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Placidi G, D'Agostino E, Maltese PE, Savastano MC, Gambini G, Rizzo S, Bonetti G, Bertelli M, Chiurazzi P, Falsini B. A novel homozygous splice site variant in ARL2BP causes a syndromic autosomal recessive rod-cone dystrophy with situs inversus, asthenozoospermia, unilateral renal agenesis and microcysts. BMC Med Genomics 2024; 17:100. [PMID: 38649918 PMCID: PMC11036775 DOI: 10.1186/s12920-024-01868-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND This report presents a clinical case of syndromic rod-cone dystrophy due to a splice site variant in the ARL2BP gene causing situs inversus, asthenozoospermia, unilateral renal agenesis and microcysts. The presence of renal agenesis and cryptorchidism expands the clinical manifestations due to ARL2BP variants. The detailed, long-term follow-up contributes valuable insights into disease progression, aiding clinical diagnosis and patient management. CASE PRESENTATION The male patient complained of photophobia as the first symptom when he was 20 years old followed by nyctalopia, loss of central visual acuity and peripheral visual field ten years later. Genetic analysis identified a likely pathogenic homozygous variant (c.294-1G > C) involving the splicing acceptor site of intron 4. Reported symptoms together with full-field stimulus threshold testing, electroretinogram and advanced multimodal imaging allowed us to recognize the typical characteristics of a mixed retinal dystrophy. Despite the end-stage retinal disease, this patient still retained a useful residual vision at 63 years and had a slow disease progression during the last 5 years of evaluation. DISCUSSION AND CONCLUSIONS Our findings underscore the variable clinical presentation of ARL2BP variants, emphasizing the importance of a nuanced approach in diagnosing and managing patients. The presence of renal cysts warrants consideration of a differential diagnosis, particularly with Senior-Loken (SLS), Bardet-Biedl (BBS) and Joubert syndromes (JS) but also with Short Rib Thoracic Dysplasia 9, highlighting the need for careful phenotypic evaluation in these cases.
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Affiliation(s)
- Giorgio Placidi
- UOC Oculistica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Gemelli 8, 00168, Rome, Italy
| | - Elena D'Agostino
- UOC Oculistica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Gemelli 8, 00168, Rome, Italy
| | | | - Maria Cristina Savastano
- UOC Oculistica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Gemelli 8, 00168, Rome, Italy
- Istituto di Oftalmologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Gloria Gambini
- UOC Oculistica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Gemelli 8, 00168, Rome, Italy
- Istituto di Oftalmologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Stanislao Rizzo
- UOC Oculistica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Gemelli 8, 00168, Rome, Italy
- Istituto di Oftalmologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
- Istituto di Neuroscienze, Consiglio Nazionale Delle Ricerche, Pisa, Italy
| | - Gabriele Bonetti
- MAGI'S LAB, 38068, Rovereto, Italy
- MAGI EUREGIO, 39100, Bolzano, Italy
| | - Matteo Bertelli
- MAGI'S LAB, 38068, Rovereto, Italy
- MAGI EUREGIO, 39100, Bolzano, Italy
- MAGISNAT, Atlanta Tech Park, 107 Technology Parkway, 30092, Peachtree Corners, GA, USA
| | - Pietro Chiurazzi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
- UOC Genetica Medica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Gemelli 8, 00168, Rome, Italy
| | - Benedetto Falsini
- UOC Oculistica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Gemelli 8, 00168, Rome, Italy
- Istituto di Oftalmologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
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Fabregat M, Niño-Rivero S, Pose S, Cárdenas-Rodríguez M, Bresque M, Hernández K, Prieto-Echagüe V, Schlapp G, Crispo M, Lagos P, Lago N, Escande C, Irigoín F, Badano JL. Generation and characterization of Ccdc28b mutant mice links the Bardet-Biedl associated gene with mild social behavioral phenotypes. PLoS Genet 2022; 18:e1009896. [PMID: 35653384 PMCID: PMC9197067 DOI: 10.1371/journal.pgen.1009896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 06/14/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
CCDC28B (coiled-coil domain-containing protein 28B) was identified as a modifier in the ciliopathy Bardet-Biedl syndrome (BBS). Our previous work in cells and zebrafish showed that CCDC28B plays a role regulating cilia length in a mechanism that is not completely understood. Here we report the generation of a Ccdc28b mutant mouse using CRISPR/Cas9 (Ccdc28b mut). Depletion of CCDC28B resulted in a mild phenotype. Ccdc28b mut animals i) do not present clear structural cilia affectation, although we did observe mild defects in cilia density and cilia length in some tissues, ii) reproduce normally, and iii) do not develop retinal degeneration or obesity, two hallmark features of reported BBS murine models. In contrast, Ccdc28b mut mice did show clear social interaction defects as well as stereotypical behaviors. This finding is indeed relevant regarding CCDC28B as a modifier of BBS since behavioral phenotypes have been documented in BBS. Overall, this work reports a novel mouse model that will be key to continue evaluating genetic interactions in BBS, deciphering the contribution of CCDC28B to modulate the presentation of BBS phenotypes. In addition, our data underscores a novel link between CCDC28B and behavioral defects, providing a novel opportunity to further our understanding of the genetic, cellular, and molecular basis of these complex phenotypes. BBS is caused by mutations in any one of 22 genes known to date. In some families, BBS can be inherited as an oligogenic trait whereby mutations in more than one BBS gene collaborate in the presentation of the syndrome. In addition, CCDC28B was originally identified as a modifier of BBS, whereby a reduction in CCDC28B levels was associated with a more severe presentation of the syndrome. Different mechanisms, all relying on functional redundancy, have been proposed to explain these genetic interactions. The characterization of BBS proteins supported this functional redundancy hypothesis: BBS proteins play a role in cilia maintenance/function and subsets of BBS proteins can even interact directly in multiprotein complexes. We have previously shown that CCDC28B also participates in cilia biology regulating the length of the organelle: knockdown of CCDC28B in cells results in cilia shortening and targeting ccdc28b in zebrafish also results in early embryonic phenotypes characteristic of other cilia mutants. In this work, we generated a Ccdc28b mutant mouse to determine whether abrogating Ccdc28b function would be sufficient to cause a ciliopathy phenotype in mammals, and to generate a tool to continue dissecting its modifying role in the context of BBS. Overall, Ccdc28b mutant mice presented a mild phenotype, a finding fully compatible with its role as a modifier, rather than a causal BBS gene. In addition, we found that Ccdc28b mutants showed behavioral phenotypes, similar to the deficits observed in rodent autism spectrum disorder (ASD) models. Thus, our results underscore a novel causal link between CCDC28B and behavioral phenotypes in mice.
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Affiliation(s)
- Matías Fabregat
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- INDICyO Institutional Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Sofía Niño-Rivero
- Departamento de Fisiología, Universidad de la República, Montevideo, Uruguay
| | - Sabrina Pose
- Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Magdalena Cárdenas-Rodríguez
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- INDICyO Institutional Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Bresque
- INDICyO Institutional Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Metabolic Diseases and Aging Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Karina Hernández
- Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Victoria Prieto-Echagüe
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- INDICyO Institutional Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Geraldine Schlapp
- Laboratory Animal Biotechnology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Martina Crispo
- Laboratory Animal Biotechnology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Patricia Lagos
- Departamento de Fisiología, Universidad de la República, Montevideo, Uruguay
| | - Natalia Lago
- Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Carlos Escande
- INDICyO Institutional Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Metabolic Diseases and Aging Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Florencia Irigoín
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- INDICyO Institutional Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (FI); (JLB)
| | - Jose L. Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- INDICyO Institutional Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
- * E-mail: (FI); (JLB)
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Gana S, Serpieri V, Valente EM. Genotype-phenotype correlates in Joubert syndrome: A review. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:72-88. [PMID: 35238134 PMCID: PMC9314610 DOI: 10.1002/ajmg.c.31963] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 01/20/2023]
Abstract
Joubert syndrome (JS) is a genetically heterogeneous primary ciliopathy characterized by a pathognomonic cerebellar and brainstem malformation, the “molar tooth sign,” and variable organ involvement. Over 40 causative genes have been identified to date, explaining up to 94% of cases. To date, gene‐phenotype correlates have been delineated only for a handful of genes, directly translating into improved counseling and clinical care. For instance, JS individuals harboring pathogenic variants in TMEM67 have a significantly higher risk of liver fibrosis, while pathogenic variants in NPHP1, RPGRIP1L, and TMEM237 are frequently associated to JS with renal involvement, requiring a closer monitoring of liver parameters, or renal functioning. On the other hand, individuals with causal variants in the CEP290 or AHI1 need a closer surveillance for retinal dystrophy and, in case of CEP290, also for chronic kidney disease. These examples highlight how an accurate description of the range of clinical symptoms associated with defects in each causative gene, including the rare ones, would better address prognosis and help guiding a personalized management. This review proposes to address this issue by assessing the available literature, to confirm known, as well as to propose rare gene‐phenotype correlates in JS.
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Affiliation(s)
- Simone Gana
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Enza Maria Valente
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
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4
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Wiegering A, Dildrop R, Vesque C, Khanna H, Schneider-Maunoury S, Gerhardt C. Rpgrip1l controls ciliary gating by ensuring the proper amount of Cep290 at the vertebrate transition zone. Mol Biol Cell 2021; 32:675-689. [PMID: 33625872 PMCID: PMC8108517 DOI: 10.1091/mbc.e20-03-0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A range of severe human diseases called ciliopathies is caused by the dysfunction of primary cilia. Primary cilia are cytoplasmic protrusions consisting of the basal body (BB), the axoneme, and the transition zone (TZ). The BB is a modified mother centriole from which the axoneme, the microtubule-based ciliary scaffold, is formed. At the proximal end of the axoneme, the TZ functions as the ciliary gate governing ciliary protein entry and exit. Since ciliopathies often develop due to mutations in genes encoding proteins that localize to the TZ, the understanding of the mechanisms underlying TZ function is of eminent importance. Here, we show that the ciliopathy protein Rpgrip1l governs ciliary gating by ensuring the proper amount of Cep290 at the vertebrate TZ. Further, we identified the flavonoid eupatilin as a potential agent to tackle ciliopathies caused by mutations in RPGRIP1L as it rescues ciliary gating in the absence of Rpgrip1l.
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Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.,Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Renate Dildrop
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Christine Vesque
- Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Hemant Khanna
- Department of Ophthalmology and Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sylvie Schneider-Maunoury
- Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
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5
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Gloeckner CJ, Porras P. Guilt-by-Association - Functional Insights Gained From Studying the LRRK2 Interactome. Front Neurosci 2020; 14:485. [PMID: 32508578 PMCID: PMC7251075 DOI: 10.3389/fnins.2020.00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
The Parkinson's disease-associated Leucine-rich repeat kinase 2 (LRRK2) is a complex multi-domain protein belonging to the Roco protein family, a unique group of G-proteins. Variants of this gene are associated with an increased risk of Parkinson's disease. Besides its well-characterized enzymatic activities, conferred by its GTPase and kinase domains, and a central dimerization domain, it contains four predicted repeat domains, which are, based on their structure, commonly involved in protein-protein interactions (PPIs). In the past decades, tremendous progress has been made in determining comprehensive interactome maps for the human proteome. Knowledge of PPIs has been instrumental in assigning functions to proteins involved in human disease and helped to understand the connectivity between different disease pathways and also significantly contributed to the functional understanding of LRRK2. In addition to an increased kinase activity observed for proteins containing PD-associated variants, various studies helped to establish LRRK2 as a large scaffold protein in the interface between cytoskeletal dynamics and the vesicular transport. This review first discusses a number of specific LRRK2-associated PPIs for which a functional consequence can at least be speculated upon, and then considers the representation of LRRK2 protein interactions in public repositories, providing an outlook on open research questions and challenges in this field.
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Affiliation(s)
- Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Center for Ophthalmology, Institute for Ophthalmic Research, Core Facility for Medical Bioanalytics, University of Tübingen, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cherry Hinton, United Kingdom
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Straub J, Gregor A, Sauerer T, Fliedner A, Distel L, Suchy C, Ekici AB, Ferrazzi F, Zweier C. Genetic interaction screen for severe neurodevelopmental disorders reveals a functional link between Ube3a and Mef2 in Drosophila melanogaster. Sci Rep 2020; 10:1204. [PMID: 31988313 PMCID: PMC6985129 DOI: 10.1038/s41598-020-58182-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically extremely heterogeneous with shared phenotypes often associated with genes from the same networks. Mutations in TCF4, MEF2C, UBE3A, ZEB2 or ATRX cause phenotypically overlapping, syndromic forms of NDDs with severe intellectual disability, epilepsy and microcephaly. To characterize potential functional links between these genes/proteins, we screened for genetic interactions in Drosophila melanogaster. We induced ubiquitous or tissue specific knockdown or overexpression of each single orthologous gene (Da, Mef2, Ube3a, Zfh1, XNP) and in pairwise combinations. Subsequently, we assessed parameters such as lethality, wing and eye morphology, neuromuscular junction morphology, bang sensitivity and climbing behaviour in comparison between single and pairwise dosage manipulations. We found most stringent evidence for genetic interaction between Ube3a and Mef2 as simultaneous dosage manipulation in different tissues including glia, wing and eye resulted in multiple phenotype modifications. We subsequently found evidence for physical interaction between UBE3A and MEF2C also in human cells. Systematic pairwise assessment of the Drosophila orthologues of five genes implicated in clinically overlapping, severe NDDs and subsequent confirmation in a human cell line revealed interactions between UBE3A/Ube3a and MEF2C/Mef2, thus contributing to the characterization of the underlying molecular commonalities.
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Affiliation(s)
- Jonas Straub
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Tatjana Sauerer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anna Fliedner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Laila Distel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christine Suchy
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany.
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Functional analysis of new human Bardet-Biedl syndrome loci specific variants in the zebrafish model. Sci Rep 2019; 9:12936. [PMID: 31506453 PMCID: PMC6736949 DOI: 10.1038/s41598-019-49217-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 08/16/2019] [Indexed: 11/09/2022] Open
Abstract
The multiple genetic approaches available for molecular diagnosis of human diseases have made possible to identify an increasing number of pathogenic genetic changes, particularly with the advent of next generation sequencing (NGS) technologies. However, the main challenge lies in the interpretation of their functional impact, which has resulted in the widespread use of animal models. We describe here the functional modelling of seven BBS loci variants, most of them novel, in zebrafish embryos to validate their in silico prediction of pathogenicity. We show that target knockdown (KD) of known BBS (BBS1, BB5 or BBS6) loci leads to developmental defects commonly associated with ciliopathies, as previously described. These KD pleiotropic phenotypes were rescued by co-injecting human wild type (WT) loci sequence but not with the equivalent mutated mRNAs, providing evidence of the pathogenic effect of these BBS changes. Furthermore, direct assessment of cilia located in Kupffer's vesicle (KV) showed a reduction of ciliary length associated with all the studied variants, thus confirming a deleterious effect. Taken together, our results seem to prove the pathogenicity of the already classified and unclassified new BBS variants, as well as highlight the usefulness of zebrafish as an animal model for in vivo assays in human ciliopathies.
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Marín Ò, Aguirre J, de la Cruz X. Compensated pathogenic variants in coagulation factors VIII and IX present complex mapping between molecular impact and hemophilia severity. Sci Rep 2019; 9:9538. [PMID: 31267011 PMCID: PMC6606640 DOI: 10.1038/s41598-019-45916-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Compensated pathogenic deviations (CPDs) are sequence variants that are pathogenic in humans but neutral in other species. In recent years, our molecular understanding of CPDs has advanced substantially. For example, it is known that their impact on human proteins is generally milder than that of average pathogenic mutations and that their impact is suppressed in non-human carriers by compensatory mutations. However, prior studies have ignored the evolutionarily relevant relationship between molecular impact and organismal phenotype. Here, we explore this topic using CPDs from FVIII and FIX and data concerning carriers' hemophilia severity. We find that, regardless of their molecular impact, these mutations can be associated with either mild or severe disease phenotypes. Only a weak relationship is found between protein stability changes and severity. We also characterize the population variability of hemostasis proteins, which constitute the genetic background of FVIII and FIX, using data from the 1000 Genome project. We observe that genetic background can vary substantially between individuals in terms of both the amount and nature of genetic variants. Finally, we discuss how these results highlight the need to include new terms in present models of protein evolution to explain the origin of CPDs.
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Affiliation(s)
- Òscar Marín
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Josu Aguirre
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035, Barcelona, Spain. .,ICREA, Barcelona, Spain.
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9
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Nikopoulos K, Cisarova K, Quinodoz M, Koskiniemi-Kuendig H, Miyake N, Farinelli P, Rehman AU, Khan MI, Prunotto A, Akiyama M, Kamatani Y, Terao C, Miya F, Ikeda Y, Ueno S, Fuse N, Murakami A, Wada Y, Terasaki H, Sonoda KH, Ishibashi T, Kubo M, Cremers FPM, Kutalik Z, Matsumoto N, Nishiguchi KM, Nakazawa T, Rivolta C. A frequent variant in the Japanese population determines quasi-Mendelian inheritance of rare retinal ciliopathy. Nat Commun 2019; 10:2884. [PMID: 31253780 PMCID: PMC6599023 DOI: 10.1038/s41467-019-10746-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Hereditary retinal degenerations (HRDs) are Mendelian diseases characterized by progressive blindness and caused by ultra-rare mutations. In a genomic screen of 331 unrelated Japanese patients, we identify a disruptive Alu insertion and a nonsense variant (p.Arg1933*) in the ciliary gene RP1, neither of which are rare alleles in Japan. p.Arg1933* is almost polymorphic (frequency = 0.6%, amongst 12,000 individuals), does not cause disease in homozygosis or heterozygosis, and yet is significantly enriched in HRD patients (frequency = 2.1%, i.e., a 3.5-fold enrichment; p-value = 9.2 × 10-5). Familial co-segregation and association analyses show that p.Arg1933* can act as a Mendelian mutation in trans with the Alu insertion, but might also associate with disease in combination with two alleles in the EYS gene in a non-Mendelian pattern of heredity. Our results suggest that rare conditions such as HRDs can be paradoxically determined by relatively common variants, following a quasi-Mendelian model linking monogenic and complex inheritance.
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Affiliation(s)
- Konstantinos Nikopoulos
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- Service of Medical Genetics, Lausanne University Hospital (CHUV), 1011, Lausanne, Switzerland
| | - Katarina Cisarova
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Hanna Koskiniemi-Kuendig
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Pietro Farinelli
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Atta Ur Rehman
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Andrea Prunotto
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Chikashi Terao
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Yasuhiro Ikeda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, 980-8573, Japan
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan
| | - Yuko Wada
- Yuko Wada Eye Clinic, Sendai, 980-0011, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tatsuro Ishibashi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, Lausanne University Hospital, 1011, Lausanne, Switzerland
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Koji M Nishiguchi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
| | - Carlo Rivolta
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland.
- University of Basel, 4001, Basel, Switzerland.
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10
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Studying how genetic variants affect mechanism in biological systems. Essays Biochem 2018; 62:575-582. [PMID: 30315099 DOI: 10.1042/ebc20180021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 11/17/2022]
Abstract
Genetic variants are currently a major component of system-wide investigations into biological function or disease. Approaches to select variants (often out of thousands of candidates) that are responsible for a particular phenomenon have many clinical applications and can help illuminate differences between individuals. Selecting meaningful variants is greatly aided by integration with information about molecular mechanism, whether known from protein structures or interactions or biological pathways. In this review we discuss the nature of genetic variants, and recent studies highlighting what is currently known about the relationship between genetic variation, biomolecular function, and disease.
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11
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Hao T, Wang Q, Zhao L, Wu D, Wang E, Sun J. Analyzing of Molecular Networks for Human Diseases and Drug Discovery. Curr Top Med Chem 2018; 18:1007-1014. [PMID: 30101711 PMCID: PMC6174636 DOI: 10.2174/1568026618666180813143408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 01/11/2023]
Abstract
Molecular networks represent the interactions and relations of genes/proteins, and also encode molecular mechanisms of biological processes, development and diseases. Among the molecular networks, protein-protein Interaction Networks (PINs) have become effective platforms for uncovering the molecular mechanisms of diseases and drug discovery. PINs have been constructed for various organisms and utilized to solve many biological problems. In human, most proteins present their complex functions by interactions with other proteins, and the sum of these interactions represents the human protein interactome. Especially in the research on human disease and drugs, as an emerging tool, the PIN provides a platform to systematically explore the molecular complexities of specific diseases and the references for drug design. In this review, we summarized the commonly used approaches to aid disease research and drug discovery with PINs, including the network topological analysis, identification of novel pathways, drug targets and sub-network biomarkers for diseases. With the development of bioinformatic techniques and biological networks, PINs will play an increasingly important role in human disease research and drug discovery.
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Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Qian Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Lingxuan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Dan Wu
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Edwin Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,University of Calgary Cumming School of Medicine, Calgary, Alberta T2N 4Z6, Canada
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,Tianjin Bohai Fisheries Research Institute, Tianjin 300221, China
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12
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Wiegering A, Rüther U, Gerhardt C. The ciliary protein Rpgrip1l in development and disease. Dev Biol 2018; 442:60-68. [DOI: 10.1016/j.ydbio.2018.07.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/13/2018] [Accepted: 07/28/2018] [Indexed: 12/28/2022]
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13
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Abstract
PURPOSE OF REVIEW The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. RECENT FINDINGS MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs. Although gene panel sequencing has evolved as a standard test for heterogeneous diseases, it is still debated, mainly because of financial issues and unsolved problems of variant interpretation, whether genome sequencing (and to a lesser extent also exome sequencing) of single patients can already be regarded as routine diagnostics. However, it has been shown that the inclusion of parents and additional family members often leads to a substantial increase in the diagnostic yield in exome-wide/genome-wide MPS approaches. In addition, MPS-based RNA sequencing just enters the research and diagnostic scene. SUMMARY Next-generation sequencing increasingly enables the detection of the genetic cause in highly heterogeneous diseases like NMDs in an efficient and affordable way. Gene panel sequencing and family-based exome sequencing have been proven as potent and cost-efficient diagnostic tools. Although clinical validation and interpretation of genome sequencing is still challenging, diagnostic RNA sequencing represents a promising tool to bypass some hurdles of diagnostics using genomic DNA.
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14
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Wiegering A, Dildrop R, Kalfhues L, Spychala A, Kuschel S, Lier JM, Zobel T, Dahmen S, Leu T, Struchtrup A, Legendre F, Vesque C, Schneider-Maunoury S, Saunier S, Rüther U, Gerhardt C. Cell type-specific regulation of ciliary transition zone assembly in vertebrates. EMBO J 2018; 37:embj.201797791. [PMID: 29650680 PMCID: PMC5978567 DOI: 10.15252/embj.201797791] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 01/07/2023] Open
Abstract
Ciliopathies are life-threatening human diseases caused by defective cilia. They can often be traced back to mutations of genes encoding transition zone (TZ) proteins demonstrating that the understanding of TZ organisation is of paramount importance. The TZ consists of multimeric protein modules that are subject to a stringent assembly hierarchy. Previous reports place Rpgrip1l at the top of the TZ assembly hierarchy in Caenorhabditis elegans By performing quantitative immunofluorescence studies in RPGRIP1L-/- mouse embryos and human embryonic cells, we recognise a different situation in vertebrates in which Rpgrip1l deficiency affects TZ assembly in a cell type-specific manner. In cell types in which the loss of Rpgrip1l alone does not affect all modules, additional truncation or removal of vertebrate-specific Rpgrip1 results in an impairment of all modules. Consequently, Rpgrip1l and Rpgrip1 synergistically ensure the TZ composition in several vertebrate cell types, revealing a higher complexity of TZ assembly in vertebrates than in invertebrates.
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Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Renate Dildrop
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Lisa Kalfhues
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - André Spychala
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Stefanie Kuschel
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Johanna Maria Lier
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Thomas Zobel
- Center for Advanced Imaging (CAi), Heinrich Heine University, Düsseldorf, Germany
| | - Stefanie Dahmen
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Tristan Leu
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Andreas Struchtrup
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Flora Legendre
- INSERM, U983, Hôpital Necker-Enfants Malades, Paris, France.,Sorbonne Paris Cité, Faculté de Médecine, Université Paris-Descartes, Paris, France
| | - Christine Vesque
- Paris-Seine (IBPS) - Developmental Biology Laboratory, Institut de Biologie, CNRS, UMR7622, INSERM U1156, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Sylvie Schneider-Maunoury
- Paris-Seine (IBPS) - Developmental Biology Laboratory, Institut de Biologie, CNRS, UMR7622, INSERM U1156, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Sophie Saunier
- INSERM, U983, Hôpital Necker-Enfants Malades, Paris, France.,Sorbonne Paris Cité, Faculté de Médecine, Université Paris-Descartes, Paris, France
| | - Ulrich Rüther
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
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15
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Katsanis N. 2017 Curt Stern Award: The Complexity of Simple Genetics. Am J Hum Genet 2018; 102:355-358. [PMID: 29499161 DOI: 10.1016/j.ajhg.2018.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 02/04/2018] [Indexed: 10/17/2022] Open
Affiliation(s)
- Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA.
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16
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Leveraging human genetic and adverse outcome pathway (AOP) data to inform susceptibility in human health risk assessment. Mamm Genome 2018; 29:190-204. [DOI: 10.1007/s00335-018-9738-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/31/2018] [Indexed: 12/19/2022]
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17
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Zentner D, Thompson T, Taylor J, Bogwitz M, Trainer A, Vohra J, Winship I, James PA. A rapid scoring tool to assess mutation probability in patients with inherited cardiac disorders. Eur J Med Genet 2018; 61:61-67. [DOI: 10.1016/j.ejmg.2017.10.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/29/2017] [Indexed: 02/01/2023]
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18
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Lee SH, Nam TS, Li W, Kim JH, Yoon W, Choi YD, Kim KH, Cai H, Kim MJ, Kim C, Choy HE, Kim N, Chay KO, Kim MK, Choi SY. Functional validation of novel MKS3/TMEM67 mutations in COACH syndrome. Sci Rep 2017; 7:10222. [PMID: 28860541 PMCID: PMC5579020 DOI: 10.1038/s41598-017-10652-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 08/10/2017] [Indexed: 12/18/2022] Open
Abstract
COACH syndrome is an autosomal recessive developmental disorder, a subtype of Joubert syndrome and related disorders, characterized by cerebellar vermis hypoplasia, oligophrenia, ataxia, coloboma, and hepatic fibrosis. Although mutations in TMEM67 (transmembrane protein 67)/MKS3 (Meckel-Gruber syndrome, type 3) were reported to cause COACH syndrome, this causality has not verified by functional studies. In a 20-year-old Korean man, we found cerebellar ataxia, isolated elevation in serum γ-glutamyl transpeptidase (γ-GTP) activity, oligophrenia, the molar tooth sign (MTS) in the brain MR images and congenital hepatic fibrosis (CHF). Two novel compound heterozygous mutations were found in TMEM67 in the patient: i) missense mutation (c.395 G > C and p.Gly132Ala) in exon 3, and ii) deletion in exon 26 (c.2758delT and p.Tyr920ThrfsX40). Western blotting showed that the p.Tyr920ThrfsX40 mutation accelerates turnover of the TMEM67 protein. Although wild-type human TMEM67 RNA rescued phenotypes of zebrafish embryos injected with anti-sense oligonucleotide morpholinos against tmem67, the two human TMEM67 RNAs individually harboring the two mutations did not. Finally, Wnt signaling, but not Hedgehog signaling, was suppressed in tmem67 morphants. To the best of our knowledge, this is the first report verifying the causality between COACH syndrome and TMEM67, which will further our understanding of molecular pathogenesis of the syndrome.
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Affiliation(s)
- So-Hyun Lee
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju, Republic of Korea.,Center for Creative Biomedical Scientists at Chonnam National University, Gwangju, Republic of Korea
| | - Tai-Seung Nam
- Department of Neurology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Wenting Li
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Jung Ha Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Woong Yoon
- Department of Radiology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yoo-Duk Choi
- Department of Pathology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Kun-Hee Kim
- Department of Microbiology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Hua Cai
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Changsoo Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Nacksung Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Kee Oh Chay
- Department of Biochemistry, Chonnam National University Medical School, Gwangju, Republic of Korea.
| | - Myeong-Kyu Kim
- Department of Neurology, Chonnam National University Medical School, Gwangju, Republic of Korea.
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju, Republic of Korea.
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19
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Khan I, Ansari IA, Singh P, Dass J FP. Prediction of functionally significant single nucleotide polymorphisms in PTEN tumor suppressor gene: An in silico approach. Biotechnol Appl Biochem 2017; 64:657-666. [PMID: 26800850 DOI: 10.1002/bab.1483] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 01/16/2016] [Indexed: 11/06/2022]
Abstract
The phosphatase and tensin homolog (PTEN) gene plays a crucial role in signal transduction by negatively regulating the PI3K signaling pathway. It is the most frequent mutated gene in many human-related cancers. Considering its critical role, a functional analysis of missense mutations of PTEN gene was undertaken in this study. Thirty five nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of the PTEN gene were selected for our in silico investigation, and five nsSNPs (G129E, C124R, D252G, H61D, and R130G) were found to be deleterious based on combinatorial predictions of different computational tools. Moreover, molecular dynamics (MD) simulation was performed to investigate the conformational variation between native and all the five mutant PTEN proteins having predicted deleterious nsSNPs. The results of MD simulation of all mutant models illustrated variation in structural attributes such as root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and total energy; which depicts the structural stability of PTEN protein. Furthermore, mutant PTEN protein structures also showed a significant variation in the solvent accessible surface area and hydrogen bond frequencies from the native PTEN structure. In conclusion, results of this study have established the deleterious effect of the all the five predicted nsSNPs on the PTEN protein structure. Thus, results of the current study can pave a new platform to sort out nsSNPs that can be undertaken for the confirmation of their phenotype and their correlation with diseased status in case of control studies.
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Affiliation(s)
- Imran Khan
- Department of Biosciences, Integral University, Lucknow, India
| | - Irfan A Ansari
- Department of Biosciences, Integral University, Lucknow, India
| | - Pratichi Singh
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - Febin Prabhu Dass J
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
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20
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Mitchison HM, Valente EM. Motile and non-motile cilia in human pathology: from function to phenotypes. J Pathol 2017; 241:294-309. [PMID: 27859258 DOI: 10.1002/path.4843] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
Ciliopathies are inherited human disorders caused by both motile and non-motile cilia dysfunction that form an important and rapidly expanding disease category. Ciliopathies are complex conditions to diagnose, being multisystem disorders characterized by extensive genetic heterogeneity and clinical variability with high levels of lethality. There is marked phenotypic overlap among distinct ciliopathy syndromes that presents a major challenge for their recognition, diagnosis, and clinical management, in addition to posing an on-going task to develop the most appropriate family counselling. The impact of next-generation sequencing and high-throughput technologies in the last decade has significantly improved our understanding of the biological basis of ciliopathy disorders, enhancing our ability to determine the possible reasons for the extensive overlap in their symptoms and genetic aetiologies. Here, we review the diverse functions of cilia in human health and disease and discuss a growing shift away from the classical clinical definitions of ciliopathy syndromes to a more functional categorization. This approach arises from our improved understanding of this unique organelle, revealed through new genetic and cell biological insights into the discrete functioning of subcompartments of the cilium (basal body, transition zone, intraflagellar transport, motility). Mutations affecting these distinct ciliary protein modules can confer different genetic diseases and new clinical classifications are possible to define, according to the nature and extent of organ involvement. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Hannah M Mitchison
- Genetics and Genomic Medicine Programme, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Enza Maria Valente
- Department of Medicine and Surgery, University of Salerno, Salerno, Italy.,Neurogenetics Unit, IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano, 00143, Rome, Italy
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21
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Gualandi F, Zaraket F, Malagù M, Parmeggiani G, Trabanelli C, Fini S, Dang X, Wei X, Fang M, Bertini M, Ferrari R, Ferlini A. Mutation Load of Multiple Ion Channel Gene Mutations in Brugada Syndrome. Cardiology 2017; 137:256-260. [PMID: 28494446 DOI: 10.1159/000471792] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/14/2017] [Indexed: 11/19/2022]
Abstract
Brugada syndrome is a primary arrhythmic syndrome that accounts for 20% of all sudden cardiac death cases in individuals with a structurally normal heart. Pathogenic variants associated with Brugada syndrome have been identified in over 19 genes, with SCN5A as a pivotal gene accounting for nearly 30% of cases. In contrast to other arrhythmogenic channelopathies (such as long QT syndrome), digenic inheritance has never been reported in Brugada syndrome. Exploring 66 cardiac genes using a new custom next-generation sequencing panel, we identified a double heterozygosity for pathogenic mutations in SCN5A and TRPM4 in a Brugada syndrome patient. The parents were heterozygous for each variation. This novel finding highlights the role of mutation load in Brugada syndrome and strongly suggests the adoption of a gene panel to obtain an accurate genetic diagnosis, which is mandatory for risk stratification, prevention, and therapy.
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Affiliation(s)
- Francesca Gualandi
- Medical Genetics Logistic Unit (UOL), Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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22
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Poretti A, Snow J, Summers AC, Tekes A, Huisman TAGM, Aygun N, Carson KA, Doherty D, Parisi MA, Toro C, Yildirimli D, Vemulapalli M, Mullikin JC, Cullinane AR, Vilboux T, Gahl WA, Gunay-Aygun M. Joubert syndrome: neuroimaging findings in 110 patients in correlation with cognitive function and genetic cause. J Med Genet 2017; 54:521-529. [PMID: 28087721 DOI: 10.1136/jmedgenet-2016-104425] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/09/2016] [Accepted: 12/10/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Joubert syndrome is a clinically and genetically heterogeneous ciliopathy. Neuroimaging findings have not been systematically evaluated in a large cohort of patients with Joubert syndrome in correlation with molecular genetic cause and cognitive function. METHODS Brain MRI of 110 patients with Joubert syndrome was included in this study. A comprehensive evaluation of brain MRI studies for infratentorial and supratentorial morphological abnormalities was performed. Genetic cause was identified by whole-exome sequencing, and cognitive functions were assessed with age-appropriate neurocognitive tests in a subset of patients. RESULTS The cerebellar hemispheres were enlarged in 18% of the patients, mimicking macrocerebellum. The posterior fossa was enlarged in 42% of the patients, resembling Dandy-Walker malformation. Abnormalities of the brainstem, such as protuberance at the ventral contour of the midbrain, were present in 66% of the patients. Abnormalities of the supratentorial brain were present in approximately one-third of the patients, most commonly malrotation of the hippocampi. Mild ventriculomegaly, which typically did not require shunting, was present in 23% of the patients. No correlation between neuroimaging findings and molecular genetic cause was apparent. A novel predictor of outcome was identified; the more severe the degree of vermis hypoplasia, the worse the neurodevelopmental outcome was. CONCLUSIONS The spectrum of neuroimaging findings in Joubert syndrome is wide. Neuroimaging does not predict the genetic cause, but may predict the neurodevelopmental outcome. A high degree of vermis hypoplasia correlates with worse neurodevelopmental outcome. This finding is important for prognostic counselling in Joubert syndrome.
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Affiliation(s)
- Andrea Poretti
- Section of Pediatric Neuroradiology, Division of Pediatric Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Joseph Snow
- Intramural Research Program, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Angela C Summers
- Intramural Research Program, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Aylin Tekes
- Section of Pediatric Neuroradiology, Division of Pediatric Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thierry A G M Huisman
- Section of Pediatric Neuroradiology, Division of Pediatric Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nafi Aygun
- Division of Neuroradiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kathryn A Carson
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.,Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Melissa A Parisi
- Intellectual and Developmental Disabilities Branch, National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Maryland, USA
| | - Deniz Yildirimli
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Meghana Vemulapalli
- NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Jim C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | | | - Andrew R Cullinane
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Department of Anatomy, Howard University College of Medicine, Washington District of Columbia, USA
| | - Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Maryland, USA.,Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Meral Gunay-Aygun
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Lee H, Song J, Jung JH, Ko HW. Primary cilia in energy balance signaling and metabolic disorder. BMB Rep 2016; 48:647-54. [PMID: 26538252 PMCID: PMC4791320 DOI: 10.5483/bmbrep.2015.48.12.229] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 12/16/2022] Open
Abstract
Energy homeostasis in our body system is maintained by balancing the intake and expenditure of energy. Excessive accumulation of fat by disrupting the balance system causes overweight and obesity, which are increasingly becoming global health concerns. Understanding the pathogenesis of obesity focused on studying the genes related to familial types of obesity. Recently, a rare human genetic disorder, ciliopathy, links the role for genes regulating structure and function of a cellular organelle, the primary cilium, to metabolic disorder, obesity and type II diabetes. Primary cilia are microtubule based hair-like membranous structures, lacking motility and functions such as sensing the environmental cues, and transducing extracellular signals within the cells. Interestingly, the subclass of ciliopathies, such as Bardet-Biedle and Alström syndrome, manifest obesity and type II diabetes in human and mouse model systems. Moreover, studies on genetic mouse model system indicate that more ciliary genes affect energy homeostasis through multiple regulatory steps such as central and peripheral actions of leptin and insulin. In this review, we discuss the latest findings in primary cilia and metabolic disorders, and propose the possible interaction between primary cilia and the leptin and insulin signal pathways which might enhance our understanding of the unambiguous link of a cell's antenna to obesity and type II diabetes.
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Affiliation(s)
- Hankyu Lee
- College of Pharmacy, Dongguk University, Goyang 10326, Korea
| | - Jieun Song
- College of Pharmacy, Dongguk University, Goyang 10326, Korea
| | - Joo Hyun Jung
- College of Pharmacy, Dongguk University, Goyang 10326, Korea
| | - Hyuk Wan Ko
- College of Pharmacy, Dongguk University, Goyang 10326, Korea
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24
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Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TMT, Texier Y, van Beersum SEC, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJC, Coene KLM, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJF, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJP, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, Roepman R. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nat Commun 2016; 7:11491. [PMID: 27173435 PMCID: PMC4869170 DOI: 10.1038/ncomms11491] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/01/2016] [Indexed: 01/12/2023] Open
Abstract
Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine. Mutations in proteins that localize to primary cilia cause devastating diseases, yet the primary cilium is a poorly understood organelle. Here the authors use interaction proteomics to identify a network of human ciliary proteins that provides new insights into several biological processes and diseases.
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Affiliation(s)
- Karsten Boldt
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Jeroen van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Qianhao Lu
- Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.,Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Konstantinos Koutroumpas
- Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Evry, 91030 Evry, France
| | - Thanh-Minh T Nguyen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Yves Texier
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.,Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science, 81377 Munich, Germany
| | - Sylvia E C van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Nicola Horn
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Dorus A Mans
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Gerard Dougherty
- Department of General Pediatrics, University Children's Hospital Muenster, 48149 Muenster, Germany
| | - Ideke J C Lamers
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Heleen H Arts
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Matthew J Betts
- Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.,Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Tina Beyer
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Emine Bolat
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholz Association, Otfried-Müller Strasse 23, 72076 Tuebingen, Germany
| | - Khatera Haidari
- Department of Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Lisette Hetterschijt
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Daniela Iaconis
- Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy
| | - Dagan Jenkins
- Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Franziska Klose
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Barbara Knapp
- Cell and Matrix Biology, Inst. of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany
| | - Brooke Latour
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Stef J F Letteboer
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Carlo L Marcelis
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Dragana Mitic
- Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy.,Department of Translational Medicine Federico II University, 80131 Naples, Italy
| | - Machteld M Oud
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Moniek Riemersma
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Susan Rix
- Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Grischa Toedt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Yasmin Wissinger
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Ka Man Wu
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Gordana Apic
- Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
| | - Philip L Beales
- Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Oliver E Blacque
- School of Biomolecular &Biomed Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Hannie Kremer
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Muenster, 48149 Muenster, Germany
| | - Erwin van Wijk
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Uwe Wolfrum
- Cell and Matrix Biology, Inst. of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany
| | - François Kepes
- Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Evry, 91030 Evry, France
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy.,Department of Translational Medicine Federico II University, 80131 Naples, Italy
| | - Rachel H Giles
- Department of Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Marius Ueffing
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Robert B Russell
- Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.,Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
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25
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Yadav SP, Sharma NK, Liu C, Dong L, Li T, Swaroop A. Centrosomal protein CP110 controls maturation of the mother centriole during cilia biogenesis. Development 2016; 143:1491-501. [PMID: 26965371 PMCID: PMC4909859 DOI: 10.1242/dev.130120] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/29/2016] [Indexed: 11/30/2022]
Abstract
Defects in cilia centrosomal genes cause pleiotropic clinical phenotypes, collectively called ciliopathies. Cilia biogenesis is initiated by the interaction of positive and negative regulators. Centriolar coiled coil protein 110 (CP110) caps the distal end of the mother centriole and is known to act as a suppressor to control the timing of ciliogenesis. Here, we demonstrate that CP110 promotes cilia formation in vivo, in contrast to findings in cultured cells. Cp110−/− mice die shortly after birth owing to organogenesis defects as in ciliopathies. Shh signaling is impaired in null embryos and primary cilia are reduced in multiple tissues. We show that CP110 is required for anchoring of basal bodies to the membrane during cilia formation. CP110 loss resulted in an abnormal distribution of core components of subdistal appendages (SDAs) and of recycling endosomes, which may be associated with premature extension of axonemal microtubules. Our data implicate CP110 in SDA assembly and ciliary vesicle docking, two requisite early steps in cilia formation. We suggest that CP110 has unique context-dependent functions, acting as both a suppressor and a promoter of ciliogenesis. Highlighted article: CP110 promotes the assembly of subdistal appendages and ciliary vesicle docking during cilia formation in vivo, thereby facilitating mammalian organogenesis.
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Affiliation(s)
- Sharda Prasad Yadav
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neel Kamal Sharma
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chunqiao Liu
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tiansen Li
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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26
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Kochinke K, Zweier C, Nijhof B, Fenckova M, Cizek P, Honti F, Keerthikumar S, Oortveld M, Kleefstra T, Kramer J, Webber C, Huynen M, Schenck A. Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. Am J Hum Genet 2016; 98:149-64. [PMID: 26748517 DOI: 10.1016/j.ajhg.2015.11.024] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022] Open
Abstract
Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders.
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27
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Zweier C. Mikrozephalie bei psychomotorischen Entwicklungsstörungen und geistiger Behinderung. MED GENET-BERLIN 2015. [DOI: 10.1007/s11825-015-0072-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Zusammenfassung
Eine geistige Behinderung kommt bei ca. 2–3 % der Bevölkerung vor. Sowohl die klinischen Erscheinungsbilder als auch die genetischen Ursachen sind extrem heterogen. Es können sowohl chromosomale als auch monogene Veränderungen ursächlich sein. Eine Mikrozephalie ist ein häufiges Symptom bei psychomotorischen Entwicklungsstörungen und geistiger Behinderung, was auf überlappende Pathomechanismen hindeutet. Etwa 23 % der bekannten, mit geistiger Behinderung assoziierten Gene sind auch mit Mikrozephalie assoziiert. Weitere häufige Komorbiditäten sind Krampfanfälle, Kleinwuchs oder Fehlbildungen. In einer Kohorte von über 700 Patienten mit psychomotorischer Entwicklungsstörung, die in der genetischen Sprechstunde des Humangenetischen Instituts in Erlangen gesehen wurden, waren 22,5 % auch mikrozephal. Dabei korrelierte die Schwere der Mikrozephalie mit der Schwere der kognitiven Einschränkung und dem Auftreten von Krampfanfällen.
In dieser Übersichtsarbeit werden genetische Ursachen für psychomotorische Entwicklungsstörungen mit Mikrozephalie sowie die Häufigkeit einer Mikrozephalie in einer Kohorte von Patienten mit ungeklärter Entwicklungsstörung und ihre Bedeutung bei der Diagnosefindung bei geistiger Behinderung diskutiert.
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Affiliation(s)
- Christiane Zweier
- Aff1 grid.5330.5 0000000121073311 Humangenetisches Institut Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg Schwabachanlage 10 91054 Erlangen Deutschland
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28
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Schock EN, Chang CF, Youngworth IA, Davey MG, Delany ME, Brugmann SA. Utilizing the chicken as an animal model for human craniofacial ciliopathies. Dev Biol 2015; 415:326-337. [PMID: 26597494 DOI: 10.1016/j.ydbio.2015.10.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/13/2015] [Accepted: 10/21/2015] [Indexed: 11/30/2022]
Abstract
The chicken has been a particularly useful model for the study of craniofacial development and disease for over a century due to their relatively large size, accessibility, and amenability for classical bead implantation and transplant experiments. Several naturally occurring mutant lines with craniofacial anomalies also exist and have been heavily utilized by developmental biologist for several decades. Two of the most well known lines, talpid(2) (ta(2)) and talpid(3) (ta(3)), represent the first spontaneous mutants to have the causative genes identified. Despite having distinct genetic causes, both mutants have recently been identified as ciliopathic. Excitingly, both of these mutants have been classified as models for human craniofacial ciliopathies: Oral-facial-digital syndrome (ta(2)) and Joubert syndrome (ta(3)). Herein, we review and compare these two models of craniofacial disease and highlight what they have revealed about the molecular and cellular etiology of ciliopathies. Furthermore, we outline how applying classical avian experiments and new technological advances (transgenics and genome editing) with naturally occurring avian mutants can add a tremendous amount to what we currently know about craniofacial ciliopathies.
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Affiliation(s)
- Elizabeth N Schock
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ching-Fang Chang
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ingrid A Youngworth
- College of Agricultural and Environmental Sciences, Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Megan G Davey
- Division of Developmental Biology, The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, UK
| | - Mary E Delany
- College of Agricultural and Environmental Sciences, Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Samantha A Brugmann
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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29
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Gerhardt C, Lier JM, Burmühl S, Struchtrup A, Deutschmann K, Vetter M, Leu T, Reeg S, Grune T, Rüther U. The transition zone protein Rpgrip1l regulates proteasomal activity at the primary cilium. J Cell Biol 2015; 210:115-33. [PMID: 26150391 PMCID: PMC4494006 DOI: 10.1083/jcb.201408060] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Rpgrip1l regulates proteasomal activity at the basal body via Psmd2 and thereby controls ciliary signaling. Mutations in RPGRIP1L result in severe human diseases called ciliopathies. To unravel the molecular function of RPGRIP1L, we analyzed Rpgrip1l−/− mouse embryos, which display a ciliopathy phenotype and die, at the latest, around birth. In these embryos, cilia-mediated signaling was severely disturbed. Defects in Shh signaling suggested that the Rpgrip1l deficiency causes an impairment of protein degradation and protein processing. Indeed, we detected a cilia-dependent decreased proteasomal activity in the absence of Rpgrip1l. We found different proteasomal components localized to cilia and identified Psmd2, a component of the regulatory proteasomal 19S subunit, as an interaction partner for Rpgrip1l. Quantifications of proteasomal substrates demonstrated that Rpgrip1l regulates proteasomal activity specifically at the basal body. Our study suggests that Rpgrip1l controls ciliary signaling by regulating the activity of the ciliary proteasome via Psmd2.
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Affiliation(s)
- Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Johanna Maria Lier
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Stephan Burmühl
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Andreas Struchtrup
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Kathleen Deutschmann
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Maik Vetter
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Tristan Leu
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Sandra Reeg
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller University Jena, 07743 Jena, Germany
| | - Tilman Grune
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller University Jena, 07743 Jena, Germany
| | - Ulrich Rüther
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
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30
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Ramsbottom S, Miles C, Sayer J. Murine Cep290 phenotypes are modified by genetic backgrounds and provide an impetus for investigating disease modifier alleles. F1000Res 2015; 4:590. [PMID: 26594343 PMCID: PMC4648220 DOI: 10.12688/f1000research.6959.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/19/2015] [Indexed: 11/20/2022] Open
Abstract
The study of primary cilia is of broad interest both in terms of disease pathogenesis and the fundamental biological role of these structures. Murine models of ciliopathies provide valuable tools for the study of these diseases. However, it is important to consider the precise phenotype of murine models and how dependant it is upon genetic background. Here we compare and contrast murine models of
Cep290, a frequent genetic cause of Joubert syndrome in order to refine our concept of genotype-phenotype correlations.
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Affiliation(s)
- Simon Ramsbottom
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Colin Miles
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - John Sayer
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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31
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Novas R, Cardenas-Rodriguez M, Irigoín F, Badano JL. Bardet-Biedl syndrome: Is it only cilia dysfunction? FEBS Lett 2015; 589:3479-91. [PMID: 26231314 DOI: 10.1016/j.febslet.2015.07.031] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 01/12/2023]
Abstract
Bardet-Biedl syndrome (BBS) is a genetically heterogeneous, pleiotropic disorder, characterized by both congenital and late onset defects. From the analysis of the mutational burden in patients to the functional characterization of the BBS proteins, this syndrome has become a model for both understanding oligogenic patterns of inheritance and the biology of a particular cellular organelle: the primary cilium. Here we briefly review the genetics of BBS to then focus on the function of the BBS proteins, not only in the context of the cilium but also highlighting potential extra-ciliary roles that could be relevant to the etiology of the disorder. Finally, we provide an overview of how the study of this rare syndrome has contributed to the understanding of cilia biology and how this knowledge has informed on the cellular basis of different clinical manifestations that characterize BBS and the ciliopathies.
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Affiliation(s)
- Rossina Novas
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | | | - Florencia Irigoín
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay; Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Montevideo, Gral. Flores 2125, Montevideo CP11800, Uruguay
| | - Jose L Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay.
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Laclef C, Anselme I, Besse L, Catala M, Palmyre A, Baas D, Paschaki M, Pedraza M, Métin C, Durand B, Schneider-Maunoury S. The role of primary cilia in corpus callosum formation is mediated by production of the Gli3 repressor. Hum Mol Genet 2015; 24:4997-5014. [PMID: 26071364 DOI: 10.1093/hmg/ddv221] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/09/2015] [Indexed: 12/13/2022] Open
Abstract
Agenesis of the corpus callosum (AgCC) is a frequent brain disorder found in over 80 human congenital syndromes including ciliopathies. Here, we report a severe AgCC in Ftm/Rpgrip1l knockout mouse, which provides a valuable model for Meckel-Grüber syndrome. Rpgrip1l encodes a protein of the ciliary transition zone, which is essential for ciliogenesis in several cell types in mouse including neuroepithelial cells in the developing forebrain. We show that AgCC in Rpgrip1l(-/-) mouse is associated with a disturbed location of guidepost cells in the dorsomedial telencephalon. This mislocalization results from early patterning defects and abnormal cortico-septal boundary (CSB) formation in the medial telencephalon. We demonstrate that all these defects primarily result from altered GLI3 processing. Indeed, AgCC, together with patterning defects and mispositioning of guidepost cells, is rescued by overexpressing in Rpgrip1l(-/-) embryos, the short repressor form of the GLI3 transcription factor (GLI3R), provided by the Gli3(Δ699) allele. Furthermore, Gli3(Δ699) also rescues AgCC in Rfx3(-/-) embryos deficient for the ciliogenic RFX3 transcription factor that regulates the expression of several ciliary genes. These data demonstrate that GLI3 processing is a major outcome of primary cilia function in dorsal telencephalon morphogenesis. Rescuing CC formation in two independent ciliary mutants by GLI3(Δ699) highlights the crucial role of primary cilia in maintaining the proper level of GLI3R required for morphogenesis of the CC.
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Affiliation(s)
- Christine Laclef
- Sorbonne Universités, UPMC Univ Paris 06, UMR7622, CNRS, Institut de Biologie Paris Seine (IBPS)-Developmental Biology Laboratory, UMR7622, INSERM, ERL1156 and
| | - Isabelle Anselme
- Sorbonne Universités, UPMC Univ Paris 06, UMR7622, CNRS, Institut de Biologie Paris Seine (IBPS)-Developmental Biology Laboratory, UMR7622, INSERM, ERL1156 and
| | - Laurianne Besse
- Sorbonne Universités, UPMC Univ Paris 06, UMR7622, CNRS, Institut de Biologie Paris Seine (IBPS)-Developmental Biology Laboratory, UMR7622, INSERM, ERL1156 and
| | - Martin Catala
- Sorbonne Universités, UPMC Univ Paris 06, UMR7622, CNRS, Institut de Biologie Paris Seine (IBPS)-Developmental Biology Laboratory, UMR7622, INSERM, ERL1156 and Fédération de Neurologie, Groupe hospitalier Pitié-Salpêtrière-APHP, F-75013 Paris, France
| | - Aurélien Palmyre
- Sorbonne Universités, UPMC Univ Paris 06, UMR7622, CNRS, Institut de Biologie Paris Seine (IBPS)-Developmental Biology Laboratory, UMR7622, INSERM, ERL1156 and
| | - Dominique Baas
- Université Claude Bernard Lyon 1 and CNRS, CGPhiMC-UMR5534, F-69622 Villeurbanne, France and
| | - Marie Paschaki
- Université Claude Bernard Lyon 1 and CNRS, CGPhiMC-UMR5534, F-69622 Villeurbanne, France and
| | - Maria Pedraza
- Institut du Fer à Moulin, INSERM S839, F-75005 Paris, France, Sorbonne Université, UPMC Univ Paris 06, S839, Paris, France
| | - Christine Métin
- Institut du Fer à Moulin, INSERM S839, F-75005 Paris, France, Sorbonne Université, UPMC Univ Paris 06, S839, Paris, France
| | - Bénédicte Durand
- Université Claude Bernard Lyon 1 and CNRS, CGPhiMC-UMR5534, F-69622 Villeurbanne, France and
| | - Sylvie Schneider-Maunoury
- Sorbonne Universités, UPMC Univ Paris 06, UMR7622, CNRS, Institut de Biologie Paris Seine (IBPS)-Developmental Biology Laboratory, UMR7622, INSERM, ERL1156 and
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Identification of G Protein-Coupled Receptors (GPCRs) in Primary Cilia and Their Possible Involvement in Body Weight Control. PLoS One 2015; 10:e0128422. [PMID: 26053317 PMCID: PMC4459993 DOI: 10.1371/journal.pone.0128422] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 11/30/2022] Open
Abstract
Primary cilia are sensory organelles that harbor various receptors such as G protein-coupled receptors (GPCRs). We analyzed subcellular localization of 138 non-odorant GPCRs. We transfected GPCR expression vectors into NIH3T3 cells, induced ciliogenesis by serum starvation, and observed subcellular localization of GPCRs by immunofluorescent staining. We found that several GPCRs whose ligands are involved in feeding behavior, including prolactin-releasing hormone receptor (PRLHR), neuropeptide FF receptor 1 (NPFFR1), and neuromedin U receptor 1 (NMUR1), localized to the primary cilia. In addition, we found that a short form of dopamine receptor D2 (DRD2S) is efficiently transported to the primary cilia, while a long form of dopamine receptor D2 (DRD2L) is rarely transported to the primary cilia. Using an anti-Prlhr antibody, we found that Prlhr localized to the cilia on the surface of the third ventricle in the vicinity of the hypothalamic periventricular nucleus. We generated the Npy2r-Cre transgenic mouse line in which Cre-recombinase is expressed under the control of the promoter of Npy2r encoding a ciliary GPCR. By mating Npy2r-Cre mice with Ift80 flox mice, we generated Ift80 conditional knockout (CKO) mice in which Npy2r-positive cilia were diminished in number. We found that Ift80 CKO mice exhibited a body weight increase. Our results suggest that Npy2r-positive cilia are important for body weight control.
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Magne F, Serpa R, Van Vliet G, Samuels ME, Deladoëy J. Somatic mutations are not observed by exome sequencing of lymphocyte DNA from monozygotic twins discordant for congenital hypothyroidism due to thyroid dysgenesis. Horm Res Paediatr 2015; 83:79-85. [PMID: 25277881 PMCID: PMC5050031 DOI: 10.1159/000365393] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/20/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Congenital primary hypothyroidism (CH) is a rare pediatric disorder estimated to occur in about 1:2,500 live births. Approximately half of these cases entail ectopic thyroid tissue, which is believed to result from a migration defect during embryogenesis. Approximately 3% of CH cases are explained by mutation(s) in known genes, most of which are transcription factors implicated in the embryology of the thyroid gland. Surprisingly, monozygotic (MZ) twins are usually discordant for CH due to thyroid dysgenesis, suggesting that most cases are not caused by transmitted genetic variation. One possible explanation is somatic mutation in genes involved in thyroid migration occurring after zygotic twinning. Such mutations should be observed only in the affected twin. METHODS To test the hypothesis of somatic mutation, we performed whole exome sequencing of DNA from three pairs of MZ twins discordant for CH with ectopic glands. RESULTS We found no somatic mutations exclusive to any of the three affected twins or in any of the unaffected twins. CONCLUSION Either somatic mutations are not significant for the etiology of CH or else such mutations lie outside regions of the genome accessible by exome sequencing technology.
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Affiliation(s)
- Fabien Magne
- Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, University of Montreal, Montreal, Que., Canada,Department of Biomedical Sciences, University of Montreal, Montreal, Que., Canada
| | - Roman Serpa
- Department of Biochemistry, University of Montreal, Montreal, Que., Canada
| | - Guy Van Vliet
- Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, University of Montreal, Montreal, Que., Canada
| | - Mark E. Samuels
- Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, University of Montreal, Montreal, Que., Canada,Department of Medicine, University of Montreal, Montreal, Que., Canada
| | - Johnny Deladoëy
- Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, University of Montreal, Montreal, Que., Canada,Department of Biomedical Sciences, University of Montreal, Montreal, Que., Canada,Department of Biochemistry, University of Montreal, Montreal, Que., Canada
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Abstract
Cilia proteins have long been characterized for their role in cilia formation and function, and their implications in ciliopathies. However, several cellular defects induced by cilia proteins deregulation suggest that they could have non-ciliary roles. Indeed, several non-ciliary functions have been recently characterized for cilia proteins including roles in intra-cellular and in vesicular transport, in spindle orientation or in the maintenance of genomic stability. These observations thus raise the crucial question of the contribution of non-ciliary functions of cilia proteins to the pathological manifestations associated with ciliopathies such as polycystic kidney disease.
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Affiliation(s)
- Nicolas Taulet
- CNRS-CRBM (centre de recherche en biochimie macromoléculaire), équipe centrosome, cil et pathologies, université de Montpellier, 1919, route de Mende, 34293 Montpellier, France
| | - Bénédicte Delaval
- CNRS-CRBM (centre de recherche en biochimie macromoléculaire), équipe centrosome, cil et pathologies, université de Montpellier, 1919, route de Mende, 34293 Montpellier, France
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A preliminary study of the relationship between breast cancer metastasis and loss of heterozygosity by using exome sequencing. Sci Rep 2014; 4:5460. [PMID: 24964733 PMCID: PMC5381542 DOI: 10.1038/srep05460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 06/09/2014] [Indexed: 11/16/2022] Open
Abstract
We explored the feasibility of studying loss of heterozygosity (LOH) by using exome sequencing and compared the differences in genetic LOH between primary breast tumors and metastatic lesions. Exome sequencing was conducted to investigate the genetic LOH in the peripheral blood, a primary tumor, and a metastatic lesion from the same patient. LOH was observed in 30 and 48 chromosomal loci of the primary tumor and metastatic lesion, respectively. The incidence of LOH was the highest on chromosome 19, followed by chromosomes 14, 3, and 11 in the metastatic lesion. Among these ‘hot' regions, LOH was observed for multiple genes of the CECAM, MMP and ZNF families. Therefore, the use of exome sequencing for studying LOH is feasible. More members of gene families appeared with LOH in ‘hot' regions, suggesting that these gene families had synergistic effects in tumorigenesis.
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Ciliopathy-associated gene Cc2d2a promotes assembly of subdistal appendages on the mother centriole during cilia biogenesis. Nat Commun 2014; 5:4207. [PMID: 24947469 PMCID: PMC4096663 DOI: 10.1038/ncomms5207] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/23/2014] [Indexed: 01/01/2023] Open
Abstract
The primary cilium originates from the mother centriole and participates in critical functions during organogenesis. Defects in cilia biogenesis or function lead to pleiotropic phenotypes. Mutations in centrosome-cilia gene CC2D2A result in Meckel and Joubert syndromes. Here we generate a Cc2d2a-/- mouse that recapitulates features of Meckel syndrome including embryonic lethality and multi-organ defects. Cilia are absent in Cc2d2a-/- embryonic node and other somatic tissues; disruption of cilia-dependent Shh signaling appears to underlie exencephaly in mutant embryos. The Cc2d2a-/- mouse embryonic fibroblasts (MEFs) lack cilia though mother centriole and pericentriolar proteins are detected. Odf2, associated with subdistal appendages, is absent and ninein is reduced in mutant MEFs. In Cc2d2a-/- MEFs, subdistal appendages are lacking or abnormal by transmission-EM. Consistent with this, CC2D2A localizes to subdistal appendages by immuno-EM in wild type cells. We conclude that CC2D2A is essential for the assembly of subdistal appendages, which anchor cytoplasmic microtubules and prime the mother centriole for axoneme biogenesis.
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The NEIGHBOR consortium primary open-angle glaucoma genome-wide association study: rationale, study design, and clinical variables. J Glaucoma 2014; 22:517-25. [PMID: 22828004 DOI: 10.1097/ijg.0b013e31824d4fd8] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Primary open-angle glaucoma (POAG) is a common disease with complex inheritance. The identification of genes predisposing to POAG is an important step toward the development of novel gene-based methods of diagnosis and treatment. Genome-wide association studies (GWAS) have successfully identified genes contributing to complex traits such as POAG however, such studies frequently require very large sample sizes, and thus, collaborations and consortia have been of critical importance for the GWAS approach. In this report we describe the formation of the NEIGHBOR consortium, the harmonized case control definitions used for a POAG GWAS, the clinical features of the cases and controls, and the rationale for the GWAS study design.
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Drosophila models of early onset cognitive disorders and their clinical applications. Neurosci Biobehav Rev 2014; 46 Pt 2:326-42. [PMID: 24661984 DOI: 10.1016/j.neubiorev.2014.01.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 12/28/2022]
Abstract
The number of genes known to cause human monogenic diseases is increasing rapidly. For the extremely large, genetically and phenotypically heterogeneous group of intellectual disability (ID) disorders, more than 600 causative genes have been identified to date. However, knowledge about the molecular mechanisms and networks disrupted by these genetic aberrations is lagging behind. The fruit fly Drosophila has emerged as a powerful model organism to close this knowledge gap. This review summarizes recent achievements that have been made in this model and envisions its future contribution to our understanding of ID genetics and neuropathology. The available resources and efficiency of Drosophila place it in a position to tackle the main challenges in the field: mapping functional modules of ID genes to provide conceptually novel insights into the genetic control of cognition, tailored functional studies to improve 'next-generation' diagnostics, and identification of reversible ID phenotypes and medication. Drosophila's behavioral repertoire and powerful genetics also open up perspectives for modeling genetically complex forms of ID and neuropsychiatric disorders, which overlap in their genetic etiologies. In conclusion, Drosophila provides many opportunities to advance future medical genomics of early onset cognitive disorders.
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Abstract
Primary cilia are generally solitary organelles that emanate from the surface of almost all vertebrate cell types. Until recently, details regarding the function of these structures were lacking; however, extensive evidence now suggests that primary cilia have critical roles in sensing the extracellular environment, and in coordinating developmental and homeostatic signalling pathways. Furthermore, disruption of these functions seems to underlie a diverse spectrum of disorders, known as primary ciliopathies. These disorders are characterized by wide-ranging clinical and genetic heterogeneity, but with substantial overlap among distinct conditions. Indeed, ciliopathies are associated with a large variety of manifestations that often include distinctive neurological findings. Herein, we review neurological features associated with primary ciliopathies, highlight genotype-phenotype correlations, and discuss potential mechanisms underlying these findings.
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Riera C, Lois S, de la Cruz X. Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Casandra Riera
- Laboratory of Translational Bioinformatics in Neuroscience; VHIR; Barcelona Spain
| | - Sergio Lois
- Laboratory of Translational Bioinformatics in Neuroscience; VHIR; Barcelona Spain
| | - Xavier de la Cruz
- Laboratory of Translational Bioinformatics in Neuroscience; VHIR; Barcelona Spain
- Institució Catalana per la Recerca i Estudis Avançats (ICREA); Barcelona Spain
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Abstract
Genomic technologies are reaching the point of being able to detect genetic variation in patients at high accuracy and reduced cost, offering the promise of fundamentally altering medicine. Still, although scientists and policy advisers grapple with how to interpret and how to handle the onslaught and ambiguity of genome-wide data, established and well-validated molecular technologies continue to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities. Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics. In parallel, we outline implementation challenges that will be necessary to address to ensure the future of genetic medicine.
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Abstract
Joubert syndrome is a congenital cerebellar ataxia with autosomal recessive or X-linked inheritance, the diagnostic hallmark of which is a unique cerebellar and brainstem malformation recognisable on brain imaging-the so-called molar tooth sign. Neurological signs are present from the neonatal period and include hypotonia progressing to ataxia, global developmental delay, ocular motor apraxia, and breathing dysregulation. These signs are variably associated with multiorgan involvement, mainly of the retina, kidneys, skeleton, and liver. 21 causative genes have been identified so far, all of which encode for proteins of the primary cilium or its apparatus. The primary cilium is a subcellular organelle that has key roles in development and in many cellular functions, making Joubert syndrome part of the expanding family of ciliopathies. Notable clinical and genetic overlap exists between distinct ciliopathies, which can co-occur even within families. Such variability is probably explained by an oligogenic model of inheritance, in which the interplay of mutations, rare variants, and polymorphisms at distinct loci modulate the expressivity of the ciliary phenotype.
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Baxter RM, Vilain E. Translational genetics for diagnosis of human disorders of sex development. Annu Rev Genomics Hum Genet 2013; 14:371-92. [PMID: 23875799 DOI: 10.1146/annurev-genom-091212-153417] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Disorders of sex development (DSDs) are congenital conditions with discrepancies between the chromosomal, gonadal, and phenotypic sex of the individual. Such disorders have historically been difficult to diagnose and cause great stress to patients and their families. Genetic analysis of human samples has been instrumental in elucidating the molecules and pathways involved in the development of the bipotential gonad into a functioning testis or ovary. However, many DSD patients still do not receive a genetic diagnosis. New genetic and genomic technologies are expanding our knowledge of the underlying mechanism of DSDs and opening new avenues for clinical diagnosis. We review the genetic technologies that have elucidated the genes that are well established in sex determination in humans, discuss findings from more recent genomic technologies, and propose a new paradigm for clinical diagnosis of DSDs.
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Yengkopiong JP, Lako JDW. Genetic background of nonmutant Piebald-Virol-Glaxo rats does not influence nephronophthisis phenotypes. Int J Nephrol Renovasc Dis 2013; 6:39-46. [PMID: 23549608 PMCID: PMC3579405 DOI: 10.2147/ijnrd.s39295] [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: 11/23/2022] Open
Abstract
BACKGROUND Nephronophthisis (NPHP), which affects multiple organs, is a hereditary cystic kidney disease (CKD), characterized by interstitial fibrosis and numerous fluid-filled cysts in the kidneys. It is caused by mutations in NPHP genes, which encode for ciliary proteins known as nephrocystins. The disorder affects many people across the world and leads to end-stage renal disease. The aim of this study was to determine if the genetic background of the nonmutant female Piebald-Virol-Glaxo (PVG/Seac(-/-)) rat influences phenotypic inheritance of NPHP from mutant male Lewis polycystic kidney rats. METHODS Mating experiments were performed between mutant Lewis polycystic kidney male rats with CKD and nonmutant PVG and Wistar Kyoto female rats without cystic kidney disease to raise second filial and backcross 1 progeny, respectively. Rats that developed cystic kidneys were identified. Systolic blood pressure was determined in each rat at 12 weeks of age using the tail and cuff method. After euthanasia, blood samples were collected and chemistry was determined. Histological examination of the kidneys, pancreas, and liver of rats with and without cystic kidney disease was performed. RESULTS It was established that the genetic background of nonmutant female PVG rats did not influence the phenotypic inheritance of the CKD from mutant male Lewis polycystic kidney rats. The disease arose as a result of a recessive mutation in a single gene (second filial generation, CKD = 13, non-CKD = 39, χ (2) = 0.00, P ≥ 0.97; backcross 1 generation, CKD = 67, non-CKD = 72, χ (2) = 0.18, P > 0.05) and inherited as NPHP. The rats with CKD developed larger fluid-filled cystic kidneys, higher systolic blood pressure, and anemia, but there were no extrarenal cysts and disease did not lead to early pup mortality. CONCLUSION The genetic background of the nonmutant PVG rats does not influence the genetic and phenotypic inheritance of CKD from mutant Lewis polycystic kidney rats. A single recessive mutation incapacitated the gene, which relaxed its functional constraints, and led to formation of multiple cysts in the kidneys of the homozygous mutant rats.
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Affiliation(s)
- Jada Pasquale Yengkopiong
- John Garang Memorial University of Science and Technology, Faculty of Science and Technology, Bor, Jonglei State, Republic of South Sudan
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Furlong LI. Human diseases through the lens of network biology. Trends Genet 2013; 29:150-9. [DOI: 10.1016/j.tig.2012.11.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/24/2012] [Accepted: 11/09/2012] [Indexed: 12/13/2022]
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Navarrete K, Pedroso I, De Jong S, Stefansson H, Steinberg S, Stefansson K, Ophoff RA, Schalkwyk LC, Collier DA. TCF4 (e2-2; ITF2): a schizophrenia-associated gene with pleiotropic effects on human disease. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:1-16. [PMID: 23129290 DOI: 10.1002/ajmg.b.32109] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/27/2012] [Indexed: 12/22/2022]
Abstract
Common SNPs in the transcription factor 4 (TCF4; ITF2, E2-2, SEF-2) gene, which encodes a basic Helix-Loop-Helix (bHLH) transcription factor, are associated with schizophrenia, conferring a small increase in risk. Other common SNPs in the gene are associated with the common eye disorder Fuch's corneal dystrophy, while rare, mostly de novo inactivating mutations cause Pitt-Hopkins syndrome. In this review, we present a systematic bioinformatics and literature review of the genomics, biological function and interactome of TCF4 in the context of schizophrenia. The TCF4 gene is present in all vertebrates, and although protein length varies, there is high conservation of primary sequence, including the DNA binding domain. Humans have a unique leucine-rich nuclear export signal. There are two main isoforms (A and B), as well as complex splicing generating many possible N-terminal amino acid sequences. TCF4 is highly expressed in the brain, where plays a role in neurodevelopment, interacting with class II bHLH transcription factors Math1, HASH1, and neuroD2. The Ca(2+) sensor protein calmodulin interacts with the DNA binding domain of TCF4, inhibiting transcriptional activation. It is also the target of microRNAs, including mir137, which is implicated in schizophrenia. The schizophrenia-associated SNPs are in linkage disequilibrium with common variants within putative DNA regulatory elements, suggesting that regulation of expression may underlie association with schizophrenia. Combined gene co-expression analyses and curated protein-protein interaction data provide a network involving TCF4 and other putative schizophrenia susceptibility genes. These findings suggest new opportunities for understanding the molecular basis of schizophrenia and other mental disorders.
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Affiliation(s)
- Katherinne Navarrete
- Social, Genetic and Developmental Psychiatry Centre, King's College London, Institute of Psychiatry, London, UK
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Fernández RM, Bleda M, Núñez-Torres R, Medina I, Luzón-Toro B, García-Alonso L, Torroglosa A, Marbà M, Enguix-Riego MV, Montaner D, Antiñolo G, Dopazo J, Borrego S. Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. Orphanet J Rare Dis 2012; 7:103. [PMID: 23270508 PMCID: PMC3575329 DOI: 10.1186/1750-1172-7-103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 12/19/2012] [Indexed: 12/23/2022] Open
Abstract
Finding gene associations in rare diseases is frequently hampered by the reduced numbers of patients accessible. Conventional gene-based association tests rely on the availability of large cohorts, which constitutes a serious limitation for its application in this scenario. To overcome this problem we have used here a combined strategy in which a pathway-based analysis (PBA) has been initially conducted to prioritize candidate genes in a Spanish cohort of 53 trios of short-segment Hirschsprung’s disease. Candidate genes have been further validated in an independent population of 106 trios. The study revealed a strong association of 11 gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other HSCR-related processes. Among the preselected candidates, a total of 4 loci, RASGEF1A, IQGAP2, DLC1 and CHRNA7, related to signal transduction and migration processes, were found to be significantly associated to HSCR. Network analysis also confirms their involvement in the network of already known disease genes. This approach, based on the study of functionally-related gene sets, requires of lower sample sizes and opens new opportunities for the study of rare diseases.
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Affiliation(s)
- Raquel Ma Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
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A New Insight into Structural and Functional Impact of Single-Nucleotide Polymorphisms in PTEN Gene. Cell Biochem Biophys 2012; 66:249-63. [DOI: 10.1007/s12013-012-9472-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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