyzed independently by whole exome sequencing and selected variants were genotyped across all available members of both pedigrees. A disease variant of SLC25A25 (OMIM 608745), encoding the mitochondrial ATP-Mg/Pi carrier 3 (APC3) was identified, and analyzed structurally and functionally with respect to its calcium-regulated transport activity. RESULTS All five patients had a heterozygous dominant SLC25A25 variant (rs140777921; GRCh37.p13: chr 9 130868670 G>C; p.Gln349His; Reference Sequence NM_001006641.3). Non-stone formers also carried the variant indicating incomplete penetrance. Modeling suggests that the variant lacks a conserved polar interaction, which may cause structural instability. Calcium-regulated ATP transport was reduced to ~20% of the wild type, showing a large reduction in function. CONCLUSION The transporter is important in regulating mitochondrial ATP production. This rare variant may increase urine lithogenicity through impaired provision of ATP for solute transport processes in the kidney, and/or for purinergic signaling. Variants found in other genes may compound this abnormality.
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Affiliation(s)
- M Reza Jabalameli
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Fiona M Fitzpatrick
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Roberto Colombo
- Faculty of Medicine 'Agostino Gemelli', Catholic University of the Sacred Heart, Rome, Italy.,Center for the Study of Rare Inherited Diseases, Niguarda Ca´Granda Metropolitan Hospital, Milan, Italy
| | - Sarah A Howles
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.,Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Gary Leggatt
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth, UK
| | - Valerie Walker
- Department of Clinical Biochemistry, University Hospital Southampton, Southampton, UK
| | - Akira Wiberg
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Jabalameli MR, Briceno I, Martinez J, Briceno I, Pengelly RJ, Ennis S, Collins A. Aarskog-Scott syndrome: phenotypic and genetic heterogeneity. AIMS Genetics 2021. [DOI: 10.3934/genet.2016.1.49] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
AbstractAarskog-Scott syndrome (AAS) is a rare developmental disorder which primarily affects males and has a relative prevalence of 1 in 25,000 in the general population. AAS patients usually present with developmental complications including short stature and facial, skeletal and urogenital anomalies. The spectrum of genotype-phenotype correlations in AAS is unclear and mutations of the FGD1 gene on the proximal short arm of chromosome X account for only 20% of the incidence of the disorder. Failure to identify pathogenic variants in patients referred for FGD1 screening suggests heterogeneity underlying pathophysiology of the condition. Furthermore, overlapping features of AAS with several other developmental disorders increase the complexity of diagnosis. Cytoskeletal signaling may be involved in the pathophysiology of AAS. The FGD1 protein family has a role in activation of CDC42 (Cell Division Control protein 42 homolog) which has a core function in remodeling of extracellular matrix and the transcriptional activation of many modulators of development. Therefore, mutations in components in the EGFR1 (Epidermal Growth Factor Receptor 1) signaling pathway, to which CDC42 belongs, may contribute to pathophysiology. Parallel sequencing strategies (so-called next generation sequencing or high throughput sequencing) enables simultaneous production of millions of sequencing reads that enormously facilitate cost-effective identification of cryptic mutations in heterogeneous monogenic disorders. Here we review the source of phenotypic and genetic heterogeneity in the context of AAS and discuss the applicability of next generation sequencing for identification of novel mutations underlying AAS.
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Affiliation(s)
- M. Reza Jabalameli
- Genetic Epidemiology & Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ignacio Briceno
- Department of Biomedical Sciences, Medical School, Universidad de La Sabana, Bogota, Colombia
| | - Julio Martinez
- Department of Biomedical Sciences, Medical School, Universidad de La Sabana, Bogota, Colombia
| | - Ignacio Briceno
- Instituto de Genética Humana, Faculty of Medicine, Pontificia Universidad Javeriana, Colombia
| | - Reuben J. Pengelly
- Genetic Epidemiology & Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarah Ennis
- Genetic Epidemiology & Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Collins
- Genetic Epidemiology & Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
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Charsouei S, Jabalameli MR, Karimi-Moghadam A. Molecular insights into the role of AMPA receptors in the synaptic plasticity, pathogenesis and treatment of epilepsy: therapeutic potentials of perampanel and antisense oligonucleotide (ASO) technology. Acta Neurol Belg 2020; 120:531-544. [PMID: 32152997 DOI: 10.1007/s13760-020-01318-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Glutamate is considered as the predominant excitatory neurotransmitter in the mammalian central nervous systems (CNS). Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are the main glutamate-gated ionotropic channels that mediate the majority of fast synaptic excitation in the brain. AMPARs are highly dynamic that constitutively move into and out of the postsynaptic membrane. Changes in the postsynaptic number of AMPARs play a key role in controlling synaptic plasticity and also brain functions such as memory formation and forgetting development. Impairments in the regulation of AMPAR function, trafficking, and signaling pathway may also contribute to neuronal hyperexcitability and epileptogenesis process, which offers AMPAR as a potential target for epilepsy therapy. Over the last decade, various types of AMPAR antagonists such as perampanel and talampanel have been developed to treat epilepsy, but they usually show limited efficacy at low doses and produce unwanted cognitive and motor side effects when administered at higher doses. In the present article, the latest findings in the field of molecular mechanisms controlling AMPAR biology, as well as the role of these mechanism dysfunctions in generating epilepsy will be reviewed. Also, a comprehensive summary of recent findings from clinical trials with perampanel, in treating epilepsy, glioma-associated epilepsy and Parkinson's disease is provided. Finally, antisense oligonucleotide therapy as an alternative strategy for the efficient treatment of epilepsy is discussed.
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Affiliation(s)
- Saeid Charsouei
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, IR, Iran
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Amin Karimi-Moghadam
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR, Iran.
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Vergara-Lope A, Jabalameli MR, Horscroft C, Ennis S, Collins A, Pengelly RJ. Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data. Sci Data 2019; 6:208. [PMID: 31624256 PMCID: PMC6797713 DOI: 10.1038/s41597-019-0227-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/29/2019] [Indexed: 11/08/2022] Open
Abstract
Quantification of linkage disequilibrium (LD) patterns in the human genome is essential for genome-wide association studies, selection signature mapping and studies of recombination. Whole genome sequence (WGS) data provides optimal source data for this quantification as it is free from biases introduced by the design of array genotyping platforms. The Malécot-Morton model of LD allows the creation of a cumulative map for each choromosome, analogous to an LD form of a linkage map. Here we report LD maps generated from WGS data for a large population of European ancestry, as well as populations of Baganda, Ethiopian and Zulu ancestry. We achieve high average genetic marker densities of 2.3-4.6/kb. These maps show good agreement with prior, low resolution maps and are consistent between populations. Files are provided in BED format to allow researchers to readily utilise this resource.
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Affiliation(s)
- Alejandra Vergara-Lope
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Reza Jabalameli
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Clare Horscroft
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarah Ennis
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Reuben J Pengelly
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK.
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Pengelly RJ, Vergara-Lope A, Alyousfi D, Jabalameli MR, Collins A. Understanding the disease genome: gene essentiality and the interplay of selection, recombination and mutation. Brief Bioinform 2017; 20:267-273. [DOI: 10.1093/bib/bbx110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 12/24/2022] Open
Affiliation(s)
- Reuben J Pengelly
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Alejandra Vergara-Lope
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Dareen Alyousfi
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Reza Jabalameli
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Collins
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
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Pengelly RJ, Greville-Heygate S, Schmidt S, Seaby EG, Jabalameli MR, Mehta SG, Parker MJ, Goudie D, Fagotto-Kaufmann C, Mercer C, Debant A, Ennis S, Baralle D. Mutations specific to the Rac-GEF domain of TRIO cause intellectual disability and microcephaly. J Med Genet 2016; 53:735-742. [PMID: 27418539 PMCID: PMC5264232 DOI: 10.1136/jmedgenet-2016-103942] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 11/03/2022]
Abstract
BACKGROUND Neurodevelopmental disorders have challenged clinical genetics for decades, with over 700 genes implicated and many whose function remains unknown. The application of whole-exome sequencing is proving pivotal in closing the genotype/phenotype gap through the discovery of new genes and variants that help to unravel the pathogenic mechanisms driving neuropathogenesis. One such discovery includes TRIO, a gene recently implicated in neurodevelopmental delay. Trio is a Dbl family guanine nucleotide exchange factor (GEF) and a major regulator of neuronal development, controlling actin cytoskeleton dynamics by activating the GTPase Rac1. METHODS Whole-exome sequencing was undertaken on a family presenting with global developmental delay, microcephaly and mild dysmorphism. Father/daughter exome analysis was performed, followed by confirmatory Sanger sequencing and segregation analysis on four individuals. Three further patients were recruited through the deciphering developmental disorders (DDD) study. Functional studies were undertaken using patient-specific Trio protein mutations. RESULTS We identified a frameshift deletion in TRIO that segregated autosomal dominantly. By scrutinising data from DDD, we further identified three unrelated children with a similar phenotype who harboured de novo missense mutations in TRIO. Biochemical studies demonstrated that in three out of four families, the Trio mutations led to a markedly reduced Rac1 activation. CONCLUSIONS We describe an inherited global developmental delay phenotype associated with a frameshift deletion in TRIO. Additionally, we identify pathogenic de novo missense mutations in TRIO associated with the same consistent phenotype, intellectual disability, microcephaly and dysmorphism with striking digital features. We further functionally validate the importance of the GEF domain in Trio protein function. Our study demonstrates how genomic technologies are yet again proving prolific in diagnosing and advancing the understanding of neurodevelopmental disorders.
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Affiliation(s)
- Reuben J Pengelly
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Susanne Schmidt
- Centre de Recherche en Biologie Cellulaire de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, Cédex, France
| | - Eleanor G Seaby
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Reza Jabalameli
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarju G Mehta
- Department of Clinical Genetics, Cambridge University Hospital Trust, Cambridge, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital NHS Foundation Trust, OPD2, Northern General Hospital, Sheffield, UK
| | - David Goudie
- Department of Clinical Genetics, Ninewells Hospital, Dundee, UK
| | - Christine Fagotto-Kaufmann
- Centre de Recherche en Biologie Cellulaire de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, Cédex, France
| | - Catherine Mercer
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | | | - Anne Debant
- Centre de Recherche en Biologie Cellulaire de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, Cédex, France
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
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Jabalameli MR, Zahednasab H. Are IL2 promoter polymorphisms associated with MS in Iranian patients? - We do not know. Int J Immunogenet 2014; 41:528-9. [PMID: 25399512 DOI: 10.1111/iji.12149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 11/29/2022]
Affiliation(s)
- M R Jabalameli
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
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Bahreini SA, Jabalameli MR, Saadatnia M, Zahednasab H. The role of non-HLA single nucleotide polymorphisms in multiple sclerosis susceptibility. J Neuroimmunol 2010; 229:5-15. [DOI: 10.1016/j.jneuroim.2010.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/19/2010] [Accepted: 08/04/2010] [Indexed: 10/19/2022]
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Zahednasab H, Saadatnia M, Jabalameli MR, Zarkesh-Esfahani H, Esmaeili A, Bahreini SA. Controversial role of MMP-9 gene in MS disease. J Neuroimmunol 2010; 230:191. [PMID: 20961624 DOI: 10.1016/j.jneuroim.2010.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
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