1
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Wang D, Ma S, Yan M, Dong M, Zhang M, Zhang T, Zhang T, Zhang X, Xu L, Huang X. DNA methylation patterns in the peripheral blood of Xinjiang brown cattle with variable somatic cell counts. Front Genet 2024; 15:1405478. [PMID: 39045327 PMCID: PMC11263093 DOI: 10.3389/fgene.2024.1405478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/10/2024] [Indexed: 07/25/2024] Open
Abstract
The use of wide-ranging dairy herd improvement (DHI) measurements has resulted in the investigation of somatic cell count (SCC) and the identification of many genes associated with mastitis resistance. In this study, blood samples of Xinjiang brown cattle with different SCCs were collected, and genome-wide DNA methylation was analyzed by MeDIP-seq. The results showed that peaks were mostly in intergenic regions, followed by introns, exons, and promoters. A total of 1,934 differentially expressed genes (DEGs) associated with mastitis resistance in Xinjiang brown cattle were identified. The enrichment of differentially methylated CpG islands of the TRAPPC9 and CD4 genes was analyzed by bisulfate genome sequencing. The methylation rate of differentially methylated CpGs was higher in the TRAPPC9 gene of cattle with clinical mastitis (mastitis group) compared with healthy cattle (control group), while methylation of differentially methylated CpGs was significantly lower in CD4 of the mastitis group compared with the control group. RT-qRCR analysis showed that the mastitis group had significantly reduced expression of CD4 and TRAPPC9 genes compared to the control group (p < 0.05). Furthermore, Mac-T cells treated with lipopolysaccharide and lipoteichoic acid showed significant downregulation of the TRAPPC9 gene in the mastitis group compared with the control group. The identified epigenetic biomarkers provide theoretical reference for treating cow mastitis, breeding management, and the genetic improvement of mastitis resistance in Xinjiang brown cattle.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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2
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Kharrat M, Triki C, Ben Isaa A, Bouchaala W, Alila O, Chouchen J, Ghouliya Y, Kamoun F, Tlili A, Fakhfakh F. Expanding the genetic and phenotypic spectrum of TRAPPC9 and MID2-related neurodevelopmental disabilities: report of two novel mutations, 3D-modelling, and molecular docking studies. J Hum Genet 2024; 69:291-299. [PMID: 38467738 DOI: 10.1038/s10038-024-01242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
Intellectual disabilities (ID) and autism spectrum disorders (ASD) have a variety of etiologies, including environmental and genetic factors. Our study reports a psychiatric clinical investigation and a molecular analysis using whole exome sequencing (WES) of two siblings with ID and ASD from a consanguineous family. Bioinformatic prediction and molecular docking analysis were also carried out. The two patients were diagnosed with profound intellectual disability, brain malformations such as cortical atrophy, acquired microcephaly, and autism level III. The neurological and neuropsychiatric examination revealed that P2 was more severely affected than P1, as he was unable to walk, presented with dysmorphic feature and exhibited self and hetero aggressive behaviors. The molecular investigations revealed a novel TRAPPC9 biallelic nonsense mutation (c.2920 C > T, p.R974X) in the two siblings. The more severely affected patient (P2) presented, along with the TRAPPC9 variant, a new missense mutation c.166 C > T (p.R56C) in the MID2 gene at hemizygous state, while his sister P1 was merely a carrier. The 3D modelling and molecular docking analysis revealed that c.166 C > T variant could affect the ability of MID2 binding to Astrin, leading to dysregulation of microtubule dynamics and causing morphological abnormalities in the brain. As our knowledge, the MID2 mutation (p.R56C) is the first one to be detected in Tunisia and causing phenotypic variability between the siblings. We extend the genetic and clinical spectrum of TRAPPC9 and MID2 mutations and highlights the possible concomitant presence of X-linked as well as autosomal recessive inheritance to causing ID, microcephaly, and autism.
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Affiliation(s)
- Marwa Kharrat
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences of Sfax University, Sfax, Tunisia.
| | - Chahnez Triki
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Abir Ben Isaa
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Wafa Bouchaala
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Olfa Alila
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences of Sfax University, Sfax, Tunisia
| | - Jihen Chouchen
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Yosra Ghouliya
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Fatma Kamoun
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences of Sfax University, Sfax, Tunisia.
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3
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Li Y, Usman M, Sapp E, Ke Y, Wang Z, Boudi A, DiFiglia M, Li X. Chronic pharmacologic manipulation of dopamine transmission ameliorates metabolic disturbance in Trappc9-linked brain developmental syndrome. JCI Insight 2024; 9:e181339. [PMID: 38889014 PMCID: PMC11383600 DOI: 10.1172/jci.insight.181339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Loss-of-function mutations of the gene encoding the trafficking protein particle complex subunit 9 (Trappc9) cause autosomal recessive intellectual disability and obesity by unknown mechanisms. Genome-wide analysis links Trappc9 to nonalcoholic fatty liver disease (NAFLD). Trappc9-deficient mice have been shown to appear overweight shortly after weaning. Here, we analyzed serum biochemistry and histology of adipose and liver tissues to determine the incidence of obesity and NAFLD in Trappc9-deficient mice and combined transcriptomic and proteomic analyses, pharmacological studies, and biochemical and histological examinations of postmortem mouse brains to unveil mechanisms involved. We found that Trappc9-deficient mice presented with systemic glucose homeostatic disturbance, obesity, and NAFLD, which were relieved upon chronic treatment combining dopamine receptor D2 (DRD2) agonist quinpirole and DRD1 antagonist SCH23390. Blood glucose homeostasis in Trappc9-deficient mice was restored upon administering quinpirole alone. RNA-sequencing analysis of DRD2-containing neurons and proteomic study of brain synaptosomes revealed signs of impaired neurotransmitter secretion in Trappc9-deficient mice. Biochemical and histological studies of mouse brains showed that Trappc9-deficient mice synthesized dopamine normally, but their dopamine-secreting neurons had a lower abundance of structures for releasing dopamine in the striatum. Our study suggests that Trappc9 loss of function causes obesity and NAFLD by constraining dopamine synapse formation.
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Affiliation(s)
- Yan Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Muhammad Usman
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Yuting Ke
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Zejian Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Xueyi Li
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
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4
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Aljuraysi S, Platt M, Pulix M, Poptani H, Plagge A. Microcephaly with a disproportionate hippocampal reduction, stem cell loss and neuronal lipid droplet symptoms in Trappc9 KO mice. Neurobiol Dis 2024; 192:106431. [PMID: 38331351 DOI: 10.1016/j.nbd.2024.106431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024] Open
Abstract
Mutations of the human TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 9 (TRAPPC9) cause a neurodevelopmental disorder characterised by microcephaly and intellectual disability. Trappc9 constitutes a subunit specific to the intracellular membrane-associated TrappII complex. The TrappII complex interacts with Rab11 and Rab18, the latter being specifically associated with lipid droplets (LDs). Here we used non-invasive imaging to characterise Trappc9 knock-out (KO) mice as a model of the human hereditary disorder. KOs developed postnatal microcephaly with many grey and white matter regions being affected. In vivo magnetic resonance imaging (MRI) identified a disproportionately stronger volume reduction in the hippocampus, which was associated with a significant loss of Sox2-positive neural stem and progenitor cells. Diffusion tensor imaging indicated a reduced organisation or integrity of white matter areas. Trappc9 KOs displayed behavioural abnormalities in several tests related to exploration, learning and memory. Trappc9-deficient primary hippocampal neurons accumulated a larger LD volume per cell following Oleic Acid stimulation, and the coating of LDs by Perilipin-2 was much reduced. Additionally, Trappc9 KOs developed obesity, which was significantly more severe in females than in males. Our findings indicate that, beyond previously reported Rab11-related vesicle transport defects, dysfunctions in LD homeostasis might contribute to the neurobiological symptoms of Trappc9 deficiency.
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Affiliation(s)
- Sultan Aljuraysi
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mark Platt
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK
| | - Michela Pulix
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Harish Poptani
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK.
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK.
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5
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Uctepe E, Yesilyurt A, Esen FN, Tumer S, Mancilar H, Sonmez FM. TRAPPC9-Related Intellectual Disability: Report of Two New Cases and Review of the Literature. Mol Syndromol 2023; 14:485-492. [PMID: 38058760 PMCID: PMC10697769 DOI: 10.1159/000531439] [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: 03/18/2023] [Accepted: 06/05/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction Hereditary forms of intellectual disability (ID), an estimated prevalence ranging between 1% and 3% in the general population, are among the most important problems in health care. Especially, autosomal-recessive ID has a very heterogeneous molecular basis and a lack of specific phenotypic features. Methods Here, we report on two unrelated patients with autosomal-recessive ID, microcephaly, and autistic features and review the patients with TRAPPC9-related ID. Whole-exome sequencing and array CGH were performed for molecular diagnosis of the patients. Results The first case has a microdeletion on chromosome 8q24.23-q24.3 region which is 1.7 Mb in length and includes the last 5 exons of TRAPPC9, and c.3435delG [p.Thr1146Profs*8] deletion. The second case has a homozygous missense c.623A>C (p.His208Pro) variant in TRAPPC9 which is detected by means of whole-exome sequencing study of the proband. We also reviewed the clinical findings and mutation spectrum of all patients with TRAPPC9-related ID reported so far. Conclusions Our study showed that the most consistent clinical findings for TRAPPC9-related ID are ID, microcephaly, and some structural brain MRI abnormalities. The mutations in the TRAPPC9 are scattered throughout all exons of TRAPPC9 indicating there is no hot spot mutation region in this gene.
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Affiliation(s)
- Eyyup Uctepe
- Acibadem Ankara Tissue Typing Laboratory, Ankara, Turkey
| | - Ahmet Yesilyurt
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Turkey
- Acibadem Maslak Hospital, Istanbul, Turkey
| | | | - Sait Tumer
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Turkey
| | | | - Fatma Mujgan Sonmez
- Karadeniz Technical University Faculty of Medicine, Department of Child Neurology, Ankara, Turkey
- Private office, Child Neurology, Ankara, Turkey
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6
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Polenghi M, Taverna E. Intracellular traffic and polarity in brain development. Front Neurosci 2023; 17:1172016. [PMID: 37859764 PMCID: PMC10583573 DOI: 10.3389/fnins.2023.1172016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023] Open
Abstract
Neurons forming the human brain are generated during embryonic development by neural stem and progenitor cells via a process called neurogenesis. A crucial feature contributing to neural stem cell morphological and functional heterogeneity is cell polarity, defined as asymmetric distribution of cellular components. Cell polarity is built and maintained thanks to the interplay between polarity proteins and polarity-generating organelles, such as the endoplasmic reticulum (ER) and the Golgi apparatus (GA). ER and GA affect the distribution of membrane components and work as a hub where glycans are added to nascent proteins and lipids. In the last decades our knowledge on the role of polarity in neural stem and progenitor cells have increased tremendously. However, the role of traffic and associated glycosylation in neural stem and progenitor cells is still relatively underexplored. In this review, we discuss the link between cell polarity, architecture, identity and intracellular traffic, and highlight how studies on neurons have shaped our knowledge and conceptual framework on traffic and polarity. We will then conclude by discussing how a group of rare diseases, called congenital disorders of glycosylation (CDG) offers the unique opportunity to study the contribution of traffic and glycosylation in the context of neurodevelopment.
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7
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Hu M, Bodnar B, Zhang Y, Xie F, Li F, Li S, Zhao J, Zhao R, Gedupoori N, Mo Y, Lin L, Li X, Meng W, Yang X, Wang H, Barbe MF, Srinivasan S, Bethea JR, Mo X, Xu H, Hu W. Defective neurite elongation and branching in Nibp/Trappc9 deficient zebrafish and mice. Int J Biol Sci 2023; 19:3226-3248. [PMID: 37416774 PMCID: PMC10321293 DOI: 10.7150/ijbs.78489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
Loss of function in transport protein particles (TRAPP) links a new set of emerging genetic disorders called "TRAPPopathies". One such disorder is NIBP syndrome, characterized by microcephaly and intellectual disability, and caused by mutations of NIBP/TRAPPC9, a crucial and unique member of TRAPPII. To investigate the neural cellular/molecular mechanisms underlying microcephaly, we developed Nibp/Trappc9-deficient animal models using different techniques, including morpholino knockdown and CRISPR/Cas mutation in zebrafish and Cre/LoxP-mediated gene targeting in mice. Nibp/Trappc9 deficiency impaired the stability of the TRAPPII complex at actin filaments and microtubules of neurites and growth cones. This deficiency also impaired elongation and branching of neuronal dendrites and axons, without significant effects on neurite initiation or neural cell number/types in embryonic and adult brains. The positive correlation of TRAPPII stability and neurite elongation/branching suggests a potential role for TRAPPII in regulating neurite morphology. These results provide novel genetic/molecular evidence to define patients with a type of non-syndromic autosomal recessive intellectual disability and highlight the importance of developing therapeutic approaches targeting the TRAPPII complex to cure TRAPPopathies.
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Affiliation(s)
- Min Hu
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Brittany Bodnar
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Yonggang Zhang
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu 610052, China
| | - Fangxin Xie
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu 610052, China
- Department of Clinical Laboratory, Xi'an NO. 3 Hospital, Xi'an, Shaanxi, 710018, China
| | - Fang Li
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Siying Li
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Jin Zhao
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Ruotong Zhao
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Naveen Gedupoori
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Yifan Mo
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Lanyi Lin
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Xue Li
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Wentong Meng
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Mary F. Barbe
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Shanthi Srinivasan
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John R. Bethea
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Hong Xu
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Wenhui Hu
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
- Center for Metabolic Disease Research, Department of Pathalogy and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
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8
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Penon-Portmann M, Hodoglugil U, Arun P W, Yip T, Slavotinek A, Tenney JL. TRAPPC9-related neurodevelopmental disorder: Report of a homozygous deletion in TRAPPC9 due to paternal uniparental isodisomy. Am J Med Genet A 2023; 191:1077-1082. [PMID: 36574751 DOI: 10.1002/ajmg.a.63100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/24/2022] [Accepted: 12/11/2022] [Indexed: 12/28/2022]
Abstract
TRAPPC9 loss-of-function biallelic variants are associated with an autosomal recessive intellectual disability syndrome (Online Mendelian Inheritance of Man no. 613192), also characterized by microcephaly, hypertelorism, obesity, growth delay, and behavioral differences. Here, we describe an 8-year-old Hispanic female with neurodevelopmental disorder, partial epilepsy, microcephaly, bilateral cleft lip and alveolus, growth delay, and dysmorphic features. She had abnormal myelination, mega cisterna magna, and colpocephaly on brain magnetic resonance imaging (MRI). Microarray showed a single ~146 Mb region of homozygosity (ROH) encompassing all of Chromosome 8, consistent with uniparental isodisomy (UPD). Exome sequencing performed in-house did not identify single nucleotide variants to explain her phenotype. Algorithms developed in-house and further evaluation of BAM files revealed a homozygous deletion overlapping Exon 2 in TRAPPC9 within the ROH. Subsequent del/dup analyses with exon-level oligo array confirmed a likely pathogenic deletion in TRAPPC9 (NM_031466.5): arr[GRCh37] 8q24.3(141460661_141461780)x0. Our case highlights the implications of downstream analyses from UPD/ROH given the increased risk for AR conditions, the strengths of combining orthologous molecular methods to establish a diagnosis and further delineates the TRAPPC9-related phenotype in an individual of Hispanic ancestry.
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Affiliation(s)
- Monica Penon-Portmann
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Ugur Hodoglugil
- Genomic Medicine Laboratory, University of California San Francisco, San Francisco, California, USA
| | - Wiita Arun P
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Tiffany Yip
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.,Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jessica L Tenney
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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9
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Dattilo V, Ulivi S, Minelli A, La Bianca M, Giacopuzzi E, Bortolomasi M, Bignotti S, Gennarelli M, Gasparini P, Concas MP. Genome-wide association studies on Northern Italy isolated populations provide further support concerning genetic susceptibility for major depressive disorder. World J Biol Psychiatry 2023; 24:135-148. [PMID: 35615967 DOI: 10.1080/15622975.2022.2082523] [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: 10/18/2022]
Abstract
OBJECTIVES Major depressive disorder (MDD) is a psychiatric disorder with pathogenesis influenced by both genetic and environmental factors. To date, the molecular-level understanding of its aetiology remains unclear. Thus, we aimed to identify genetic variants and susceptibility genes for MDD with a genome-wide association study (GWAS) approach. METHODS We performed a meta-analysis of GWASs and a gene-based analysis on two Northern Italy isolated populations (cases/controls n = 166/472 and 33/320), followed by replication and polygenic risk score (PRS) analyses in Italian independent samples (cases n = 464, controls n = 339). RESULTS We identified two novel MDD-associated genes, KCNQ5 (lead SNP rs867262, p = 3.82 × 10-9) and CTNNA2 (rs6729523, p = 1.25 × 10-8). The gene-based analysis revealed another six genes (p < 2.703 × 10-6): GRM7, CTNT4, SNRK, SRGAP3, TRAPPC9, and FHIT. No replication of the genome-wide significant SNPs was found in the independent cohort, even if 14 SNPs around CTNNA2 showed association with MDD and related phenotypes at the nominal level of p (<0.05). Furthermore, the PRS model developed in the discovery cohort discriminated cases and controls in the replication cohort. CONCLUSIONS Our work suggests new possible genes associated with MDD, and the PRS analysis confirms the polygenic nature of this disorder. Future studies are required to better understand the role of these findings in MDD.
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Affiliation(s)
- Vincenzo Dattilo
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Sheila Ulivi
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Alessandra Minelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Martina La Bianca
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Edoardo Giacopuzzi
- Wellcome Centre for Human Genetics, Oxford University, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Stefano Bignotti
- Unit of Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Science, University of Trieste, Trieste, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
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10
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Touhami R, Foddha H, Alix E, Jalloul A, Mougou-Zerelli S, Saad A, Sanlaville D, Haj Khelil A. Case report: 7p22.3 deletion and 8q24.3 duplication in a patient with epilepsy and psychomotor delay-Does both possibly act to modulate a candidate gene region for the patient's phenotype? Front Genet 2023; 13:1061539. [PMID: 36778913 PMCID: PMC9909830 DOI: 10.3389/fgene.2022.1061539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Background: Psychomotor delay, epilepsy and dysmorphic features are clinical signs which are described in multiple syndromes due to chromosomal imbalances or mutations involving key genes implicated in the stages of Early Embryonic Development. In this context, we report a 10 years old Tunisian patient with these three signs. Our objective is to determine the cause of developmental, behavioral and facial abnormalities in this patient. Methods: We used banding cytogenetics (karyotype) and Array Comparative Genomic Hybridization (Array CGH) to this purpose. Results: The karyotype was in favor of a derivative of chromosome 7 in the patient and Array CGH analysis revealed a loss of genetic material in 7p22.3-p22.1 (4,56 Mb) with a gain at 8q24.23-q24 (9.20 Mb) resulting from maternal 7/8 reciprocal translocation. An in silico analysis of the unbalanced region was carried out and showed that the 7p22.3-p22.1 deletion contains eight genes. Among them, BRAT1 gene, previously described in several neurodevelopmental diseases, may be a candidate gene which absence could be correlated to the patient's phenotype. However, the 8q24.23-q24 duplication could be involved in the phenotype of this patient. Conclusion: In this study, we report for the first time a 7p deletion/8q duplication in a patient with psychomoteur delay, epilepsy and facial dysmorphism. Our study showed that Array CGH still useful for delivering a conclusive genetic diagnosis for patients having neurodevelopmental abnormalities in the era of next-generation sequencing.
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Affiliation(s)
- Rahma Touhami
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia,Department of Cellular and Molecular Biology, Superior Institute of Biotechnology, University of Monastir, Monastir, Tunisia,Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Hajer Foddha
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Eudeline Alix
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Afef Jalloul
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Soumaya Mougou-Zerelli
- Laboratory of Cytogenetics, molecular genetics, and human reproduction biology, CHU Farhat Hached, Sousse, Tunisia
| | - Ali Saad
- Laboratory of Cytogenetics, molecular genetics, and human reproduction biology, CHU Farhat Hached, Sousse, Tunisia
| | - Damien Sanlaville
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Amel Haj Khelil
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia,Department of Cellular and Molecular Biology, Superior Institute of Biotechnology, University of Monastir, Monastir, Tunisia,*Correspondence: Amel Haj Khelil,
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11
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Muacevic A, Adler JR, Verma R, Shah SD, Vattikuti B, Khan AZ, Shahzadi A, Abdi P, Anthony M, Farkouh CS, Farkouh M, Santiago N, Zepeda D, Nunez A. Non-syndromic Intellectual Disability: An Experimental In-Depth Exploration of Inheritance Pattern, Phenotypic Presentation, and Genomic Composition. Cureus 2023; 15:e34085. [PMID: 36843831 PMCID: PMC9946902 DOI: 10.7759/cureus.34085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 01/25/2023] Open
Abstract
Background Intellectual disability (ID), also termed mental retardation (MR), is a neurodevelopmental disorder characterized by an intelligence quotient (IQ) of 70 or below and a deficit in at least two behaviors associated with adaptive functioning. The condition is further classified into syndromic intellectual disability (S-ID) and non-syndromic intellectual disability (NS-ID). This study highlights the genes associated with NS-ID. Objectives A genetic study was performed on two Pakistani families to know the inheritance patterns, clinical phenotypes, and molecular genetics of affected individuals with NS-ID. Methodology Samples were collected from two families: families A and B. All affected individuals in both families were diagnosed by a neurologist. Written informed consent was taken from the affected individuals and guardians before collecting the data and sample. Family A belongs to the Swabi District of Pakistan having four affected individuals, out of whom three were male and one was female. Family B also belongs to the Swabi District of Pakistan having two affected individuals, out of whom one was male and one was female. A total of 10 candidate genes were selected and were further screened by microarray analysis. Results In family A, this analysis identified a region of 9.6 Mb on chromosome 17q11.2-q12 between the single nucleotide polymorphisms (SNPs) rs953527 and rs2680398. The region was genotyped using microsatellite markers to confirm the haplotypes in all family members. Based on the phenotype-genotype relationship, 10 possible candidate genes were selected out of more than 140 genes in this critical region of 9.6 Mb. In family B, homozygosity mapping through microarray identified four homozygous areas of affected individuals: two (27,324,822-59,122,062 and 96,423,252123,656,241) on chromosome 8, one (14,785,224-19,722,760) on chromosome 9, and one (126173647-126215644) on chromosome 11. Conclusion An autosomal recessive pattern was found in the pedigrees of both families A and B. Phenotypically affected individuals showed IQ levels below 70. Three genes, CDK5R1, OMG, and EV12A, were found on chromosome 17q11.2-q12 region of affected individuals in family A with high expression in the frontal cortex of the brain, hippocampus, and spinal cord, respectively. Other regions on chromosomes 8, 9, and 11 as evident from the affected individuals in family B can also contribute to the non-syndromic autosomal recessive intellectual disability (NS-ARID). Further research is needed to find the association of these genes with intelligence and other neuropsychiatric conditions.
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12
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Sultana P, Novotny J. Rab11 and Its Role in Neurodegenerative Diseases. ASN Neuro 2022; 14:17590914221142360. [PMID: 36464817 PMCID: PMC9726856 DOI: 10.1177/17590914221142360] [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: 12/08/2022] Open
Abstract
Vesicles mediate the trafficking of membranes/proteins in the endocytic and secretory pathways. These pathways are regulated by small GTPases of the Rab family. Rab proteins belong to the Ras superfamily of GTPases, which are significantly involved in various intracellular trafficking and signaling processes in the nervous system. Rab11 is known to play a key role especially in recycling many proteins, including receptors important for signal transduction and preservation of functional activities of nerve cells. Rab11 activity is controlled by GEFs (guanine exchange factors) and GAPs (GTPase activating proteins), which regulate its function through modulating GTP/GDP exchange and the intrinsic GTPase activity, respectively. Rab11 is involved in the transport of several growth factor molecules important for the development and repair of neurons. Overexpression of Rab11 has been shown to significantly enhance vesicle trafficking. On the other hand, a reduced expression of Rab11 was observed in several neurodegenerative diseases. Current evidence appears to support the notion that Rab11 and its cognate proteins may be potential targets for therapeutic intervention. In this review, we briefly discuss the function of Rab11 and its related interaction partners in intracellular pathways that may be involved in neurodegenerative processes.
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Affiliation(s)
| | - Jiri Novotny
- Jiri Novotny, Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic.
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13
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Amin M, Vignal C, Eltaraifee E, Mohammed IN, Hamed AAA, Elseed MA, Babai A, Elbadi I, Mustafa D, Abubaker R, Mustafa M, Drunat S, Elsayed LEO, Ahmed AE, Boespflug-Tanguy O, Dorboz I. A novel homozygous mutation in TRAPPC9 gene causing autosomal recessive non-syndromic intellectual disability. BMC Med Genomics 2022; 15:236. [PMID: 36348459 PMCID: PMC9644490 DOI: 10.1186/s12920-022-01354-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background The etiology of intellectual disabilities is diverse and includes both genetic and environmental factors. The genetic causes of intellectual disabilities range from chromosomal aberrations to single gene disorders. The TRAPPC9 gene has been reported to cause autosomal recessive forms of intellectual disabilities in 56 patients from consanguineous and non-consanguineous families around the world. Methods We analyzed two siblings with intellectual disability, microcephaly and delayed motor and speech development from a consanguineous Sudanese family. Genomic DNA was screened for mutations using NGS panel (NextSeq500 Illumina) testing 173 microcephaly associated genes in the Molecular Genetics service in Robert Debre hospital in Paris, France. Results A novel homozygous mutation (NM_031466.7 (TRAPPC9):c.2288dup, p. (Val764Glyfs*7) in exon 14 of TRAPPC9 gene was found in the two patients. The mutation was predicted to cause nonsense mediated decay (NSMD) using SIFT prediction tool. The variant has not been found in either gnomAD or Exac databases. Both parents were heterozygous (carriers) to the mutation. Conclusion This is the first study to report patients with TRAPPC9-related disorder from Sub-Saharan Africa.
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14
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Chhetri G, Ke Y, Wang P, Usman M, Li Y, Sapp E, Wang J, Ghosh A, Islam MA, Wang X, Boudi A, DiFiglia M, Li X. Impaired XK recycling for importing manganese underlies striatal vulnerability in Huntington's disease. J Cell Biol 2022; 221:213461. [PMID: 36099524 PMCID: PMC9475296 DOI: 10.1083/jcb.202112073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/15/2022] [Accepted: 07/29/2022] [Indexed: 02/08/2023] Open
Abstract
Mutant huntingtin, which causes Huntington's disease (HD), is ubiquitously expressed but induces preferential loss of striatal neurons by unclear mechanisms. Rab11 dysfunction mediates homeostatic disturbance of HD neurons. Here, we report that Rab11 dysfunction also underscores the striatal vulnerability in HD. We profiled the proteome of Rab11-positive endosomes of HD-vulnerable striatal cells to look for protein(s) linking Rab11 dysfunction to striatal vulnerability in HD and found XK, which triggers the selective death of striatal neurons in McLeod syndrome. XK was trafficked together with Rab11 and was diminished on the surface of immortalized HD striatal cells and striatal neurons in HD mouse brains. We found that XK participated in transporting manganese, an essential trace metal depleted in HD brains. Introducing dominantly active Rab11 into HD striatal cells improved XK dynamics and increased manganese accumulation in an XK-dependent manner. Our study suggests that impaired Rab11-based recycling of XK onto cell surfaces for importing manganese is a driver of striatal dysfunction in Huntington's disease.
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Affiliation(s)
- Gaurav Chhetri
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yuting Ke
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Ping Wang
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA.,Department of Neurology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Muhammad Usman
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Jing Wang
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Arabinda Ghosh
- Department of Botany, Microbiology Division, Gauhati University, Guwahati, Assam, India
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolong Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Xueyi Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
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15
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Trappc9 Deficiency Impairs the Plasticity of Stem Cells. Int J Mol Sci 2022; 23:ijms23094900. [PMID: 35563289 PMCID: PMC9101649 DOI: 10.3390/ijms23094900] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Genetic mutations of trappc9 cause intellectual disability with the atrophy of brain structures and variable obesity by poorly understood mechanisms. Trappc9-deficient mice develop phenotypes resembling pathological changes in humans and appear overweight shortly after weaning, and thus are useful for studying the pathogenesis of obesity. Here, we investigated the effects of trappc9 deficiency on the proliferation and differentiation capacity of adipose-derived stem cells (ASCs). We isolated ASCs from mice before overweight was developed and found that trappc9-null ASCs exhibited signs of premature senescence and cell death. While the lineage commitment was retained, trappc9-null ASCs preferred adipogenic differentiation. We observed a profound accumulation of lipid droplets in adipogenic cells derived from trappc9-deficient ASCs and marked differences in the distribution patterns and levels of calcium deposited in osteoblasts obtained from trappc9-null ASCs. Biochemical studies revealed that trappc9 deficiency resulted in an upregulated expression of rab1, rab11, and rab18, and agitated autophagy in ASCs. Moreover, we found that the content of neural stem cells in both the subventricular zone of the lateral ventricle and the subgranular zone of the dentate gyrus vastly declined in trappc9-null mice. Collectively, our results suggest that obesity, as well as brain structure hypoplasia induced by the deficiency of trappc9, involves an impairment in the plasticity of stem cells.
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16
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TRAPPC9-CDG: A novel congenital disorder of glycosylation with dysmorphic features and intellectual disability. Genet Med 2022; 24:894-904. [PMID: 35042660 DOI: 10.1016/j.gim.2021.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023] Open
Abstract
PURPOSE TRAPPC9 deficiency is an autosomal recessive disorder mainly associated with intellectual disability (ID), microcephaly, and obesity. Previously, TRAPPC9 deficiency has not been associated with biochemical abnormalities. METHODS Exome sequencing was performed in 3 individuals with ID and dysmorphic features. N-Glycosylation analyses were performed in the patients' blood samples to test for possible congenital disorder of glycosylation (CDG). TRAPPC9 gene, TRAPPC9 protein expression, and N-glycosylation markers were assessed in patient fibroblasts. Complementation with wild-type TRAPPC9 and immunofluorescence studies to assess TRAPPC9 expression and localization were performed. The metabolic consequences of TRAPPC9 deficiency were evaluated using tracer metabolomics. RESULTS All 3 patients carried biallelic missense variants in TRAPPC9 and presented with an N-glycosylation defect in blood, consistent with CDG type I. Extensive investigations in patient fibroblasts corroborated TRAPPC9 deficiency and an N-glycosylation defect. Tracer metabolomics revealed global metabolic changes with several affected glycosylation-related metabolites. CONCLUSION We identified 3 TRAPPC9 deficient patients presenting with ID, dysmorphic features, and abnormal glycosylation. On the basis of our findings, we propose that TRAPPC9 deficiency could lead to a CDG (TRAPPC9-CDG). The finding of abnormal glycosylation in these patients is highly relevant for diagnosis, further elucidation of the pathophysiology, and management of the disease.
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17
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Rawlins LE, Almousa H, Khan S, Collins SC, Milev MP, Leslie J, Saint-Dic D, Khan V, Hincapie AM, Day JO, McGavin L, Rowley C, Harlalka GV, Vancollie VE, Ahmad W, Lelliott CJ, Gul A, Yalcin B, Crosby AH, Sacher M, Baple EL. Biallelic variants in TRAPPC10 cause a microcephalic TRAPPopathy disorder in humans and mice. PLoS Genet 2022; 18:e1010114. [PMID: 35298461 PMCID: PMC8963566 DOI: 10.1371/journal.pgen.1010114] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/29/2022] [Accepted: 02/20/2022] [Indexed: 11/25/2022] Open
Abstract
The highly evolutionarily conserved transport protein particle (TRAPP) complexes (TRAPP II and III) perform fundamental roles in subcellular trafficking pathways. Here we identified biallelic variants in TRAPPC10, a component of the TRAPP II complex, in individuals with a severe microcephalic neurodevelopmental disorder. Molecular studies revealed a weakened interaction between mutant TRAPPC10 and its putative adaptor protein TRAPPC2L. Studies of patient lymphoblastoid cells revealed an absence of TRAPPC10 alongside a concomitant absence of TRAPPC9, another key TRAPP II complex component associated with a clinically overlapping neurodevelopmental disorder. The TRAPPC9/10 reduction phenotype was recapitulated in TRAPPC10-/- knockout cells, which also displayed a membrane trafficking defect. Notably, both the reduction in TRAPPC9 levels and the trafficking defect in these cells could be rescued by wild type but not mutant TRAPPC10 gene constructs. Moreover, studies of Trappc10-/- knockout mice revealed neuroanatomical brain defects and microcephaly, paralleling findings seen in the human condition as well as in a Trappc9-/- mouse model. Together these studies confirm autosomal recessive TRAPPC10 variants as a cause of human disease and define TRAPP-mediated pathomolecular outcomes of importance to TRAPPC9 and TRAPPC10 mediated neurodevelopmental disorders in humans and mice. Microcephalic neurodevelopmental disorders are a group of conditions that are often inherited in families, involving small head size and abnormal brain development and function. This often results in delayed development of an affected child, affecting their movement, language and/or non-verbal communication and learning, as well as seizures and neuropsychiatric problems. A group of proteins called the transport protein particles (TRAPPs) are important for the transport of cargos inside cells. Alterations within a number of the TRAPP proteins have previously been associated with human inherited diseases called the ‘TRAPPopathies’, which involve neurodevelopmental and skeletal abnormalities. Here we show that TRAPPC10 gene alterations cause a new TRAPPopathy microcephalic neurodevelopmental disorder, and we provide a detailed clinical description of the condition termed ‘TRAPPC10-related disorder’. Our studies in mice lacking the TRAPPC10 gene identified similar features to those of affected humans, including small brain size and skeletal abnormalities. Our molecular studies showed that an affected individual with an alteration in the TRAPPC10 gene has no functional TRAPPC10 protein in their cells, which in turn causes a reduction in levels of another important TRAPP molecule, TRAPPC9. Cells lacking TRAPPC10 also display abnormalities in cellular transport processes. Together our data confirm alterations in TRAPPC10 as a cause of a microcephalic neurodevelopmental disorder in both humans and mice.
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Affiliation(s)
- Lettie E. Rawlins
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Hashem Almousa
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Shazia Khan
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Stephan C. Collins
- Institute of Genetics and Molecular and Cellular Biology, Inserm, Illkirch, France
- Inserm, University of Bourgogne Franche-Comté, Dijon, France
| | - Miroslav P. Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Joseph Leslie
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
| | - Djenann Saint-Dic
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Valeed Khan
- Department of Molecular Diagnostics, Rehman Medical Institute, Peshawar, Pakistan
| | | | - Jacob O. Day
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Faculty of Health, University of Plymouth, Plymouth, United Kingdom
| | - Lucy McGavin
- University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | | | - Gaurav V. Harlalka
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Department of Pharmacology, Rajarshi Shahu College of Pharmacy, Malvihir, Buldana, India
| | | | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Asma Gul
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Binnaz Yalcin
- Institute of Genetics and Molecular and Cellular Biology, Inserm, Illkirch, France
- Inserm, University of Bourgogne Franche-Comté, Dijon, France
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Emma L. Baple
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
- * E-mail:
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18
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Biallelic loss of TRAPPC9 function links vesicle trafficking pathway to autosomal recessive intellectual disability. J Hum Genet 2022; 67:279-284. [PMID: 34983975 DOI: 10.1038/s10038-021-01007-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND The trafficking protein particle (TRAPP) complex subunit 9 (C9) protein is a member of TRAPP-II complexes and regulates vesicle trafficking. Biallelic mutations in the TRAPPC9 gene are responsible for intellectual disability with expanded developmental delay, epilepsy, microcephaly, and brain atrophy. TRAPPC9-related disease list is still expanding, however, the functional effects of only a limited fraction of these have been studied. METHODS In a patient with a pathological variant in TRAPPC9, clinical examination and cranial imaging findings were evaluated. Whole-exome sequencing, followed by Sanger sequencing was performed to detect and verify the variant. To confirm the functional effect of the mutation; variant mRNA and protein expression levels were evaluated by qRT-PCR and Western blotting. Immunostaining for TRAPPC9 and lipid droplet accumulation were examined. RESULTS We have identified a novel homozygous c.696C>G (p.Phe232Leu) pathogenic variant in TRAPPC9 (NM_031466.6) gene as a cause of severe developmental delay. Functional characterization of the TRAPPC9 variant resulted in decreased mRNA and protein expression. The intracellular findings showed that TRAPPC9 protein build-up around the nucleus in mutant type while there was no specific accumulation in the control cell line. This disrupted protein pattern affected the amount of neutral lipid-carrying vesicles and their homogenous distribution at a decreasing level. CONCLUSION Biallelic variants in the TRAPPC9 gene have been reported as the underlying cause of intellectual disability. This study provides functional evidence of the novel variant in TRAPPC9 We demonstrated that the loss of function variant exclusively targeting TRAPPC9 may explicate the neurological findings through vesicle trafficking.
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19
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Cai Y, Zhang Y, Chen H, Sun XH, Zhang P, Zhang L, Liao MY, Zhang F, Xia ZY, Man RYK, Feinberg MW, Leung SWS. MicroRNA-17-3p suppresses NF-κB-mediated endothelial inflammation by targeting NIK and IKKβ binding protein. Acta Pharmacol Sin 2021; 42:2046-2057. [PMID: 33623121 PMCID: PMC8633290 DOI: 10.1038/s41401-021-00611-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/03/2021] [Indexed: 01/31/2023] Open
Abstract
Nuclear factor kappa B (NF-κB) activation contributes to many vascular inflammatory diseases. The present study tested the hypothesis that microRNA-17-3p (miR-17-3p) suppresses the pro-inflammatory responses via NF-κB signaling in vascular endothelium. Human umbilical vein endothelial cells (HUVECs), transfected with or without miR-17-3p agomir/antagomir, were exposed to lipopolysaccharide (LPS), and the inflammatory responses were determined. The cellular target of miR-17-3p was examined with dual-luciferase reporter assay. Mice were treated with miR-17-3p agomir and the degree of LPS-induced inflammation was determined. In HUVECs, LPS caused upregulation of miR-17-3p. Overexpression of miR-17-3p in HUVECs inhibited NIK and IKKβ binding protein (NIBP) protein expression and suppressed LPS-induced phosphorylation of inhibitor of kappa Bα (IκBα) and NF-κB-p65. The reduced NF-κB activity was paralleled by decreased protein levels of NF-κB-target gene products including pro-inflammatory cytokine [interleukin 6], chemokines [interleukin 8 and monocyte chemoattractant protein-1] and adhesion molecules [vascular cell adhesion molecule-1, intercellular adhesion molecule-1 and E-selectin]. Immunostaining revealed that overexpression of miR-17-3p reduced monocyte adhesion to LPS-stimulated endothelial cells. Inhibition of miR-17-3p with antagomir has the opposite effect on LPS-induced inflammatory responses in HUVECs. The anti-inflammatory effect of miR-17-3p was mimicked by NIBP knockdown. In mice treated with LPS, miR-17-3p expression was significantly increased. Systemic administration of miR-17-3p for 3 days suppressed LPS-induced NF-κB activation and monocyte adhesion to endothelium in lung tissues of the mice. In conclusion, miR-17-3p inhibits LPS-induced NF-κB activation in HUVECs by targeting NIBP. The findings therefore suggest that miR-17-3p is a potential therapeutic target/agent in the management of vascular inflammatory diseases.
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Affiliation(s)
- Yin Cai
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
- Department of Anaesthesiology, The University of Hong Kong, Hong Kong, China
| | - Yu Zhang
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Hui Chen
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Xing-Hui Sun
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peng Zhang
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Lu Zhang
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Meng-Yang Liao
- Department of Cardiology, Institute of Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Fang Zhang
- Department of Pharmacology, Medical College of Qingdao University, Qingdao, 266021, China
| | - Zheng-Yuan Xia
- Department of Anaesthesiology, The University of Hong Kong, Hong Kong, China
| | - Ricky Ying-Keung Man
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Susan Wai-Sum Leung
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China.
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20
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Tang BL. Defects in early secretory pathway transport machinery components and neurodevelopmental disorders. Rev Neurosci 2021; 32:851-869. [PMID: 33781010 DOI: 10.1515/revneuro-2021-0020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/12/2021] [Indexed: 12/23/2022]
Abstract
The early secretory pathway, provisionally comprising of vesicular traffic between the endoplasmic reticulum (ER) and the Golgi apparatus, occurs constitutively in mammalian cells. Critical for a constant supply of secretory and plasma membrane (PM) materials, the pathway is presumably essential for general cellular function and survival. Neurons exhibit a high intensity in membrane dynamics and protein/lipid trafficking, with differential and polarized trafficking towards the somatodendritic and axonal PM domains. Mutations in genes encoding early secretory pathway membrane trafficking machinery components are known to result in neurodevelopmental or neurological disorders with disease manifestation in early life. Here, such rare disorders associated with autosomal recessive mutations in coat proteins, membrane tethering complexes and membrane fusion machineries responsible for trafficking in the early secretory pathway are summarily discussed. These mutations affected genes encoding subunits of coat protein complex I and II, subunits of transport protein particle (TRAPP) complexes, members of the YIP1 domain family (YIPF) and a SNAP receptor (SNARE) family member. Why the ubiquitously present and constitutively acting early secretory pathway machinery components could specifically affect neurodevelopment is addressed, with the plausible underlying disease etiologies and neuropathological mechanisms resulting from these mutations explored.
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Affiliation(s)
- Bor Luen Tang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore117597, Singapore
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21
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Rasool IG, Zahoor MY, Iqbal M, Anjum AA, Ashraf F, Abbas HQ, Baig HMA, Mahmood T, Shehzad W. Whole exome sequencing revealed novel variants in consanguineous Pakistani families with intellectual disability. Genes Genomics 2021; 43:503-512. [PMID: 33710595 DOI: 10.1007/s13258-021-01070-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Intellectual disability (ID) is a heterogeneous disorder affecting 1-3% of the population. Elucidation of monogenic variants for ID is a current challenge. These variants can be better demonstrated in consanguineous affected families. OBJECTIVE The study was designed to find the genetic variants of ID in consanguineous families. METHODS We analyzed five unrelated consanguineous Pakistani families affected with ID using whole exome sequencing (WES). Data was analyzed using different bioinformatics tools and software. RESULTS We mapped four variants including three novels in four different ID known genes. Each variant is found in a different family, co-segregating with a recessive pattern of inheritance. The novel variants found are; c. 2_4del (p.?) mapped in ROS1 and c. 718G>A (p.Gly240Arg) in GRM1. Another novel causative variant, c.2673del (p.Gly892Aspfs*17) identified in COL18A1 in a recessive form, a gene reported for Knobloch syndrome that manifests ID along with typical retinal abnormalities, and this phenotype was confirmed on reverse phenotyping. A mutation c.2134C>T (p.Arg712*) in TRAPPC9 has been found first time in the homozygous recessive form in our enrolled three affected siblings while it was previously reported in compound heterozygous form in a Caucasian descent. While fifth family remained unsolved. CONCLUSION These mutations in four different genes with a recessive inheritance would be a contribution to the disease variant database of this devastating disorder.
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Affiliation(s)
- Iqra Ghulam Rasool
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Muhammad Iqbal
- Department of Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Aftab Ahmad Anjum
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Fatima Ashraf
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Hafiz Qamar Abbas
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | | | - Tariq Mahmood
- Department of Statistics and Computer Science, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
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22
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Krämer J, Beer M, Bode H, Winter B. Two Novel Compound Heterozygous Mutations in the TRAPPC9 Gene Reveal a Connection of Non-syndromic Intellectual Disability and Autism Spectrum Disorder. Front Genet 2021; 11:972. [PMID: 33719327 PMCID: PMC7947907 DOI: 10.3389/fgene.2020.00972] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/31/2020] [Indexed: 12/28/2022] Open
Abstract
Introduction Autism spectrum disorder (ASD) is characterized by deficits in communication, social interaction, and repetitive behavior. Up to 70% of ASD cases are linked with intellectual disability (ID). The major genetic causes for ASD and ID are largely unknown, however, a shared genetic etiology between ASD and ID must be assumed. The trafficking protein particle complex subunit 9 (TRAPPC9) is highly expressed in postmitotic neurons of the cerebral cortex, playing a key role in development. Among 43 reported cases with mutations in TRAPPC9, all (100%) showed ID and developmental delay. Among the cases including information about ASD, 26% were affected (19 cases with information, among them 5 with ASD). Nevertheless, in some cases not classified as ASD, descriptions of autistic features like hand-flapping movements were present. Clinical Findings The affected individual presented with delay of speech development. Physical development was normal. Besides lateral slope of the eye-lid axis no facial abnormalities were evident. The individual was diagnosed with ID and ASD by structured testing. Cerebral MRI revealed associated abnormalities. Genetical Findings The chromosome set was 46,XY without structural changes. Array-CGH showed a normal molecular karyotype (arr(1-22)x2,(X,Y)x1). PCR for the FMR1 gene showed 41 ± 1 CGG repeats, and therefore no evidence of fragile X syndrome. A panel diagnostic for syndromal ID (CASK, EP300, HIVEP2, KIF1A, TRAPPC9) revealed two structural changes in TRAPPC9 in the compound heterozygosity. The mutations c.1678C > T (p.Arg560Cys) and c.3370C > T (p.Pro1124Ser) are classified as missense mutations and are both not described in the literature. Conclusion We report two new missense mutations in the TRAPPC9 gene in one individual with ID and ASD. The TRAPPC9 gene should be part of the diagnostic assessment in ID. ASD must be considered as a feature of TRAPPC9-associated ID. It might have been neglected in the literature and should result in specific testing for ASD in affected individuals.
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Affiliation(s)
- Johannes Krämer
- Division of Pediatric Neurology and Inborn Errors of Metabolism, Children's Hospital, Ulm University, Ulm, Germany
| | - Meinrad Beer
- Department of Radiology, Ulm University, Ulm, Germany
| | - Harald Bode
- Division of Pediatric Neurology and Inborn Errors of Metabolism, Children's Hospital, Ulm University, Ulm, Germany
| | - Benedikt Winter
- Division of Pediatric Neurology and Inborn Errors of Metabolism, Children's Hospital, Ulm University, Ulm, Germany
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23
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Diaz J, Gérard X, Emerit MB, Areias J, Geny D, Dégardin J, Simonutti M, Guerquin MJ, Collin T, Viollet C, Billard JM, Métin C, Hubert L, Larti F, Kahrizi K, Jobling R, Agolini E, Shaheen R, Zigler A, Rouiller-Fabre V, Rozet JM, Picaud S, Novelli A, Alameer S, Najmabadi H, Cohn R, Munnich A, Barth M, Lugli L, Alkuraya FS, Blaser S, Gashlan M, Besmond C, Darmon M, Masson J. YIF1B mutations cause a post-natal neurodevelopmental syndrome associated with Golgi and primary cilium alterations. Brain 2021; 143:2911-2928. [PMID: 33103737 DOI: 10.1093/brain/awaa235] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/29/2020] [Accepted: 06/13/2020] [Indexed: 12/30/2022] Open
Abstract
Human post-natal neurodevelopmental delay is often associated with cerebral alterations that can lead, by themselves or associated with peripheral deficits, to premature death. Here, we report the clinical features of 10 patients from six independent families with mutations in the autosomal YIF1B gene encoding a ubiquitous protein involved in anterograde traffic from the endoplasmic reticulum to the cell membrane, and in Golgi apparatus morphology. The patients displayed global developmental delay, motor delay, visual deficits with brain MRI evidence of ventricle enlargement, myelination alterations and cerebellar atrophy. A similar profile was observed in the Yif1b knockout (KO) mouse model developed to identify the cellular alterations involved in the clinical defects. In the CNS, mice lacking Yif1b displayed neuronal reduction, altered myelination of the motor cortex, cerebellar atrophy, enlargement of the ventricles, and subcellular alterations of endoplasmic reticulum and Golgi apparatus compartments. Remarkably, although YIF1B was not detected in primary cilia, biallelic YIF1B mutations caused primary cilia abnormalities in skin fibroblasts from both patients and Yif1b-KO mice, and in ciliary architectural components in the Yif1b-KO brain. Consequently, our findings identify YIF1B as an essential gene in early post-natal development in human, and provide a new genetic target that should be tested in patients developing a neurodevelopmental delay during the first year of life. Thus, our work is the first description of a functional deficit linking Golgipathies and ciliopathies, diseases so far associated exclusively to mutations in genes coding for proteins expressed within the primary cilium or related ultrastructures. We therefore propose that these pathologies should be considered as belonging to a larger class of neurodevelopmental diseases depending on proteins involved in the trafficking of proteins towards specific cell membrane compartments.
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Affiliation(s)
- Jorge Diaz
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Xavier Gérard
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Michel-Boris Emerit
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Julie Areias
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - David Geny
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Julie Dégardin
- INSERM UMR-S968, Institut de la vision, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris F-75012, Université Pierre et Marie Curie, France
| | - Manuel Simonutti
- INSERM UMR-S968, Institut de la vision, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris F-75012, Université Pierre et Marie Curie, France
| | | | - Thibault Collin
- Saint Pères Paris Institute for the Neurosciences CNRS - UMR 8003 Université de Paris, Paris 75006, France
| | - Cécile Viollet
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Jean-Marie Billard
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Christine Métin
- INSERM, UMR-S1270, Institut du Fer à Moulin, Sorbonne Université, Paris F-75005, France
| | - Laurence Hubert
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Farzaneh Larti
- University of Social Welfare and Rehabilitation Sciences, Genetics Research Center, Tehran 19834, Iran
| | - Kimia Kahrizi
- University of Social Welfare and Rehabilitation Sciences, Genetics Research Center, Tehran 19834, Iran
| | - Rebekah Jobling
- The Hospital for Sick Children, Molecular Genetics, Toronto, Canada
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Ranad Shaheen
- King Faisal Specialist Hospital and Research Center, Developmental Genetics Unit, Riyadh 11211, Saudi Arabia
| | | | | | - Jean-Michel Rozet
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Serge Picaud
- INSERM UMR-S968, Institut de la vision, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris F-75012, Université Pierre et Marie Curie, France
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Seham Alameer
- Department of Pediatrics, King Khaled National Guard Hospital, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Hossein Najmabadi
- University of Social Welfare and Rehabilitation Sciences, Genetics Research Center, Tehran 19834, Iran
| | - Ronald Cohn
- The Hospital for Sick Children, Molecular Genetics, Toronto, Canada
| | - Arnold Munnich
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | | | - Licia Lugli
- Division of Neonatal Intensive Care Unit, Department of Pediatrics, University Hospital, 41125 Modena, Italy
| | - Fowzan S Alkuraya
- King Faisal Specialist Hospital and Research Center, Developmental Genetics Unit, Riyadh 11211, Saudi Arabia
| | - Susan Blaser
- Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Maha Gashlan
- King Faisal Specialist Hospital and Research Center, Developmental Genetics Unit, Riyadh 11211, Saudi Arabia
| | - Claude Besmond
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Michèle Darmon
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France.,INSERM, UMR-S1270, Institut du Fer à Moulin, Sorbonne Université, Paris F-75005, France
| | - Justine Masson
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France.,INSERM, UMR-S1270, Institut du Fer à Moulin, Sorbonne Université, Paris F-75005, France
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24
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Yousefipour F, Mozhdehipanah H, Mahjoubi F. Identification of two novel homozygous nonsense mutations in TRAPPC9 in two unrelated consanguineous families with intellectual Disability from Iran. Mol Genet Genomic Med 2021; 9:e1610. [PMID: 33513295 PMCID: PMC8683625 DOI: 10.1002/mgg3.1610] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 11/12/2022] Open
Abstract
Background Pathogenic mutations in TRAPPC9 are associated with autosomal recessive Intellectual Disability (ID), a major public health issue that affects about 1–3% of children worldwide. Method Clinical evaluation, magnetic resonance imaging, peripheral blood karyotype, Multiplex ligation‐dependent probe amplification (MLPA), array CGH, and whole‐exome sequencing were used to characterize etiology in three patients from two unrelated consanguineous families of Iranian descent with intellectual disability. Results Whole‐exome sequencing showed two novel homozygous nonsense mutations (c.937C>T) in exon 3 and (c.3103C>T) in exon 19 of TRAPPC9 (NM_031466.7) in two unrelated consanguineous families. Conclusion The two novel variants found in TRAPPC9 caused truncated protein and clinical manifestations such as ID, developmental delay, microcephaly, and brain abnormalities in three patients.
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Affiliation(s)
| | - Hossein Mozhdehipanah
- Department of Neurology, Bou Ali Sina Hospital, Qazvin University of Medical Sciences, Qazvin, Iran
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25
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A novel homozygous variant in the TRAPPC9 gene causing intellectual disability and autism Spectrum disorder. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Aslanger AD, Demiral E, Sonmez-Sahin S, Guler S, Goncu B, Yucesan E, Iscan A, Saltik S, Yesil G. Expanding Clinical Phenotype of TRAPPC12-Related Childhood Encephalopathy: Two Cases and Review of Literature. Neuropediatrics 2020; 51:430-434. [PMID: 32369837 DOI: 10.1055/s-0040-1710526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Biallelic mutations in the TRAPPC12 gene are responsible for early-onset progressive encephalopathy with brain atrophy and spasticity (PEBAS). To date, three different allelic variants have been reported. Next-generation sequencing allowed discovery of unique alternations in this gene with different phenotypes. We report two patients carrying TRAPPC12 variants, one previously reported and one unknown mutation, with severe neurodevelopmental delay and brain atrophy. Standard clinical examination and cranial imaging studies were performed in these two unrelated patients. In addition, whole-exome sequencing was performed, followed by Sanger sequencing for verification. The first patient, a 2-year-old boy, was found to be homozygous for the previously reported c.1880C > T (p.Ala627Val) mutation. He presented with a phenotype including severe progressive cortical atrophy, moderate cerebellar atrophy, epilepsy, and microcephaly, very similar to the previously reported cases. The second case, a 9-year-old boy, carried a novel homozygous c.679T > G (p.Phe227Val) variant and presented with mild cortical atrophy, severe cerebellar atrophy, and neither clinically manifest epilepsy nor microcephaly, which were previously considered typical findings in PEBAS with TRAPPC12 mutations. Our findings suggest that clinical and brain imaging findings might be more variable than previously anticipated; however, a larger number of observations would benefit for broader phenotypic spectrum.
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Affiliation(s)
- Ayca Dilruba Aslanger
- Department of Medical Genetics, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
| | - Emine Demiral
- Department of Medical Genetics, Istanbul Training and Research Hospital, Istanbul, Turkey
| | - Seyma Sonmez-Sahin
- Department of Pediatric Neurology, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
| | - Serhat Guler
- Department of Pediatric Neurology, Cerrahpasa Faculty of Medicine Hospital, Istanbul University, Istanbul, Turkey
| | - Beyza Goncu
- Experimental Research Center, Bezmialem Vakıf University, Istanbul, Turkey
| | - Emrah Yucesan
- Institute of Life Sciences and Biotechnology, Bezmialem Vakıf University, Istanbul, Turkey
| | - Akın Iscan
- Department of Pediatric Neurology, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
| | - Sema Saltik
- Department of Pediatric Neurology, Cerrahpasa Faculty of Medicine Hospital, Istanbul University, Istanbul, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
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27
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Ke Y, Weng M, Chhetri G, Usman M, Li Y, Yu Q, Ding Y, Wang Z, Wang X, Sultana P, DiFiglia M, Li X. Trappc9 deficiency in mice impairs learning and memory by causing imbalance of dopamine D1 and D2 neurons. SCIENCE ADVANCES 2020; 6:6/47/eabb7781. [PMID: 33208359 PMCID: PMC7673810 DOI: 10.1126/sciadv.abb7781] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/01/2020] [Indexed: 05/06/2023]
Abstract
Genetic mutations in the gene encoding transport protein particle complex 9 (trappc9), a subunit of TRAPP that acts as a guanine nucleotide exchange factor for rab proteins, cause intellectual disability with brain structural malformations by elusive mechanisms. Here, we report that trappc9-deficient mice exhibit a broad range of behavioral deficits and postnatal delay in growth of the brain. Contrary to volume decline of various brain structures, the striatum of trappc9 null mice was enlarged. An imbalance existed between dopamine D1 and D2 receptor containing neurons in the brain of trappc9-deficient mice; pharmacological manipulation of dopamine receptors improved performances of trappc9 null mice to levels of wild-type mice on cognitive tasks. Loss of trappc9 compromised the activation of rab11 in the brain and resulted in retardation of endocytic receptor recycling in neurons. Our study elicits a pathogenic mechanism and a potential treatment for trappc9-linked disorders including intellectual disability.
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Affiliation(s)
- Yuting Ke
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Meiqian Weng
- Mucosal Immunology Laboratory, Combined Program in Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gaurav Chhetri
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Muhammad Usman
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Yan Li
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Qing Yu
- Department of Nephrology, Shanghai General Hospital, 650 Songjiang Road, Songjiang District, Shanghai 201620, China
| | - Yingzhuo Ding
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Zejian Wang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Xiaolong Wang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Pinky Sultana
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Xueyi Li
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
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28
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Bodnar B, DeGruttola A, Zhu Y, Lin Y, Zhang Y, Mo X, Hu W. Emerging role of NIK/IKK2-binding protein (NIBP)/trafficking protein particle complex 9 (TRAPPC9) in nervous system diseases. Transl Res 2020; 224:55-70. [PMID: 32434006 PMCID: PMC7442628 DOI: 10.1016/j.trsl.2020.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 02/05/2023]
Abstract
NFκB signaling and protein trafficking network play important roles in various biological and pathological processes. NIK-and-IKK2-binding protein (NIBP), also known as trafficking protein particle complex 9 (TRAPPC9), is a prototype member of a novel protein family, and has been shown to regulate both NFκB signaling pathway and protein transport/trafficking. NIBP is extensively expressed in the nervous system and plays an important role in regulating neurogenesis and neuronal differentiation. NIBP/TRAPPC9 mutations have been linked to an autosomal recessive intellectual disability syndrome, called NIBP Syndrome, which is characterized by nonsyndromic autosomal recessive intellectual disability along with other symptoms such as obesity, microcephaly, and facial dysmorphia. As more cases of NIBP Syndrome are identified, new light is being shed on the role of NIBP/TRAPPC9 in the central nervous system developments and diseases. NIBP is also involved in the enteric nervous system. This review will highlight the importance of NIBP/TRAPPC9 in central and enteric nervous system diseases, and the established possible mechanisms for developing a potential therapeutic.
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Affiliation(s)
- Brittany Bodnar
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Arianna DeGruttola
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Yuanjun Zhu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Yuan Lin
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Yonggang Zhang
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Wenhui Hu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.
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29
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Khan MZ, Khan A, Xiao J, Ma J, Ma Y, Chen T, Shao D, Cao Z. Overview of Research Development on the Role of NF-κB Signaling in Mastitis. Animals (Basel) 2020; 10:E1625. [PMID: 32927884 PMCID: PMC7552152 DOI: 10.3390/ani10091625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Mastitis is the inflammation of the mammary gland. Escherichia coli and Staphylococcus aureus are the most common bacteria responsible for mastitis. When mammary epithelial cells are infected by microorganisms, this activates an inflammatory response. The bacterial infection is recognized by innate pattern recognition receptors (PRRs) in the mammary epithelial cells, with the help of Toll-like receptors (TLRs). Upon activation by lipopolysaccharides, a virulent agent of bacteria, the TLRs further trigger nuclear factor-κB (NF-κB) signaling to accelerate its pathogenesis. The NF-κB has an essential role in many biological processes, such as cell survival, immune response, inflammation and development. Therefore, the NF-κB signaling triggered by the TLRs then regulates the transcriptional expression of specific inflammatory mediators to initiate inflammation of the mammary epithelial cells. Thus, any aberrant regulation of NF-κB signaling may lead to many inflammatory diseases, including mastitis. Hence, the inhibiting of NF-κB signaling has potential therapeutic applications in mastitis control strategies. In this review, we highlighted the regulation and function of NF-κB signaling in mastitis. Furthermore, the role of NF-κB signaling for therapeutic purposes in mastitis control has been explored in the current review.
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Affiliation(s)
- Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (J.X.); (J.M.); (Y.M.); (T.C.)
| | - Adnan Khan
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (J.X.); (J.M.); (Y.M.); (T.C.)
| | - Jiaying Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (J.X.); (J.M.); (Y.M.); (T.C.)
| | - Yulin Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (J.X.); (J.M.); (Y.M.); (T.C.)
| | - Tianyu Chen
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (J.X.); (J.M.); (Y.M.); (T.C.)
| | - Dafu Shao
- Institute of Agricultural Information of CAAS, Beijing 100081, China;
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (J.X.); (J.M.); (Y.M.); (T.C.)
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30
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Liang ZS, Cimino I, Yalcin B, Raghupathy N, Vancollie VE, Ibarra-Soria X, Firth HV, Rimmington D, Farooqi IS, Lelliott CJ, Munger SC, O’Rahilly S, Ferguson-Smith AC, Coll AP, Logan DW. Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity. PLoS Genet 2020; 16:e1008916. [PMID: 32877400 PMCID: PMC7467316 DOI: 10.1371/journal.pgen.1008916] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 11/30/2022] Open
Abstract
Some imprinted genes exhibit parental origin specific expression bias rather than being transcribed exclusively from one copy. The physiological relevance of this remains poorly understood. In an analysis of brain-specific allele-biased expression, we identified that Trappc9, a cellular trafficking factor, was expressed predominantly (~70%) from the maternally inherited allele. Loss-of-function mutations in human TRAPPC9 cause a rare neurodevelopmental syndrome characterized by microcephaly and obesity. By studying Trappc9 null mice we discovered that homozygous mutant mice showed a reduction in brain size, exploratory activity and social memory, as well as a marked increase in body weight. A role for Trappc9 in energy balance was further supported by increased ad libitum food intake in a child with TRAPPC9 deficiency. Strikingly, heterozygous mice lacking the maternal allele (70% reduced expression) had pathology similar to homozygous mutants, whereas mice lacking the paternal allele (30% reduction) were phenotypically normal. Taken together, we conclude that Trappc9 deficient mice recapitulate key pathological features of TRAPPC9 mutations in humans and identify a role for Trappc9 and its imprinting in controlling brain development and metabolism.
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Affiliation(s)
- Zhengzheng S. Liang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Irene Cimino
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Binnaz Yalcin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, France
| | | | | | - Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Helen V. Firth
- Department of Clinical Genetics, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Debra Rimmington
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Stephen O’Rahilly
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | | | - Anthony P. Coll
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Darren W. Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
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31
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Al-Deri N, Okur V, Ahimaz P, Milev M, Valivullah Z, Hagen J, Sheng Y, Chung W, Sacher M, Ganapathi M. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function. J Med Genet 2020; 58:592-601. [PMID: 32843486 DOI: 10.1136/jmedgenet-2020-107016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 06/26/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Next-generation sequencing has facilitated the diagnosis of neurodevelopmental disorders with variable and non-specific clinical findings. Recently, a homozygous missense p.(Asp37Tyr) variant in TRAPPC2L, a core subunit of TRAPP complexes which function as tethering factors during membrane trafficking, was reported in two unrelated individuals with neurodevelopmental delay, post-infectious encephalopathy-associated developmental arrest, tetraplegia and accompanying rhabdomyolysis. METHODS We performed whole genome sequencing on members of an Ashkenazi Jewish pedigree to identify the underlying genetic aetiology of global developmental delay/intellectual disability in three affected siblings. To assess the effect of the identified TRAPPC2L variant, we performed biochemical and cell biological functional studies on the TRAPPC2L protein. RESULTS A rare homozygous predicted deleterious missense variant, p.(Ala2Gly), in TRAPPC2L was identified in the affected siblings and it segregated with the neurodevelopmental phenotype within the family. Using a yeast two-hybrid assay and in vitro binding, we demonstrate that the p.(Ala2Gly) variant, but not the p.(Asp37Tyr) variant, disrupted the interaction between TRAPPC2L and another core TRAPP protein, TRAPPC6a. Size exclusion chromatography suggested that this variant affects the assembly of TRAPP complexes. Employing two different membrane trafficking assays using fibroblasts from one of the affected siblings, we found a delay in traffic into and out of the Golgi. Similar to the p.(Asp37Tyr) variant, the p.(Ala2Gly) variant resulted in an increase in the levels of active RAB11. CONCLUSION Our data fill in a gap in the knowledge of TRAPP architecture with TRAPPC2L interacting with TRAPPC6a, positioning it as a putative adaptor for other TRAPP subunits. Collectively, our findings support the pathogenicity of the TRAPPC2L p.(Ala2Gly) variant.
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Affiliation(s)
- Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Volkan Okur
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Miroslav Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zaheer Valivullah
- Center for Mendelian Genomics, Broad Institute Harvard, Cambridge, Massachusetts, USA
| | - Jacob Hagen
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Yufeng Sheng
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Wendy Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA.,Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada .,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
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Kaur P, Kadavigere R, Girisha KM, Shukla A. Recurrent bi-allelic splicing variant c.454+3A>G in TRAPPC4 is associated with progressive encephalopathy and muscle involvement. Brain 2020; 143:e29. [PMID: 32125366 DOI: 10.1093/brain/awaa046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis and Imaging, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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Yarwood R, Hellicar J, Woodman PG, Lowe M. Membrane trafficking in health and disease. Dis Model Mech 2020; 13:13/4/dmm043448. [PMID: 32433026 PMCID: PMC7197876 DOI: 10.1242/dmm.043448] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Membrane trafficking pathways are essential for the viability and growth of cells, and play a major role in the interaction of cells with their environment. In this At a Glance article and accompanying poster, we outline the major cellular trafficking pathways and discuss how defects in the function of the molecular machinery that mediates this transport lead to various diseases in humans. We also briefly discuss possible therapeutic approaches that may be used in the future treatment of trafficking-based disorders. Summary: This At a Glance article and poster summarise the major intracellular membrane trafficking pathways and associated molecular machineries, and describe how defects in these give rise to disease in humans.
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Affiliation(s)
- Rebecca Yarwood
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - John Hellicar
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Philip G Woodman
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Martin Lowe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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34
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Wilton KM, Gunderson LB, Hasadsri L, Wood CP, Schimmenti LA. Profound intellectual disability caused by homozygous TRAPPC9 pathogenic variant in a man from Malta. Mol Genet Genomic Med 2020; 8:e1211. [PMID: 32162493 PMCID: PMC7216808 DOI: 10.1002/mgg3.1211] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/24/2020] [Indexed: 01/02/2023] Open
Abstract
Background Intellectual disability is a complex multi‐faceted condition with diverse underlying etiologies. One rare form of intellectual disability is secondary to the loss of TRAPPC9, an activator of NF‐κB and a mediator of intracellular protein processing and trafficking. TRAPPC9 deficiency has been described in 48 patients with more than 15 pathologic variants. Method Clinical evaluation, magnetic resonance imaging, and whole‐exome sequencing were used to characterize the underlying cause of absent speech, restricted/repetitive behaviors, and worsening behavioral outbursts in 27‐year‐old man from Malta. Results Magnetic Resonance Imaging showed morphologic abnormalities, including global cerebral and cerebellar hypoplasia. Genetic analysis through Whole Exome Sequencing identified a homozygous deletion (c.568_574del) in TRAPPC9 resulting in a frameshift, premature stop codon, and ultimately a truncated protein (p.Trp190Argfs*95). In this case, the pathogenic variant was homozygous, identified in both of the parents without known consanguinity. Conclusion Given the phenotype and genotype consistent with a deficiency in TRAPPC9, it is likely that this patient represents a novel case of this rare genetic syndrome. Specifically, this case, in the context of 48 total reported patients, raises questions as to the geographic origin of the pathologic variant and optimal detection and therapeutic intervention for this condition.
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Affiliation(s)
- Katelynn M Wilton
- Mayo Clinic Alix School of Medicine Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
| | | | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Otorhinolaryngology, Mayo Clinic, Rochester, MN, USA
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35
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Van Bergen NJ, Guo Y, Al-Deri N, Lipatova Z, Stanga D, Zhao S, Murtazina R, Gyurkovska V, Pehlivan D, Mitani T, Gezdirici A, Antony J, Collins F, Willis MJH, Coban Akdemir ZH, Liu P, Punetha J, Hunter JV, Jhangiani SN, Fatih JM, Rosenfeld JA, Posey JE, Gibbs RA, Karaca E, Massey S, Ranasinghe TG, Sleiman P, Troedson C, Lupski JR, Sacher M, Segev N, Hakonarson H, Christodoulou J. Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability. Brain 2020; 143:112-130. [PMID: 31794024 PMCID: PMC6935753 DOI: 10.1093/brain/awz374] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
The conserved transport protein particle (TRAPP) complexes regulate key trafficking events and are required for autophagy. TRAPPC4, like its yeast Trs23 orthologue, is a core component of the TRAPP complexes and one of the essential subunits for guanine nucleotide exchange factor activity for Rab1 GTPase. Pathogenic variants in specific TRAPP subunits are associated with neurological disorders. We undertook exome sequencing in three unrelated families of Caucasian, Turkish and French-Canadian ethnicities with seven affected children that showed features of early-onset seizures, developmental delay, microcephaly, sensorineural deafness, spastic quadriparesis and progressive cortical and cerebellar atrophy in an effort to determine the genetic aetiology underlying neurodevelopmental disorders. All seven affected subjects shared the same identical rare, homozygous, potentially pathogenic variant in a non-canonical, well-conserved splice site within TRAPPC4 (hg19:chr11:g.118890966A>G; TRAPPC4: NM_016146.5; c.454+3A>G). Single nucleotide polymorphism array analysis revealed there was no haplotype shared between the tested Turkish and Caucasian families suggestive of a variant hotspot region rather than a founder effect. In silico analysis predicted the variant to cause aberrant splicing. Consistent with this, experimental evidence showed both a reduction in full-length transcript levels and an increase in levels of a shorter transcript missing exon 3, suggestive of an incompletely penetrant splice defect. TRAPPC4 protein levels were significantly reduced whilst levels of other TRAPP complex subunits remained unaffected. Native polyacrylamide gel electrophoresis and size exclusion chromatography demonstrated a defect in TRAPP complex assembly and/or stability. Intracellular trafficking through the Golgi using the marker protein VSVG-GFP-ts045 demonstrated significantly delayed entry into and exit from the Golgi in fibroblasts derived from one of the affected subjects. Lentiviral expression of wild-type TRAPPC4 in these fibroblasts restored trafficking, suggesting that the trafficking defect was due to reduced TRAPPC4 levels. Consistent with the recent association of the TRAPP complex with autophagy, we found that the fibroblasts had a basal autophagy defect and a delay in autophagic flux, possibly due to unsealed autophagosomes. These results were validated using a yeast trs23 temperature sensitive variant that exhibits constitutive and stress-induced autophagic defects at permissive temperature and a secretory defect at restrictive temperature. In summary we provide strong evidence for pathogenicity of this variant in a member of the core TRAPP subunit, TRAPPC4 that associates with vesicular trafficking and autophagy defects. This is the first report of a TRAPPC4 variant, and our findings add to the growing number of TRAPP-associated neurological disorders.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Yiran Guo
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Daniela Stanga
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah Zhao
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Rakhilya Murtazina
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Valeriya Gyurkovska
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, 34303, Turkey
| | - Jayne Antony
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - Felicity Collins
- Western Sydney Genetics Program, Children’s Hospital at Westmead, Sydney, Australia
- Medical Genomics Department, Royal Prince Alfred Hospital, Sydney, Australia
| | - Mary J H Willis
- Department of Pediatrics, Naval Medical Center San Diego, San Diego, California, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Thisara G Ranasinghe
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Patrick Sleiman
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Chris Troedson
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
- Kids Research, The Children’s Hospital at Westmead, Sydney, NSW, Australia
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36
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Yang Z, Lian Z, Liu G, Deng M, Sun B, Guo Y, Liu D, Li Y. Identification of genetic markers associated with milk production traits in Chinese Holstein cattle based on post genome-wide association studies. Anim Biotechnol 2019; 32:67-76. [PMID: 31424326 DOI: 10.1080/10495398.2019.1653901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
With the rapid development of dairy industry, the breeding process of dairy cows has been accelerated. In previous genome-wide association studies (GWAS), a large number of genetic markers have been reported which may contribute to the selection of Holstein populations with superior milk-producing traits, but they remain to be further verified before practical application. In this study, 90 single nucleotide polymorphisms (SNPs) were selected, which were reported to be significantly associated with five milk production traits, including 305-day milk yield (305MY), 305-day milk fat percent (305FC), 305-day milk protein percent (305PC), 305-day milk fat yield (305FY) and 305-day milk protein yield (305PY). Effective 305-day data and fresh DNA samples were obtained from 295 healthy cows with gestational age of 1-4. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) was used to perform precise genotyping of these loci, followed by site association and haplotype analysis. Results showed that 36 out of 90 loci were supported to be used as genetic markers. In particular, several novel and effective haplotypes were also presented. Overall, our results verified tens of useful markers and provided a basis for further development of breeding strategies.
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Affiliation(s)
- Zhenwei Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Zhiquan Lian
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, China.,National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
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Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers HH, Najmabadi H. Genetics of intellectual disability in consanguineous families. Mol Psychiatry 2019; 24:1027-1039. [PMID: 29302074 DOI: 10.1038/s41380-017-0012-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 01/17/2023]
Abstract
Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.
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Affiliation(s)
- Hao Hu
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Guangzhou Women and Children's Medical Center, 510623, Guangzhou, China
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Luciana Musante
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ralf Herwig
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Cornelia Oppitz
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Vanessa Suckow
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sabine Otto
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, 36156, Iran
| | - Faezeh Mojahedi
- Mashhad Medical Genetic Counseling Center, Mashhad, 91767, Iran
| | - Maryam Taghdiri
- Shiraz Genetic Counseling Center, Welfare Office, Shiraz, Iran
| | - Elaheh Papari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Saeide Akbari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Seyed Hassan Tonekaboni
- Pediatric Neurology Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, 15468, Iran
| | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Mohammad Reza Ebrahimpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ingrid Bader
- Kinderzentrum München, Technische Universität München, 81377, München, Germany
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Monika Cohen
- Children's Center Munich, 81377, Munich, Germany
| | - Hossein Khodaei
- Meybod Genetics Research Center, Welfare Organization, Yazd, 89651, Iran
| | - Beate Albrecht
- Institute of Human Genetics, University Hospital Essen, 45122, Essen, Germany
| | - Sarah Azimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Birgit Zirn
- Genetikum Counseling Center, 70173, Stuttgart, Germany
| | - Milad Bastami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Dagmar Wieczorek
- Institute of Human Genetics and Anthropology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Gholamreza Bahrami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Krystyna Keleman
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Leila Nouri Vahid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Andreas Tzschach
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Jutta Gärtner
- University Medical Center, Georg August University Göttingen, 37075, Göttingen, Germany
| | | | | | - Bernd Timmermann
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | | | - Aria Jankhah
- Shiraz Genetic Counseling Center, Shiraz, 71346, Iran
| | - Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Thomas F Wienker
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Hans-Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany. .,Institute of Human Genetics, University Medicine, Mainz, Germany.
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran. .,Kariminejad - Najmabadi Pathology & Genetics Centre, Tehran, 14667-13713, Iran.
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38
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Andres EM, Hafeez H, Yousaf A, Riazuddin S, Rice ML, Basra MAR, Raza MH. A genome-wide analysis in consanguineous families reveals new chromosomal loci in specific language impairment (SLI). Eur J Hum Genet 2019; 27:1274-1285. [PMID: 30976110 DOI: 10.1038/s41431-019-0398-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Abstract
Language is a uniquely human ability, and failure to attain this ability can have a life-long impact on the affected individuals. This is particularly true for individuals with specific language impairment (SLI), which is defined as an impairment in normal language development in the absence of any other developmental disability. Although SLI displays high heritability, family-based linkage studies have been hampered by an unclear mode of Mendelian segregation, variable disease penetrance, and heterogeneity of diagnostic criteria. We performed genome-wide parametric linkage analysis and homozygosity mapping in 14 consanguineous families from Pakistan segregating SLI. Linkage analysis revealed a multipoint LOD score of 4.18 at chromosome 2q in family PKSLI05 under a recessive mode of inheritance. A second linkage score of 3.85 was observed in family PKSLI12 at a non-overlapping locus on chromosome 2q. Two other suggestive linkage loci were found in family PKSLI05 on 14q and 22q with LOD scores of 2.37 and 2.23, respectively, that were also identified in homozygosity mapping. Reduction to homozygosity was observed on chromosomes 2q, 5p, 8q, 14q, 17q, and 22q. Each homozygosity region occurred in multiple PKSLI families. We report new SLI loci on chromosomes 2 and 8 and confirm suggestive SLI linkage loci on chromosomes 5, 14, 17, and 22 reported previously in the population of Robinson Crusoe Island. These findings indicate that linkage and homozygosity mapping in consanguineous families can improve genetic analyses in SLI and suggest the involvement of additional genes in the causation of this disorder.
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Affiliation(s)
- Erin M Andres
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | - Huma Hafeez
- Institute of Chemistry, University of the Punjab, Lahore, Pakistan
| | - Adnan Yousaf
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.,Department of Biotechnology, International Islamic University, Islamabad, Pakistan
| | | | - Mabel L Rice
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | | | - Muhammad Hashim Raza
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.
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Rasika S, Passemard S, Verloes A, Gressens P, El Ghouzzi V. Golgipathies in Neurodevelopment: A New View of Old Defects. Dev Neurosci 2019; 40:396-416. [PMID: 30878996 DOI: 10.1159/000497035] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/16/2019] [Indexed: 11/19/2022] Open
Abstract
The Golgi apparatus (GA) is involved in a whole spectrum of activities, from lipid biosynthesis and membrane secretion to the posttranslational processing and trafficking of most proteins, the control of mitosis, cell polarity, migration and morphogenesis, and diverse processes such as apoptosis, autophagy, and the stress response. In keeping with its versatility, mutations in GA proteins lead to a number of different disorders, including syndromes with multisystem involvement. Intriguingly, however, > 40% of the GA-related genes known to be associated with disease affect the central or peripheral nervous system, highlighting the critical importance of the GA for neural function. We have previously proposed the term "Golgipathies" in relation to a group of disorders in which mutations in GA proteins or their molecular partners lead to consequences for brain development, in particular postnatal-onset microcephaly (POM), white-matter defects, and intellectual disability (ID). Here, taking into account the broader role of the GA in the nervous system, we refine and enlarge this emerging concept to include other disorders whose symptoms may be indicative of altered neurodevelopmental processes, from neurogenesis to neuronal migration and the secretory function critical for the maturation of postmitotic neurons and myelination.
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Affiliation(s)
- Sowmyalakshmi Rasika
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP HP, Hôpital Robert Debré, UF de Génétique Clinique, Paris, France
| | - Sandrine Passemard
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP HP, Hôpital Robert Debré, UF de Génétique Clinique, Paris, France
| | - Alain Verloes
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP HP, Hôpital Robert Debré, UF de Génétique Clinique, Paris, France
| | - Pierre Gressens
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Centre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King's College London, King's Health Partners, St. Thomas' Hospital, London, United Kingdom
| | - Vincent El Ghouzzi
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France,
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40
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Hnoonual A, Graidist P, Kritsaneepaiboon S, Limprasert P. Novel Compound Heterozygous Mutations in the TRAPPC9 Gene in Two Siblings With Autism and Intellectual Disability. Front Genet 2019; 10:61. [PMID: 30853973 PMCID: PMC6396715 DOI: 10.3389/fgene.2019.00061] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/24/2019] [Indexed: 12/11/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder with many contributing risk genes and loci. To date, several intellectual disability (ID) susceptibility genes have frequently been identified in ASD. Here, whole exome sequencing was carried out on a proband with ASD and identified compound heterozygous mutations of the TRAPPC9, which plays a role in the neuronal NF-κB signaling pathway. These mutations consisted of a novel frameshift mutation (c.2415_2416insC, p.His806Profs∗9) and a rare splice site mutation (c.3349+1G>A) that were segregated from an unaffected father and unaffected mother, respectively. These two heterozygous mutations were also identified in the patient’s older brother with ID. Quantitative RT-PCR revealed a significant reduction of TRAPPC9 transcript in two siblings. This study first describes compound heterozygous mutations of the TRAPPC9 gene in two siblings with ASD and ID, which is notable as only homozygous mutations or compound heterozygous for copy number variations and rare variant in this gene have been reported to date and associated with autosomal recessive intellectual disability. The two siblings carrying compound heterozygous TRAPPC9 mutations presented with ID, developmental delay, microcephaly and brain abnormalities similarly to the clinical features found in almost cases with homozygous TRAPPC9 mutation in previous studies. Together this study provides evidence that clinical manifestations of TRAPPC9 mutations as seen in our patients with ID and autism may be broader than previous case reports have indicated.
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Affiliation(s)
- Areerat Hnoonual
- Division of Human Genetics, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Potchanapond Graidist
- Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.,The Excellent Research Laboratory of Cancer Molecular Biology, Prince of Songkla University, Songkhla, Thailand
| | - Supika Kritsaneepaiboon
- Department of Radiology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Pornprot Limprasert
- Division of Human Genetics, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.,Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
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Hsu CL, Chou CH, Huang SC, Lin CY, Lin MY, Tung CC, Lin CY, Lai IP, Zou YF, Youngson NA, Lin SP, Yang CH, Chen SK, Gau SSF, Huang HS. Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics. Hum Mol Genet 2019; 27:1039-1054. [PMID: 29346572 DOI: 10.1093/hmg/ddy023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022] Open
Abstract
Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism through which monoallelic gene expression occurs in a parent-of-origin-specific manner. It is unknown if genomic imprinting contributes to visual system development. We profiled the transcriptome and imprintome during critical periods of mouse visual system development under normal- and dark-rearing conditions using B6/CAST F1 hybrid mice. We identified experience-regulated, isoform-specific and brain-region-specific imprinted genes. We also found imprinted microRNAs were predominantly clustered into the Dlk1-Dio3 imprinted locus with light experience affecting some imprinted miRNA expression. Our findings provide the first comprehensive analysis of light-experience regulation of the transcriptome and imprintome during critical periods of visual system development. Our results may contribute to therapeutic strategies for visual impairments and circadian rhythm disorders resulting from a dysfunctional imprintome.
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Affiliation(s)
- Chi-Lin Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chih-Hsuan Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Shih-Chuan Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chia-Yi Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Meng-Ying Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chun-Che Tung
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chun-Yen Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Department of Pediatrics, Yong-He Cardinal Tien Hospital, Taipei 234, Taiwan
| | - Ivan Pochou Lai
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yan-Fang Zou
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Neil A Youngson
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Shau-Ping Lin
- Institute of Biotechnology, College of Bio-Resources & Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chang-Hao Yang
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Shih-Kuo Chen
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan.,Neurodevelopment Club in Taiwan, Taipei 10051, Taiwan
| | - Susan Shur-Fen Gau
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Department of Psychiatry, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Neurodevelopment Club in Taiwan, Taipei 10051, Taiwan
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42
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Kazeminasab S, Taskiran II, Fattahi Z, Bazazzadegan N, Hosseini M, Rahimi M, Oladnabi M, Haddadi M, Celik A, Ropers HH, Najmabadi H, Kahrizi K. CNKSR1 gene defect can cause syndromic autosomal recessive intellectual disability. Am J Med Genet B Neuropsychiatr Genet 2018; 177:691-699. [PMID: 30450701 DOI: 10.1002/ajmg.b.32648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The advent of high-throughput sequencing technologies has led to an exponential increase in the identification of novel disease-causing genes in highly heterogeneous diseases. A novel frameshift mutation in CNKSR1 gene was detected by Next-Generation Sequencing (NGS) in an Iranian family with syndromic autosomal recessive intellectual disability (ARID). CNKSR1 encodes a connector enhancer of kinase suppressor of Ras 1, which acts as a scaffold component for receptor tyrosine kinase in mitogen-activated protein kinase (MAPK) cascades. CNKSR1 interacts with proteins which have already been shown to be associated with intellectual disability (ID) in the MAPK signaling pathway and promotes cell migration through RhoA-mediated c-Jun N-terminal kinase (JNK) activation. Lack of CNKSR1 transcripts and protein was observed in lymphoblastoid cells derived from affected patients using qRT-PCR and western blot analysis, respectively. Furthermore, RNAi-mediated knockdown of cnk, the CNKSR1 orthologue in Drosophila melanogaster brain, led to defects in eye and mushroom body (MB) structures. In conclusion, our findings support the possible role of CNKSR1 in brain development which can lead to cognitive impairment.
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Affiliation(s)
- Somayeh Kazeminasab
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Rahimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Haddadi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
| | - Arzu Celik
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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43
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Sacher M, Shahrzad N, Kamel H, Milev MP. TRAPPopathies: An emerging set of disorders linked to variations in the genes encoding transport protein particle (TRAPP)-associated proteins. Traffic 2018; 20:5-26. [PMID: 30152084 DOI: 10.1111/tra.12615] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/23/2018] [Accepted: 08/26/2018] [Indexed: 02/06/2023]
Abstract
The movement of proteins between cellular compartments requires the orchestrated actions of many factors including Rab family GTPases, Soluble NSF Attachment protein REceptors (SNAREs) and so-called tethering factors. One such tethering factor is called TRAnsport Protein Particle (TRAPP), and in humans, TRAPP proteins are distributed into two related complexes called TRAPP II and III. Although thought to act as a single unit within the complex, in the past few years it has become evident that some TRAPP proteins function independently of the complex. Consistent with this, variations in the genes encoding these proteins result in a spectrum of human diseases with diverse, but partially overlapping, phenotypes. This contrasts with other tethering factors such as COG, where variations in the genes that encode its subunits all result in an identical phenotype. In this review, we present an up-to-date summary of all the known disease-related variations of genes encoding TRAPP-associated proteins and the disorders linked to these variations which we now call TRAPPopathies.
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Affiliation(s)
- Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Nassim Shahrzad
- Department of Medicine, University of California, San Francisco, California
| | - Hiba Kamel
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Miroslav P Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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44
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Mbimba T, Hussein NJ, Najeed A, Safadi FF. TRAPPC9: Novel insights into its trafficking and signaling pathways in health and disease (Review). Int J Mol Med 2018; 42:2991-2997. [PMID: 30272317 DOI: 10.3892/ijmm.2018.3889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/14/2018] [Indexed: 11/06/2022] Open
Abstract
Trafficking protein particle complex 9 (TRAPPC9) is a protein subunit of the transport protein particle II (TRAPPII), which has been reported to be important in the trafficking of cargo from the endoplasmic reticulum (ER) to the Golgi, and in intra‑Golgi and endosome‑to‑Golgi transport in yeast cells. In mammalian cells, TRAPPII has been shown to be important in Golgi vesicle tethering and intra‑Golgi transport. TRAPPC9 is considered to be a novel molecule capable of modulating the activation of nuclear factor‑κB (NF‑κB). Mutations in TRAPPC9 have been linked to a rare consanguineous hereditary form of mental retardation, as part of the NF‑κB pathways. In addition, TRAPPC9 has been reported to be involved in breast and colon cancer and liver diseases. The present review highlights the most recent publications on the structure, expression and function of TRAPPC9, and its association with various human diseases.
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Affiliation(s)
- Thomas Mbimba
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Nazar J Hussein
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Ayesha Najeed
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Fayez F Safadi
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
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Santos-Cortez RLP, Khan V, Khan FS, Mughal ZUN, Chakchouk I, Lee K, Rasheed M, Hamza R, Acharya A, Ullah E, Saqib MAN, Abbe I, Ali G, Hassan MJ, Khan S, Azeem Z, Ullah I, Bamshad MJ, Nickerson DA, Schrauwen I, Ahmad W, Ansar M, Leal SM. Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability. Hum Genet 2018; 137:735-752. [PMID: 30167849 PMCID: PMC6201268 DOI: 10.1007/s00439-018-1928-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/10/2018] [Indexed: 01/30/2023]
Abstract
Identification of Mendelian genes for neurodevelopmental disorders using exome sequencing to study autosomal recessive (AR) consanguineous pedigrees has been highly successful. To identify causal variants for syndromic and non-syndromic intellectual disability (ID), exome sequencing was performed using DNA samples from 22 consanguineous Pakistani families with ARID, of which 21 have additional phenotypes including microcephaly. To aid in variant identification, homozygosity mapping and linkage analysis were performed. DNA samples from affected family member(s) from every pedigree underwent exome sequencing. Identified rare damaging exome variants were tested for co-segregation with ID using Sanger sequencing. For seven ARID families, variants were identified in genes not previously associated with ID, including: EI24, FXR1 and TET3 for which knockout mouse models have brain defects; and CACNG7 and TRAPPC10 where cell studies suggest roles in important neural pathways. For two families, the novel ARID genes CARNMT1 and GARNL3 lie within previously reported ID microdeletion regions. We also observed homozygous variants in two ID candidate genes, GRAMD1B and TBRG1, for which each has been previously reported in a single family. An additional 14 families have homozygous variants in established ID genes, of which 11 variants are novel. All ARID genes have increased expression in specific structures of the developing and adult human brain and 91% of the genes are differentially expressed in utero or during early childhood. The identification of novel ARID candidate genes and variants adds to the knowledge base that is required to further understand human brain function and development.
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Affiliation(s)
- Regie Lyn P Santos-Cortez
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
- Department of Otolaryngology, University of Colorado School of Medicine, 12700 E. 19th Ave., Aurora, CO, 80045, USA
| | - Valeed Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Falak Sher Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zaib-Un-Nisa Mughal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Imen Chakchouk
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Kwanghyuk Lee
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Memoona Rasheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rifat Hamza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Anushree Acharya
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Ehsan Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Arif Nadeem Saqib
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Pakistan Health Research Council, Shahrah-e-Jamhuriat, G-5/2, Islamabad, Pakistan
| | - Izoduwa Abbe
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Muhammad Jawad Hassan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, KPK, Pakistan
| | - Zahid Azeem
- Department of Biochemistry, Azad Jammu and Kashmir Medical College, Muzaffarabad, Pakistan
| | - Irfan Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave. NE, Seattle, WA, 98195, USA
- Department of Pediatrics, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave. NE, Seattle, WA, 98195, USA
| | - Isabelle Schrauwen
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA.
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46
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Milev MP, Graziano C, Karall D, Kuper WFE, Al-Deri N, Cordelli DM, Haack TB, Danhauser K, Iuso A, Palombo F, Pippucci T, Prokisch H, Saint-Dic D, Seri M, Stanga D, Cenacchi G, van Gassen KLI, Zschocke J, Fauth C, Mayr JA, Sacher M, van Hasselt PM. Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts. J Med Genet 2018; 55:753-764. [DOI: 10.1136/jmedgenet-2018-105441] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/18/2018] [Accepted: 07/12/2018] [Indexed: 12/28/2022]
Abstract
BackgroundThe combination of febrile illness-induced encephalopathy and rhabdomyolysis has thus far only been described in disorders that affect cellular energy status. In the absence of specific metabolic abnormalities, diagnosis can be challenging.ObjectiveThe objective of this study was to identify and characterise pathogenic variants in two individuals from unrelated families, both of whom presented clinically with a similar phenotype that included neurodevelopmental delay, febrile illness-induced encephalopathy and episodes of rhabdomyolysis, followed by developmental arrest, epilepsy and tetraplegia.MethodsWhole exome sequencing was used to identify pathogenic variants in the two individuals. Biochemical and cell biological analyses were performed on fibroblasts from these individuals and a yeast two-hybrid analysis was used to assess protein-protein interactions.ResultsProbands shared a homozygous TRAPPC2L variant (c.109G>T) resulting in a p.Asp37Tyr missense variant. TRAPPC2L is a component of transport protein particle (TRAPP), a group of multisubunit complexes that function in membrane traffic and autophagy. Studies in patient fibroblasts as well as in a yeast system showed that the p.Asp37Tyr protein was present but not functional and resulted in specific membrane trafficking delays. The human missense mutation and the analogous mutation in the yeast homologue Tca17 ablated the interaction between TRAPPC2L and TRAPPC10/Trs130, a component of the TRAPP II complex. Since TRAPP II activates the GTPase RAB11, we examined the activation state of this protein and found increased levels of the active RAB, correlating with changes in its cellular morphology.ConclusionsOur study implicates a RAB11 pathway in the aetiology of the TRAPPC2L disorder and has implications for other TRAPP-related disorders with similar phenotypes.
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Lo CL, Lumeng L, Bell RL, Liang T, Lossie AC, Muir WM, Zhou FC. CIS-Acting Allele-Specific Expression Differences Induced by Alcohol and Impacted by Sex as Well as Parental Genotype of Origin. Alcohol Clin Exp Res 2018; 42:1444-1453. [PMID: 29786868 PMCID: PMC7560966 DOI: 10.1111/acer.13776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/09/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Alcohol use disorders (AUDs) are influenced by complex interactions between the genetics of the individual and their environment. We have previously identified hundreds of polygenic genetic variants between the selectively bred high- and low-alcohol drinking (HAD and LAD) rat lines. Here, we report allele-specific expression (ASE) differences, between the HAD2 and LAD2 rat lines. METHODS The HAD2 and LAD2 rats, which have been sequenced, were reciprocally crossed to generate 10 litters of F1 progeny. For 5 of these litters, the sire was HAD2, and for the other 5 litters, the sire was a LAD2. From these 10 litters, 2 males and 2 females were picked from each F1 litter (N = 40 total). The F1 pups were divided, balancing for sex and direction of cross, into an alcohol (15%) versus a water control group. Alcohol drinking started in the middle of adolescence (~postnatal day 35) and lasted 9 weeks. At the end of these treatments, rats were euthanized, the nucleus accumbens was dissected, and RNA was processed for RNA-sequencing and ASE analyses. RESULTS Analyses revealed that adolescent ethanol (EtOH) drinking, individual EtOH drinking levels, parentage, and sex-of-animal affected ASEs of about 300 genes. The identified genes included those associated with EtOH metabolism (e.g., Aldh2); neuromodulatory function (e.g., Cckbr, Slc6a7, and Slc1a1); ion channel activity (e.g., Kcnc3); and other synaptic and epigenetic functions. CONCLUSIONS These data indicate that EtOH drinking differentially amplified paternal versus maternal allelic contribution to the transcriptome. We hypothesize that this was due, at least in part, to EtOH-induced changes in cis-regulation of polymorphisms previously identified between the HAD2 and LAD2 rat lines. This report highlights the complexity of gene-by-environment interactions mediating a genetic predisposition for, and/or the active development of, AUDs.
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Affiliation(s)
- Chiao-Ling Lo
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Lawrence Lumeng
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Richard L. Bell
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Tiebing Liang
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Amy C. Lossie
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Williams M. Muir
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Feng C. Zhou
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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Mapping autosomal recessive intellectual disability: combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguineous families. Mol Psychiatry 2018; 23:973-984. [PMID: 28397838 DOI: 10.1038/mp.2017.60] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/06/2017] [Accepted: 02/10/2017] [Indexed: 12/14/2022]
Abstract
Approximately 1% of the global population is affected by intellectual disability (ID), and the majority receive no molecular diagnosis. Previous studies have indicated high levels of genetic heterogeneity, with estimates of more than 2500 autosomal ID genes, the majority of which are autosomal recessive (AR). Here, we combined microarray genotyping, homozygosity-by-descent (HBD) mapping, copy number variation (CNV) analysis, and whole exome sequencing (WES) to identify disease genes/mutations in 192 multiplex Pakistani and Iranian consanguineous families with non-syndromic ID. We identified definite or candidate mutations (or CNVs) in 51% of families in 72 different genes, including 26 not previously reported for ARID. The new ARID genes include nine with loss-of-function mutations (ABI2, MAPK8, MPDZ, PIDD1, SLAIN1, TBC1D23, TRAPPC6B, UBA7 and USP44), and missense mutations include the first reports of variants in BDNF or TET1 associated with ID. The genes identified also showed overlap with de novo gene sets for other neuropsychiatric disorders. Transcriptional studies showed prominent expression in the prenatal brain. The high yield of AR mutations for ID indicated that this approach has excellent clinical potential and should inform clinical diagnostics, including clinical whole exome and genome sequencing, for populations in which consanguinity is common. As with other AR disorders, the relevance will also apply to outbred populations.
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Riedel F, Galindo A, Muschalik N, Munro S. The two TRAPP complexes of metazoans have distinct roles and act on different Rab GTPases. J Cell Biol 2017; 217:601-617. [PMID: 29273580 PMCID: PMC5800803 DOI: 10.1083/jcb.201705068] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/19/2017] [Accepted: 11/27/2017] [Indexed: 12/03/2022] Open
Abstract
In yeast, the TRAPP complexes activate Rab1 with TRAPPII also activating Rab11, but less is known about the two TRAPPs in metazoans. Riedel et al. show that in Drosophila melanogaster, TRAPPIII is an essential Rab1 activator, and TRAPPII activates Rab1 and Rab11 and becomes essential when an unrelated Rab11 activator is deleted. Originally identified in yeast, transport protein particle (TRAPP) complexes are Rab GTPase exchange factors that share a core set of subunits. TRAPPs were initially found to act on Ypt1, the yeast orthologue of Rab1, but recent studies have found that yeast TRAPPII can also activate the Rab11 orthologues Ypt31/32. Mammals have two TRAPP complexes, but their role is less clear, and they contain subunits that are not found in the yeast complexes but are essential for cell growth. To investigate TRAPP function in metazoans, we show that Drosophila melanogaster have two TRAPP complexes similar to those in mammals and that both activate Rab1, whereas one, TRAPPII, also activates Rab11. TRAPPII is not essential but becomes so in the absence of the gene parcas that encodes the Drosophila orthologue of the SH3BP5 family of Rab11 guanine nucleotide exchange factors (GEFs). Thus, in metazoans, Rab1 activation requires TRAPP subunits not found in yeast, and Rab11 activation is shared by TRAPPII and an unrelated GEF that is metazoan specific.
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Affiliation(s)
- Falko Riedel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Antonio Galindo
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Nadine Muschalik
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Sean Munro
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
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50
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Abbasi AA, Blaesius K, Hu H, Latif Z, Picker-Minh S, Khan MN, Farooq S, Khan MA, Kaindl AM. Identification of a novel homozygous TRAPPC9 gene mutation causing non-syndromic intellectual disability, speech disorder, and secondary microcephaly. Am J Med Genet B Neuropsychiatr Genet 2017; 174:839-845. [PMID: 29031008 DOI: 10.1002/ajmg.b.32602] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/24/2017] [Accepted: 09/11/2017] [Indexed: 11/11/2022]
Abstract
TRAPPC9 gene mutations have been linked recently to autosomal recessive mental retardation 13 (MRT13; MIM#613192) with only eight families reported world-wide. We assessed patients from two consanguineous pedigrees of Pakistani descent with non-syndromic intellectual disability and postnatal microcephaly through whole exome sequencing (WES) and cosegregation analysis. Here we report six further patients from two pedigrees with homozygous TRAPPC9 gene mutations, the novel nonsense mutation c.2065G>T (p.E689*) and the previously identified nonsense mutation c.1423C>T (p.R475*). We provide an overview of previously reported clinical features and highlight common symptoms and variability of MRT13. Common findings are intellectual disability and absent speech, and frequently microcephaly, motor delay and pathological findings on MRI including diminished cerebral white matter volume are present. Mutations in TRAPPC9 should be considered in non-syndromic autosomal recessive intellectual disability with severe speech disorder.
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Affiliation(s)
- Ansar A Abbasi
- Department of Zoology, Mirpur University of Science and Technology (MUST), Mirpur, Pakistan
| | - Kathrin Blaesius
- Charité - Universitätsmedizin Berlin, Institute of Neuroanatomy and Cell Biology, Berlin, Germany.,Berlin Insitute of Health (BIH), Anna-Louisa-Karsch Strasse 2, 10178, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany
| | - Hao Hu
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zahid Latif
- Department of Zoology, University of Azad Jammu and Kashmir Muzaffarabad, Muzaffarabad, Pakistan
| | - Sylvie Picker-Minh
- Charité - Universitätsmedizin Berlin, Institute of Neuroanatomy and Cell Biology, Berlin, Germany.,Berlin Insitute of Health (BIH), Anna-Louisa-Karsch Strasse 2, 10178, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Muhammad N Khan
- Department of Zoology, University of Azad Jammu and Kashmir Muzaffarabad, Muzaffarabad, Pakistan
| | - Sundas Farooq
- Department of Zoology, Mirpur University of Science and Technology (MUST), Mirpur, Pakistan
| | - Muzammil A Khan
- Gomal Centre of Biochemistry and Biotechnology (GCBB), Gomal University, Dera Ismail Khan, Pakistan
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Institute of Neuroanatomy and Cell Biology, Berlin, Germany.,Berlin Insitute of Health (BIH), Anna-Louisa-Karsch Strasse 2, 10178, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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