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Wang L, Bu T, Wu X, Li L, Sun F, Cheng CY. Motor proteins, spermatogenesis and testis function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:381-445. [PMID: 38960481 DOI: 10.1016/bs.apcsb.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The role of motor proteins in supporting intracellular transports of vesicles and organelles in mammalian cells has been known for decades. On the other hand, the function of motor proteins that support spermatogenesis is also well established since the deletion of motor protein genes leads to subfertility and/or infertility. Furthermore, mutations and genetic variations of motor protein genes affect fertility in men, but also a wide range of developmental defects in humans including multiple organs besides the testis. In this review, we seek to provide a summary of microtubule and actin-dependent motor proteins based on earlier and recent findings in the field. Since these two cytoskeletons are polarized structures, different motor proteins are being used to transport cargoes to different ends of these cytoskeletons. However, their involvement in germ cell transport across the blood-testis barrier (BTB) and the epithelium of the seminiferous tubules remains relatively unknown. It is based on recent findings in the field, we have provided a hypothetical model by which motor proteins are being used to support germ cell transport across the BTB and the seminiferous epithelium during the epithelial cycle of spermatogenesis. In our discussion, we have highlighted the areas of research that deserve attention to bridge the gap of research in relating the function of motor proteins to spermatogenesis.
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Affiliation(s)
- Lingling Wang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Tiao Bu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Xiaolong Wu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Linxi Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Fei Sun
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - C Yan Cheng
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China.
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2
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Gupta M, Pazour GJ. Intraflagellar transport: A critical player in photoreceptor development and the pathogenesis of retinal degenerative diseases. Cytoskeleton (Hoboken) 2023:10.1002/cm.21823. [PMID: 38140908 PMCID: PMC11193844 DOI: 10.1002/cm.21823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
In vertebrate vision, photons are detected by highly specialized sensory cilia called outer segments. Photoreceptor outer segments form by remodeling the membrane of a primary cilium into a stack of flattened disks. Intraflagellar transport (IFT) is critical to the formation of most types of eukaryotic cilia including the outer segments. This review covers the state of knowledge of the role of IFT in the formation and maintenance of outer segments and the human diseases that result from mutations in genes encoding the IFT complex and associated motors.
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Affiliation(s)
- Mohona Gupta
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Suite 213 Biotech II, 373 Plantation Street, Worcester MA USA 01605
- Morningside Graduate School of Biological Sciences, University of Massachusetts Chan Medical School, 55 Lake Avenue North, Worcester MA USA 01655
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Suite 213 Biotech II, 373 Plantation Street, Worcester MA USA 01605
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3
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Maksiutenko EM, Barbitoff YA, Nasykhova YA, Pachuliia OV, Lazareva TE, Bespalova ON, Glotov AS. The Landscape of Point Mutations in Human Protein Coding Genes Leading to Pregnancy Loss. Int J Mol Sci 2023; 24:17572. [PMID: 38139401 PMCID: PMC10743817 DOI: 10.3390/ijms242417572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Pregnancy loss is the most frequent complication of a pregnancy which is devastating for affected families and poses a significant challenge for the health care system. Genetic factors are known to play an important role in the etiology of pregnancy loss; however, despite advances in diagnostics, the causes remain unexplained in more than 30% of cases. In this review, we aggregated the results of the decade-long studies into the genetic risk factors of pregnancy loss (including miscarriage, termination for fetal abnormality, and recurrent pregnancy loss) in euploid pregnancies, focusing on the spectrum of point mutations associated with these conditions. We reviewed the evolution of molecular genetics methods used for the genetic research into causes of pregnancy loss, and collected information about 270 individual genetic variants in 196 unique genes reported as genetic cause of pregnancy loss. Among these, variants in 18 genes have been reported by multiple studies, and two or more variants were reported as causing pregnancy loss for 57 genes. Further analysis of the properties of all known pregnancy loss genes showed that they correspond to broadly expressed, highly evolutionary conserved genes involved in crucial cell differentiation and developmental processes and related signaling pathways. Given the features of known genes, we made an effort to construct a list of candidate genes, variants in which may be expected to contribute to pregnancy loss. We believe that our results may be useful for prediction of pregnancy loss risk in couples, as well as for further investigation and revealing genetic etiology of pregnancy loss.
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Affiliation(s)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
| | | | | | | | | | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
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4
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Atique Tacla M, de Mello Copelli M, Pairet E, Monlleó IL, Ribeiro EM, Lustosa Mendes E, Helaers R, Vieira TP, Vikkula M, Gil-da-Silva-Lopes VL. Molecular investigation in individuals with orofacial clefts and microphthalmia-anophthalmia-coloboma spectrum. Eur J Hum Genet 2023:10.1038/s41431-023-01488-5. [PMID: 37932364 DOI: 10.1038/s41431-023-01488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/29/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
This study describes genomic findings among individuals with both orofacial clefts (OC) and microphthalmia/anophthalmia/coloboma (MAC) recorded in the Brazilian Database on Craniofacial Anomalies (BDCA). Chromosomal microarray analysis (CMA) and Whole Exome Sequencing (WES) were performed in 17 individuals with OC-MAC. Clinical interpretation of molecular findings was based on data available at the BDCA and on re-examination. No copy number variants (CNVs) classified as likely pathogenic or pathogenic were detected by CMA. WES allowed a conclusive diagnosis in six individuals (35.29%), two of them with variants in the CHD7 gene, and the others with variants in the TFAP2A, POMT1, PTPN11, and TP63 genes with the following syndromes: CHARGE, CHD7-spectrum, Branchiooculofacial, POMT1-spectrum, LEOPARD, and ADULT. Variants of uncertain significance (VUS) possibly associated to the phenotypes were found in six other individuals. Among the individuals with VUSes, three individuals presented variants in genes associated to defects of cilia structure and/or function, including DYNC2H1, KIAA0586, WDR34, INTU, RPGRIP1L, KIF7, and LMNA. These results show that WES was the most effective molecular approach for OC-MAC in this cohort. This study also reinforces the genetic heterogeneity of OC-MAC, and the importance of genes related to ciliopathies in this phenotype.
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Affiliation(s)
- Milena Atique Tacla
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Matheus de Mello Copelli
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Eleonore Pairet
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Isabella Lopes Monlleó
- Clinical Genetics Service, University Hospital, Medical Genetics Sector, Faculty of Medicine, Federal University of Alagoas - UFAL, Maceió, AL, Brazil
| | | | | | - Raphaël Helaers
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Tarsis Paiva Vieira
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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5
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Gopalakrishnan J, Feistel K, Friedrich BM, Grapin‐Botton A, Jurisch‐Yaksi N, Mass E, Mick DU, Müller R, May‐Simera H, Schermer B, Schmidts M, Walentek P, Wachten D. Emerging principles of primary cilia dynamics in controlling tissue organization and function. EMBO J 2023; 42:e113891. [PMID: 37743763 PMCID: PMC10620770 DOI: 10.15252/embj.2023113891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/07/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Primary cilia project from the surface of most vertebrate cells and are key in sensing extracellular signals and locally transducing this information into a cellular response. Recent findings show that primary cilia are not merely static organelles with a distinct lipid and protein composition. Instead, the function of primary cilia relies on the dynamic composition of molecules within the cilium, the context-dependent sensing and processing of extracellular stimuli, and cycles of assembly and disassembly in a cell- and tissue-specific manner. Thereby, primary cilia dynamically integrate different cellular inputs and control cell fate and function during tissue development. Here, we review the recently emerging concept of primary cilia dynamics in tissue development, organization, remodeling, and function.
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Affiliation(s)
- Jay Gopalakrishnan
- Institute for Human Genetics, Heinrich‐Heine‐UniversitätUniversitätsklinikum DüsseldorfDüsseldorfGermany
| | - Kerstin Feistel
- Department of Zoology, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | | | - Anne Grapin‐Botton
- Cluster of Excellence Physics of Life, TU DresdenDresdenGermany
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at The University Hospital Carl Gustav Carus and Faculty of Medicine of the TU DresdenDresdenGermany
| | - Nathalie Jurisch‐Yaksi
- Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
| | - Elvira Mass
- Life and Medical Sciences Institute, Developmental Biology of the Immune SystemUniversity of BonnBonnGermany
| | - David U Mick
- Center for Molecular Signaling (PZMS), Center of Human and Molecular Biology (ZHMB)Saarland School of MedicineHomburgGermany
| | - Roman‐Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Helen May‐Simera
- Institute of Molecular PhysiologyJohannes Gutenberg‐UniversityMainzGermany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Miriam Schmidts
- Pediatric Genetics Division, Center for Pediatrics and Adolescent MedicineUniversity Hospital FreiburgFreiburgGermany
- CIBSS‐Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
| | - Peter Walentek
- CIBSS‐Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
- Renal Division, Internal Medicine IV, Medical CenterUniversity of FreiburgFreiburgGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical FacultyUniversity of BonnBonnGermany
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Green TE, Fujita A, Ghaderi N, Heinzen EL, Matsumoto N, Klein KM, Berkovic SF, Hildebrand MS. Brain mosaicism of hedgehog signalling and other cilia genes in hypothalamic hamartoma. Neurobiol Dis 2023; 185:106261. [PMID: 37579995 DOI: 10.1016/j.nbd.2023.106261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023] Open
Abstract
Hypothalamic hamartoma (HH) is a rare benign developmental brain lesion commonly associated with a well characterized epilepsy phenotype. Most individuals with HH are non-syndromic without additional developmental anomalies nor a family history of disease. Nonetheless, HH is a feature of Pallister-Hall (PHS) and Oro-Facial-Digital Type VI (OFD VI) syndromes, both characterized by additional developmental anomalies. Initial genetic of analysis HH began with syndromic HH, where germline inherited or de novo variants in GLI3, encoding a central transcription factor in the sonic hedgehog (Shh) signalling pathway, were identified in most individuals with PHS. Following these discoveries in syndromic HH, the hypothesis that post-zygotic mosaicism in related genes may underly non-syndromic HH was tested. We discuss the identified mosaic variants within individuals with non-syndromic HH, review the analytical methodologies and diagnostic yields, and explore understanding of the functional role of the implicated genes with respect to Shh signalling, and cilia development and function. We also outline future challenges in studying non-syndromic HH and suggest potential novel strategies to interrogate brain mosaicism in HH.
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Affiliation(s)
- Timothy E Green
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria 3084, Australia
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Navid Ghaderi
- Departments of Clinical Neurosciences, Medical Genetics and Community Health Sciences, Hotchkiss Brain Institute & Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Canada
| | - Erin L Heinzen
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Karl Martin Klein
- Departments of Clinical Neurosciences, Medical Genetics and Community Health Sciences, Hotchkiss Brain Institute & Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Canada; Epilepsy Center Frankfurt Rhine-Main and Department of Neurology, Goethe University and University Hospital Frankfurt, Frankfurt am Main, Germany; LOEWE Center for Personalized Translational Epilepsy Research (CePTER), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria 3084, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria 3084, Australia; Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia.
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7
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Aubert-Mucca M, Huber C, Baujat G, Michot C, Zarhrate M, Bras M, Boutaud L, Malan V, Attie-Bitach T, Cormier-Daire V. Ellis-Van Creveld Syndrome: Clinical and Molecular Analysis of 50 Individuals. J Med Genet 2023; 60:337-345. [PMID: 35927022 DOI: 10.1136/jmg-2022-108435] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/09/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Ellis-Van Creveld (EVC) syndrome is one of the entities belonging to the skeletal ciliopathies short rib-polydactyly subgroup. Major signs are ectodermal dysplasia, chondrodysplasia, polydactyly and congenital cardiopathy, with a high degree of variability in phenotypes ranging from lethal to mild clinical presentations. The EVC and EVC2 genes are the major genes causative of EVC syndrome. However, an increased number of genes involved in the ciliopathy complex have been identified in EVC syndrome, leading to a better understanding of its physiopathology, namely, WDR35, GLI1, DYNC2LI1, PRKACA, PRKACB and SMO. They all code for proteins located in the primary cilia, playing a key role in signal transduction of the Hedgehog pathways. METHODS The aim of this study was the analysis of 50 clinically identified EVC cases from 45 families to further define the phenotype and molecular bases of EVC. RESULTS Our detection rate in the cohort of 45 families was of 91.11%, with variants identified in EVC/EVC2 (77.8%), DYNC2H1 (6.7%), DYNC2LI1 (2.2%), SMO (2.2%) or PRKACB (2.2%). No distinctive feature was remarkable of a specific genotype-phenotype correlation. Interestingly, we identified a high proportion of heterozygous deletions in EVC/EVC2 of variable sizes (26.92%), mostly inherited from the mother, and probably resulting from recombinations involving Alu sequences. CONCLUSION We confirmed that EVC and EVC2 are the major genes involved in the EVC phenotype and highlighted the high prevalence of previously unreported CNVs (Copy Number Variation).
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Affiliation(s)
- Marion Aubert-Mucca
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Céline Huber
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Genevieve Baujat
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Caroline Michot
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Mohammed Zarhrate
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UMS3633, Imagine Institute, Paris, France
| | - Marc Bras
- Bioinformatics Platform, Imagine Institute, Paris, France
| | - Lucile Boutaud
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hopital Universitaire Necker-Enfants Malades, Paris, France
| | - Valérie Malan
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hopital Universitaire Necker-Enfants Malades, Paris, France
| | - Tania Attie-Bitach
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hopital Universitaire Necker-Enfants Malades, Paris, France
| | | | - Valerie Cormier-Daire
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
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8
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Piceci-Sparascio F, Micale L, Torres B, Guida V, Consoli F, Torrente I, Onori A, Frustaci E, D'Asdia MC, Petrizzelli F, Bernardini L, Mancini C, Soli F, Cocciadiferro D, Guadagnolo D, Mastromoro G, Putotto C, Fontana F, Brunetti-Pierri N, Novelli A, Pizzuti A, Marino B, Digilio MC, Mazza T, Dallapiccola B, Ruiz-Perez VL, Tartaglia M, Castori M, De Luca A. Clinical variability in DYNC2H1-related skeletal ciliopathies includes Ellis-van Creveld syndrome. Eur J Hum Genet 2023; 31:479-484. [PMID: 36599940 PMCID: PMC10133340 DOI: 10.1038/s41431-022-01276-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/17/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
Deleterious variants of DYNC2H1 gene are associated with a wide spectrum of skeletal ciliopathies (SC). We used targeted parallel sequencing to analyze 25 molecularly unsolved families with different SCs. Deleterious DYNC2H1 variants were found in six sporadic patients and two monozygotic (MZ) twins. Clinical diagnoses included short rib-polydactyly type 3 in two cases, and asphyxiating thoracic dystrophy (ATD) in one case. Remarkably, clinical diagnosis fitted with EvC, mixed ATD/EvC and short rib-polydactyly/EvC phenotypes in three sporadic patients and the MZ twins. EvC/EvC-like features always occurred in compound heterozygotes sharing a previously unreported splice site change (c.6140-5A>G) or compound heterozygotes for two missense variants. These results expand the DYNC2H1 mutational repertoire and its clinical spectrum, suggesting that EvC may be occasionally caused by DYNC2H1 variants presumably acting as hypomorphic alleles.
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Affiliation(s)
- Francesca Piceci-Sparascio
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Lucia Micale
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Barbara Torres
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Valentina Guida
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Federica Consoli
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Isabella Torrente
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Annamaria Onori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Frustaci
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Cecilia D'Asdia
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesco Petrizzelli
- Laboratory of Bioinformatics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Laura Bernardini
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Fiorenza Soli
- Medical Genetic Unit, Santa Chiara Hospital APSS, Trento, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, Rome, Italy
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Carolina Putotto
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | | | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Bruno Marino
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Tommaso Mazza
- Laboratory of Bioinformatics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Victor Luis Ruiz-Perez
- Instituto de Investigaciones Biomédicas 'Alberto Sols', CSIC-UAM, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPaz-UAM, Madrid, Spain
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Alessandro De Luca
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
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9
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Huang W, Zhu X, Sun G, Gao Z, Kong X. Whole-exome sequencing in deceased fetuses with ultrasound anomalies: a retrospective analysis. BMC Med Genomics 2023; 16:25. [PMID: 36797717 PMCID: PMC9936674 DOI: 10.1186/s12920-022-01427-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/23/2022] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) is an effective method in the prenatal setting for identification of the underlying genetic etiology of fetal ultrasound abnormalities. To investigate the diagnostic value of WES in fetuses with ultrasound abnormalities that resulted in fetal demise or pregnancy termination. METHODS 61 deceased fetuses with ultrasound abnormalities and normal copy number variation Sequencing were retrospectively collected. Proband-only or trio-WES were performed on the products of conception. RESULT Collectively, 28 cases were positive with 39 variants (10 pathogenic, 22 likely pathogenic and 7 variants of uncertain significance) of 18 genes, and the overall diagnostic rate was 45.9% (28/61), of which 39.2% (11/28) were de novo variants. In addition, 21 variants in 11 genes among the positive cases had not been previously reported. The diagnostic yield for definitive findings for trio analysis was 55.9% (19/34) compared to 33.3% (9/27) for singletons. The most common ultrasound abnormalities were skeletal system abnormalities 39.2% (11/28), followed by multiple system abnormalities (17.9%, 5/28) and genitourinary abnormalities (17.9%, 5/28). CONCLUSION Our results support the use of WES to identify genetic etiologies of ultrasound abnormalities and improve understanding of pathogenic variants. The identification of disease-related variants provided information for subsequent genetic counseling of recurrence risk and management of subsequent pregnancies.
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Affiliation(s)
- Wei Huang
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaofan Zhu
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Gege Sun
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Zhi Gao
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiangdong Kong
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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10
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Chen W, Li Y, Zhang J, Yuan Y, Sun D, Yuan J, Yang K, Liang Y, Guo Q. Genetic variations in the DYNC2H1 gene causing SRTD3 (short-rib thoracic dysplasia 3 with or without polydactyly). Front Genet 2023; 14:1125473. [PMID: 37091781 PMCID: PMC10116042 DOI: 10.3389/fgene.2023.1125473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Background and aims: Short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3) represents a type of severe fetal skeletal dysplasia (SD) characterized by shortened limbs, narrow thorax with or without polydactyly, which is caused by the homozygous or compound heterozygous mutations in the DYNC2H1 gene. SRTD3 is a recessive disorder, identification of the responsible genetic variation would be beneficial to an accurate prenatal diagnosis and well-grounded counseling for the affected families. Material and methods: Two families having experienced recurrent fetal SDs were recruited and submitted to a multiplatform genetic investigation. Whole-exome sequencing (WES) was performed with samples collected from the probands. Sanger sequencing and fluorescent quantitative PCR (qPCR) were conducted as validation assays for suspected variations. Results: WES identified two compound heterozygous variations in the DYNC2H1(NM_001080463.2) gene, namely c.2386C>T (p.Arg796Trp) and c.7289T>C (p.Ile2430Thr) for one; and exon (64-83)del and c.8190G>T (p.Leu2730Phe) for the other, respectively. One variant in them, exon (64-83)del, was novelly identified. Conclusion: The study detected two compound heterozygous variation in DYNC2H1 including one novel deletion: exon (64-83) del. Our findings clarified the cause of fetal skeletal dysplasia in the subject families, provided guidance for their future pregnancies, and highlighted the value of WES in diagnosis of skeletal dysplasia with unclear prenatal indications.
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Affiliation(s)
- Wenqi Chen
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Yazhou Li
- Department of Pediatric Orthopaedic, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jing Zhang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Yufan Yuan
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Donglan Sun
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Jiayu Yuan
- Department of Pediatric Orthopaedic, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Kai Yang
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Healthcare Hospital, Capital Medical University, Beijing, China
| | - Ying Liang
- Reproductive Medicine Center, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, Hebei, China
- *Correspondence: Qing Guo, ; Ying Liang,
| | - Qing Guo
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
- *Correspondence: Qing Guo, ; Ying Liang,
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11
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Buchh M, Gillespie PJ, Treat K, Abreu MA, Schwantes-An THL, Helm BM, Fang F, Xuei X, Mantcheva L, Suhrie KR, Graham BH, Conboy E, Vetrini F. Characterization of a novel deep-intronic variant in DYNC2H1 identified by whole-exome sequencing in a patient with a lethal form of a short-rib thoracic dysplasia type III. Cold Spring Harb Mol Case Stud 2022; 8:a006254. [PMID: 36442996 PMCID: PMC9808550 DOI: 10.1101/mcs.a006254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Abstract
Biallelic pathogenic variants in DYNC2H1 are the cause of short-rib thoracic dysplasia type III with or without polydactyly (OMIM #613091), a skeletal ciliopathy characterized by thoracic hypoplasia due to short ribs. In this report, we review the case of a patient who was admitted to the Neonatal Intensive Care Unit (NICU) of Indiana University Health (IUH) for respiratory support after experiencing respiratory distress secondary to a small, narrow chest causing restrictive lung disease. Additional phenotypic features include postaxial polydactyly, short proximal long bones, and ambiguous genitalia were noted. Exome sequencing (ES) revealed a maternally inherited likely pathogenic variant c.10322C > T p.(Leu3448Pro) in the DYNC2H1 gene. However, there was no variant found on the paternal allele. Microarray analysis to detect deletion or duplication in DYNC2H1 was normal. Therefore, there was insufficient evidence to establish a molecular diagnosis. To further explore the data and perform additional investigations, the patient was subsequently enrolled in the Undiagnosed Rare Disease Clinic (URDC) at Indiana University School of Medicine (IUSM). The investigators at the URDC performed a reanalysis of the ES raw data, which revealed a paternally inherited DYNC2H1 deep-intronic variant c.10606-14A > G predicted to create a strong cryptic acceptor splice site. Additionally, the RNA sequencing of fibroblasts demonstrated partial intron retention predicted to cause a premature stop codon and nonsense-mediated mRNA decay (NMD). Droplet digital RT-PCR (RT-ddPCR) showed a drastic reduction by 74% of DYNCH2H1 mRNA levels. As a result, the intronic variant was subsequently reclassified as likely pathogenic resulting in a definitive clinical and genetic diagnosis for this patient. Reanalysis of ES and fibroblast mRNA experiments confirmed the pathogenicity of the splicing variants to supplement critical information not revealed in original ES or CMA reports. The NICU and URDC collaboration ended the diagnostic odyssey for this family; furthermore, its importance is emphasized by the possibility of prenatally diagnosing the mother's current pregnancy.
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Affiliation(s)
- Muqsit Buchh
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | | | - Kayla Treat
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Marco A Abreu
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Tae-Hwi Linus Schwantes-An
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Benjamin M Helm
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Fang Fang
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Lili Mantcheva
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Kristen R Suhrie
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Brett H Graham
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Erin Conboy
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Francesco Vetrini
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
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12
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Zhao X, Sui A, Cui L, Liu Z, Zhang R, Han Y, Shao L. A novel WDR60 variant contributes to a late diagnosis of Jeune asphyxiating thoracic dystrophy in a Chinese patient: A case report. Clin Case Rep 2022; 10:e6561. [PMID: 36381051 PMCID: PMC9653168 DOI: 10.1002/ccr3.6561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 10/07/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022] Open
Abstract
We report a Chinese patient with JATD presenting a mild skeletal phenotype and with renal insufficiency as the initial symptom of the disease. A novel homozygous c.2789C>T (p.S930L) variant in the WDR60 gene was identified. Our report will help to improve awareness and diagnosability for this disease.
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Affiliation(s)
- Xiangzhong Zhao
- Medical Research CenterThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Aihua Sui
- Medical Research CenterThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Li Cui
- Department of NephrologyThe Affiliated Hospital of Qingdao UniversityQingdaoPeople's Republic of China
| | - Zhiying Liu
- Medical Research CenterThe Affiliated Hospital of Qingdao UniversityQingdaoChina
- Department of NephrologyThe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Ruixiao Zhang
- Department of NephrologyThe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Yue Han
- Department of NephrologyThe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Leping Shao
- Department of NephrologyThe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
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13
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Deichaite I, Hopper A, Krockenberger L, Sears TJ, Sutton L, Ray X, Sharabi A, Navon A, Sanghvi P, Carter H, Moiseenko V. Germline genetic biomarkers to stratify patients for personalized radiation treatment. J Transl Med 2022; 20:360. [PMID: 35962345 PMCID: PMC9373374 DOI: 10.1186/s12967-022-03561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Precision medicine incorporating genetic profiling is becoming a standard of care in medical oncology. However, in the field of radiation oncology there is limited use of genetic profiling and the impact of germline genetic biomarkers on radiosensitivity, radioresistance, or patient outcomes after radiation therapy is poorly understood. In HNSCC, the toxicity associated with treatment can cause delays or early cessation which has been associated with worse outcomes. Identifying potential biomarkers which can help predict toxicity, as well as response to treatment, is of significant interest. Methods Patients with HNSCC who received RT and underwent next generation sequencing of somatic tumor samples, transcriptome RNA-seq with matched normal tissue samples were included. Patients were then grouped by propensity towards increased late vs. early toxicity (Group A) and those without (Group B), assessed by CTCAE v5.0. The groups were then analyzed for association of specific germline variants with toxicity and clinical outcomes. Results In this study we analyzed 37 patients for correlation between germline variants and toxicity. We observed that TSC2, HLA-A, TET2, GEN1, NCOR2 and other germline variants were significantly associated with long term toxicities. 34 HNSCC patients treated with curative intent were evaluated for clinical outcomes. Group A had significantly improved overall survival as well as improved rates of locoregional recurrence and metastatic disease. Specific variants associated with improved clinical outcomes included TSC2, FANCD2, and PPP1R15A, while the HLA-A and GEN1 variants were not correlated with survival or recurrence. A group of five HLA-DMA/HLA-DMB variants was only found in Group B and was associated with a higher risk of locoregional recurrence. Conclusions This study indicates that germline genetic biomarkers may have utility in predicting toxicity and outcomes after radiation therapy and deserve further investigation in precision radiation medicine approaches.
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Affiliation(s)
- Ida Deichaite
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA. .,Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
| | - Austin Hopper
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lena Krockenberger
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Leisa Sutton
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Xenia Ray
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
| | - Andrew Sharabi
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ami Navon
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Parag Sanghvi
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Vitali Moiseenko
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
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14
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Zhao W, Ye G, Li Q, Zhou Y, Yu X, Li Y, Yu M, Wang H. Pathogenic variant of
DYNC2H1
associated with lingual hamartoma in a Chinese pedigree. J Oral Pathol Med 2022; 51:755-761. [DOI: 10.1111/jop.13339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/17/2022] [Accepted: 06/25/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Wenquan Zhao
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Zhejiang University School of Medicine, School of Stomatology, and Key Laboratory of Oral Biomedical Research of Zhejiang Province Hangzhou Zhejiang China
| | - Guanchen Ye
- Stomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University Hangzhou Zhejiang China
| | - Qi Li
- Stomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University Hangzhou Zhejiang China
| | - Yu Zhou
- Stomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University Hangzhou Zhejiang China
| | - Xiaowen Yu
- Stomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University Hangzhou Zhejiang China
| | - Yining Li
- Stomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University Hangzhou Zhejiang China
| | - Mengfei Yu
- Stomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University Hangzhou Zhejiang China
| | - Huiming Wang
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Zhejiang University School of Medicine, School of Stomatology, and Key Laboratory of Oral Biomedical Research of Zhejiang Province Hangzhou Zhejiang China
- Stomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University Hangzhou Zhejiang China
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15
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Prenatal Diagnosis of Jeune Syndrome Caused by Compound Heterozygous Variants in DYNC2H1 Gene-Case Report with Rapid WES Procedure and Differential Diagnosis of Lethal Skeletal Dysplasias. Genes (Basel) 2022; 13:genes13081339. [PMID: 35893076 PMCID: PMC9332837 DOI: 10.3390/genes13081339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Skeletal dysplasias (SDs) are a large, heterogeneous group of mostly genetic disorders that affect the bones and cartilage, resulting in abnormal growth and development of skeletal structures. The high clinical and genetic diversity in SDs cause difficulties in prenatal diagnosis. To establish a correct prognosis and better management, it is very important to distinguish SDs with poor life-limiting prognosis or lethal SDs from other ones. Bad prognosis in foetuses is assessed on the basis of the size of the thorax, lung volumes, long bones’ length, bones’ echogenicity, bones’ angulation or presented fractures, and the concomitant presence of non-immune hydrops or visceral abnormalities. To confirm SD diagnosis and perform family genetic consultation, rapid molecular diagnostics are needed; therefore, the NGS method using a panel of genes corresponding to SD or whole-exome sequencing (WES) is commonly used. We report a case of a foetus showing long bones’ shortening and a narrow chest with short ribs, diagnosed prenatally with asphyxiating thoracic dystrophy, also known as Jeune syndrome (ATD; OMIM 208500), caused by compound heterozygous variants in the DYNC2H1 gene, identified by prenatally performed rapid-WES analysis. The missense variants in the DYNC2H1 gene were inherited from the mother (c.7289T>C; p.Ile2430Thr) and from the father (c.12716T>G; p.Leu4239Arg). The DYNC2H1 gene is one of at least 17 ATD-associated genes. This disorder belongs to the ninth group of SD, ciliopathies with major skeletal involvement. An extremely narrow, bell-shaped chest, and abnormalities of the kidneys, liver, and retinas were observed in most cases of ATD. Next to lethal and severe forms, clinically mild forms have also been reported. A diagnosis of ATD is important to establish the prognosis and management for the patient, as well as the recurrence risk for the family.
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16
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Green TE, Motelow JE, Bennett MF, Ye Z, Bennett CA, Griffin NG, Damiano JA, Leventer RJ, Freeman JL, Harvey AS, Lockhart PJ, Sadleir LG, Boys A, Scheffer IE, Major H, Darbro BW, Bahlo M, Goldstein DB, Kerrigan JF, Heinzen EL, Berkovic SF, Hildebrand MS. Sporadic hypothalamic hamartoma is a ciliopathy with somatic and bi-allelic contributions. Hum Mol Genet 2022; 31:2307-2316. [PMID: 35137044 PMCID: PMC9307310 DOI: 10.1093/hmg/ddab366] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Hypothalamic hamartoma with gelastic seizures is a well-established cause of drug-resistant epilepsy in early life. The development of novel surgical techniques has permitted the genomic interrogation of hypothalamic hamartoma tissue. This has revealed causative mosaic variants within GLI3, OFD1 and other key regulators of the sonic-hedgehog pathway in a minority of cases. Sonic-hedgehog signalling proteins localize to the cellular organelle primary cilia. We therefore explored the hypothesis that cilia gene variants may underlie hitherto unsolved cases of sporadic hypothalamic hamartoma. We performed high-depth exome sequencing and chromosomal microarray on surgically resected hypothalamic hamartoma tissue and paired leukocyte-derived DNA from 27 patients. We searched for both germline and somatic variants under both dominant and bi-allelic genetic models. In hamartoma-derived DNA of seven patients we identified bi-allelic (one germline, one somatic) variants within one of four cilia genes-DYNC2I1, DYNC2H1, IFT140 or SMO. In eight patients, we identified single somatic variants in the previously established hypothalamic hamartoma disease genes GLI3 or OFD1. Overall, we established a plausible molecular cause for 15/27 (56%) patients. Here, we expand the genetic architecture beyond single variants within dominant disease genes that cause sporadic hypothalamic hamartoma to bi-allelic (one germline/one somatic) variants, implicate three novel cilia genes and reconceptualize the disorder as a ciliopathy.
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Affiliation(s)
- Timothy E Green
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
| | - Joshua E Motelow
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Mark F Bennett
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Zimeng Ye
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
| | - Caitlin A Bennett
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
| | - Nicole G Griffin
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - John A Damiano
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
| | - Richard J Leventer
- Department of Neurology, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
| | - Jeremy L Freeman
- Department of Neurology, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
| | - A Simon Harvey
- Department of Neurology, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
| | - Paul J Lockhart
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand
| | - Amber Boys
- Victorian Clinical Genetics Services, Parkville, VIC 3052, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
- Department of Neurology, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3052, Australia
| | - Heather Major
- Department of Pediatrics, The University of Iowa, Iowa City, IA 52246, USA
| | - Benjamin W Darbro
- Department of Pediatrics, The University of Iowa, Iowa City, IA 52246, USA
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - John F Kerrigan
- Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85013, USA
| | - Erin L Heinzen
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, and Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC 3052, Australia
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17
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Cheng C, Li X, Zhao S, Feng Q, Ren X, Chen X. Compound heterozygous variants in DYNC2H1 in a foetus with type III short rib-polydactyly syndrome and situs inversus totalis. BMC Med Genomics 2022; 15:55. [PMID: 35277174 PMCID: PMC8917749 DOI: 10.1186/s12920-022-01205-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/01/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3, OMIM: 613091) is an autosomal recessive disorder. SRTD3 presents clinically with a narrow thorax, short ribs, shortened tubular bones, and acetabular roof abnormalities. Clinical signs of SRTD3 vary among individuals. Pathogenic variants of DYNC2H1 (OMIM: 603297) have been reported to cause SRTD3.
Methods
We performed a detailed clinical prenatal sonographic characterization of a foetus with SRTD3. Trio whole-exome sequencing was used to identify causative variants in the family. The identified variants in the families were validated by Sanger sequencing and mass spectrometry. Multiple computational tools were used to predict the harmfulness of the two variants. A minigene splicing assay was carried out to evaluate the impact of the splice-site variant.
Results
We evaluated prenatal sonographic images of the foetus with SRTD3, including abnormal rib curvature, narrow thorax, bilateral hypoplastic lungs, bilateral polydactyly, syndactyly, and foetal visceral situs inversus with mirror-image dextrocardia. We revealed novel compound variants of DYNC2H1 (NM_001377.3:c.11483T > G (p.Ile3828Arg) and c.2106 + 3A > T). Various statistical methods predicted that the variants would cause harmful effects on genes or gene products. The minigene assay findings suggested that c.2106 + 3A > T caused the skipping over exon 14, producing an exon 14 loss in the protein.
Conclusion
This study identified a foetus with SRTD3 with situs inversus totalis with mirror-image dextrocardia in a Chinese family, revealing two novel compound heterozygous dynein cytoplasmic 2 heavy chain 1 (DYNC2H1) variants, expanding the phenotypic spectrum of SRTD3. The minigene study of c.2106 + 3A > T was predicted to cause an inframe exclusion of exon 14, which was predicted to have important molecular functions. Our findings strongly supported the use of WES in prenatal diagnosis and helped to understand the correlation of genotype and phenotypes of DYNC2H1. The specific sonographic findings and the molecular diagnosis helped add experience to further our expertise in prenatal counselling for SRTD3.
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Stranks L, Barry S, Yeo A. A curious case of asphyxiating thoracic dystrophy in an adult. Respirol Case Rep 2021; 9:e0876. [PMID: 34795902 PMCID: PMC8580865 DOI: 10.1002/rcr2.876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 11/11/2022] Open
Abstract
Asphyxiating thoracic dystrophy (ATD), also known as Jeune syndrome, is a rare autosomal recessive chondrodysplasia that most commonly manifests as shortening of long bones and ribs, as well as frequent extra-skeletal organ involvement. It is typically diagnosed in infancy or early childhood following episodes of respiratory distress or failure, in conjunction with characteristic physical findings, and is often fatal. The genetic heterogeneity of this disease, however, means there is varying severity of symptoms and physical manifestations. In this report, we describe a 57-year-old man with his first presentation of respiratory failure, with a history and physical findings consistent with ATD, a diagnosis previously unknown to the patient.
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Affiliation(s)
- Lachlan Stranks
- Department of Thoracic MedicineRoyal Adelaide HospitalAdelaideSouth AustraliaAustralia
- Faculty of Health and Medical SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Simone Barry
- Department of Thoracic MedicineRoyal Adelaide HospitalAdelaideSouth AustraliaAustralia
| | - Aeneas Yeo
- Department of Thoracic MedicineRoyal Adelaide HospitalAdelaideSouth AustraliaAustralia
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19
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Liu Y, Wang H, Jin X, Shao Q, Pan Q. Molecular Diagnosis and Prenatal Phenotype Analysis of Eight Fetuses With Ciliopathies. Front Genet 2021; 12:705808. [PMID: 34675960 PMCID: PMC8523853 DOI: 10.3389/fgene.2021.705808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Human ciliopathies are hereditary conditions caused by variants in ciliary-associated genes. Ciliopathies are often characterized by multiple system defects. However, it is not easy to make a definite diagnosis in the prenatal period only based on the imageology. In this report, eight new prenatal cases from five unrelated families diagnosed with ciliopathies were systematically examined. The clinical manifestations of these fetuses showed such prenatal diagnostic features as occipital encephalocele, and polydactyly and polycystic kidneys. Situs inversus caused by CPLANE1 variant was first reported. In Family 1 and Family 3, homozygous variants of CPLANE1 and NPHP4 caused by consanguineous marriage and uniparental disomy were detected by whole-exome sequencing, respectively. In Family 2, Family 4 and Family 5, compound heterozygotes of TMEM67 and DYNC2H1 including two novel missense variants and one novel nonsense variant were identified. The distribution of pathogenic missense variants along TMEM67 gene mainly clustered in the extracellular cysteine rich region, extracellular area with unknown structure, and the transmembrane regions. Genotype-phenotype relationship between CPLANE1 and TMEM67 genes was concluded. This report describes new clinical manifestations and novel variants in CPLANE1, TMEM67, NPHP4, and DYNC2H1.
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Affiliation(s)
- Yuefang Liu
- Department of Clinical Genetics, Huai'an Maternity and Child Clinical College of Xuzhou Medical University, Huai'an, China
| | - Hui Wang
- Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Zhenjiang, China
| | - Xin Jin
- Department of Clinical Genetics, Huai'an Maternity and Child Clinical College of Xuzhou Medical University, Huai'an, China
| | - Qixiang Shao
- Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Zhenjiang, China.,Jiangsu College of Nursing, School of Medical Science and Laboratory Medicine, Huai'an, China
| | - Qiong Pan
- Department of Clinical Genetics, Huai'an Maternity and Child Clinical College of Xuzhou Medical University, Huai'an, China
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20
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Fetal ciliopathies: a retrospective observational single-center study. Arch Gynecol Obstet 2021; 306:71-83. [PMID: 34596737 PMCID: PMC9300526 DOI: 10.1007/s00404-021-06265-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/15/2021] [Indexed: 12/04/2022]
Abstract
Purpose Report on the diagnosis of prenatally suspected multisystem ciliopathies in a single center between 2002 and 2020. Methods Retrospective observational single-center study including pregnancies with prenatal ultrasound features of multisystem ciliopathies, such as hyperechogenic kidneys together with polydactyly and/or other skeletal and extraskeletal findings. Cases were compared according to their prenatal findings and outcomes. Results 36 cases of multisystem ciliopathies were diagnosed. Meckel-Gruber syndrome (MKS) was the most common ciliopathy (n = 19/36, 52.8%), followed by disorders that belong to the group of short-rib thoracic dysplasia (SRTD, n = 10/36, 27.8%) McKusick–Kaufmann syndrome (MKKS, n = 4/36, 11.1%), Bardet–Biedl syndrome (BBS, n = 2/36, 5.5%) and Joubert syndrome (n = 1/36, 2.8%). All cases showed abnormalities of the kidneys, most often hyperechogenic parenchyma (n = 26/36, 72.2%), cystic dysplasia (n = 24/36, 66.7%), and/or bilateral kidney enlargement (n = 22/36, 61.1%). Oligohydramnios was mainly present in fetuses with MKS. Polydactyly (n = 18/36), abnormalities of the CNS (n = 25/36), and heart defects (n = 10/36) were associated in 50%, 69.4%, and 27.8%, respectively. Conclusion Prenatal detection of renal abnormalities associated with skeletal or brain abnormalities should raise the suspicion for multisystem ciliopathies. Prenatal ultrasound can help to differentiate between different diseases and pave the way for subsequent targeted genetic testing.
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21
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Primary cilia in hard tissue development and diseases. Front Med 2021; 15:657-678. [PMID: 34515939 DOI: 10.1007/s11684-021-0829-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/13/2020] [Indexed: 10/20/2022]
Abstract
Bone and teeth are hard tissues. Hard tissue diseases have a serious effect on human survival and quality of life. Primary cilia are protrusions on the surfaces of cells. As antennas, they are distributed on the membrane surfaces of almost all mammalian cell types and participate in the development of organs and the maintenance of homeostasis. Mutations in cilium-related genes result in a variety of developmental and even lethal diseases. Patients with multiple ciliary gene mutations present overt changes in the skeletal system, suggesting that primary cilia are involved in hard tissue development and reconstruction. Furthermore, primary cilia act as sensors of external stimuli and regulate bone homeostasis. Specifically, substances are trafficked through primary cilia by intraflagellar transport, which affects key signaling pathways during hard tissue development. In this review, we summarize the roles of primary cilia in long bone development and remodeling from two perspectives: primary cilia signaling and sensory mechanisms. In addition, the cilium-related diseases of hard tissue and the manifestations of mutant cilia in the skeleton and teeth are described. We believe that all the findings will help with the intervention and treatment of related hard tissue genetic diseases.
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22
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Dahl TM, Baehr W. Review: Cytoplasmic dynein motors in photoreceptors. Mol Vis 2021; 27:506-517. [PMID: 34526758 PMCID: PMC8410232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/30/2021] [Indexed: 12/04/2022] Open
Abstract
Cytoplasmic dyneins (dynein-1 and dynein-2) transport cargo toward the minus end of microtubules and thus, are termed the "retrograde" cellular motor. Dynein-1 cargo may include nuclei, mitochondria, membrane vesicles, lysosomes, phagosomes, and other organelles. For example, dynein-1 works in the cell body of eukaryotes to move cargo toward the microtubule minus end and positions the Golgi complex. Dynein-1 also participates in the movement of chromosomes and the positioning of mitotic spindles during cell division. In contrast, dynein-2 is present almost exclusively within cilia where it participates in retrograde intraflagellar transport (IFT) along the axoneme to return kinesin-2 subunits, BBSome, and IFT particles to the cell body. Cytoplasmic dyneins are hefty 1.5 MDa complexes comprised of dimers of heavy, intermediate, light intermediate, and light chains. Missense mutations of human DYNC1H1 are associated with malformations of cortical development (MCD) or spinal muscular atrophy with lower extremity predominance (SMA-LED). Missense mutations in DYNC2H1 are causative of short-rib polydactyly syndrome type III and nonsyndromic retinitis pigmentosa. We review mutations of the two dynein heavy chains and their effect on postnatal retina development and discuss consequences of deletion of DYNC1H1 in the mouse retina.
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Affiliation(s)
- Tiffanie M. Dahl
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT
| | - Wolfgang Baehr
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT,Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT,Department of Biology, University of Utah, Salt Lake City, UT
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23
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Ding R, Qiu Y, Zhuang Z, Ruan D, Wu J, Zhou S, Ye J, Cao L, Hong L, Xu Z, Zheng E, Li Z, Wu Z, Yang J. Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs. Theriogenology 2021; 173:269-278. [PMID: 34403972 DOI: 10.1016/j.theriogenology.2021.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 01/02/2023]
Abstract
With continuous improvement of sow litter size, breeders are gradually paying more attention to the quality of litter traits that directly impact the production efficiency of pig companies, such as the rate of piglets born alive (RBA) and the rate of healthy births (RHB). The objectives of this study are to dissect the genetic basis of litter traits in pig and to identify valuable genes and genetic markers, especially pleiotropic, for pig breeding. Herein, 1140 Duroc pigs and 2046 reproduction records, 5 litter traits, including the number of healthy births (NHB), number of deformed fetuses (NDF), number of stillborn (NSB), RBA, and RHB, were used in this study. Subsequently, a genome-wide association study (GWAS) was performed for the five litter traits in the first two parities from two Duroc populations. A total of 76 significantly related SNPs and 10 potential candidate genes (CAV1, DAB2, FGF12, FHOD3, DYNC2H1, GRHL1, TCTN3, PYROXD2, MMP8, MMP13, and PGR) were detected, including 13 pleiotropic SNPs that affected more than one litter trait. Finally, the functional enrichment analysis of functional genes that were closest to these significant SNPs indicated that most of the significant pathways were associated with hormone secretion and embryo and organ development. This study advances our understanding of the genetic mechanisms of litter traits, especially the survival rate of piglets born, and provides an opportunity to increase the quality of litter using marker-assisted selection or genomic selection in pigs.
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Affiliation(s)
- Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China
| | - Lu Cao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China.
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24
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Antony D, Brunner HG, Schmidts M. Ciliary Dyneins and Dynein Related Ciliopathies. Cells 2021; 10:cells10081885. [PMID: 34440654 PMCID: PMC8391580 DOI: 10.3390/cells10081885] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
Although ubiquitously present, the relevance of cilia for vertebrate development and health has long been underrated. However, the aberration or dysfunction of ciliary structures or components results in a large heterogeneous group of disorders in mammals, termed ciliopathies. The majority of human ciliopathy cases are caused by malfunction of the ciliary dynein motor activity, powering retrograde intraflagellar transport (enabled by the cytoplasmic dynein-2 complex) or axonemal movement (axonemal dynein complexes). Despite a partially shared evolutionary developmental path and shared ciliary localization, the cytoplasmic dynein-2 and axonemal dynein functions are markedly different: while cytoplasmic dynein-2 complex dysfunction results in an ultra-rare syndromal skeleto-renal phenotype with a high lethality, axonemal dynein dysfunction is associated with a motile cilia dysfunction disorder, primary ciliary dyskinesia (PCD) or Kartagener syndrome, causing recurrent airway infection, degenerative lung disease, laterality defects, and infertility. In this review, we provide an overview of ciliary dynein complex compositions, their functions, clinical disease hallmarks of ciliary dynein disorders, presumed underlying pathomechanisms, and novel developments in the field.
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Affiliation(s)
- Dinu Antony
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106 Freiburg, Germany;
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands;
- Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands
| | - Han G. Brunner
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands;
- Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands
| | - Miriam Schmidts
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106 Freiburg, Germany;
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands;
- Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands
- Correspondence: ; Tel.: +49-761-44391; Fax: +49-761-44710
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25
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Cell-based assay for ciliopathy patients to improve accurate diagnosis using ALPACA. Eur J Hum Genet 2021; 29:1677-1689. [PMID: 34040173 PMCID: PMC8560805 DOI: 10.1038/s41431-021-00907-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/01/2021] [Accepted: 05/06/2021] [Indexed: 11/26/2022] Open
Abstract
Skeletal ciliopathies are a group of disorders caused by dysfunction of the cilium, a small signaling organelle present on nearly every vertebrate cell. This group of disorders is marked by genetic and clinical heterogeneity, which complicates accurate diagnosis. In this study, we developed a robust, standardized immunofluorescence approach to accurately diagnose a subset of these disorders. Hereto we determined and compared the cilium phenotype of healthy individuals to patients from three different ciliopathy subgroups, using skin-derived fibroblasts. The cilium phenotype assay consists of three parameters; (1) ciliogenesis, based on the presence or absence of cilium markers, (2) cilium length, measured by the combined signal of an axonemal and a cilium membrane marker, and (3) retrograde intraflagellar transport (IFT), quantified by the area of the ciliary tip. Analysis of the cilium phenotypic data yielded comparable and reproducible results and in addition, displayed identifiable clusters for healthy individuals and two ciliopathy subgroups, i.e. ATD and CED. Our results illustrate that standardized analysis of the cilium phenotype can be used to discriminate between ciliopathy subgroups. Therefore, we believe that standardization of functional assays analyzing cilium phenotypic data can provide additional proof for conclusive diagnosis of ciliopathies, which is essential for routine diagnostic care.
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26
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Hammarsjö A, Pettersson M, Chitayat D, Handa A, Anderlid BM, Bartocci M, Basel D, Batkovskyte D, Beleza-Meireles A, Conner P, Eisfeldt J, Girisha KM, Chung BHY, Horemuzova E, Hyodo H, Korņejeva L, Lagerstedt-Robinson K, Lin AE, Magnusson M, Moosa S, Nayak SS, Nilsson D, Ohashi H, Ohashi-Fukuda N, Stranneheim H, Taylan F, Traberg R, Voss U, Wirta V, Nordgren A, Nishimura G, Lindstrand A, Grigelioniene G. High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses. J Hum Genet 2021; 66:995-1008. [PMID: 33875766 PMCID: PMC8472897 DOI: 10.1038/s10038-021-00925-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 12/11/2022]
Abstract
Skeletal ciliopathies are a heterogenous group of disorders with overlapping clinical and radiographic features including bone dysplasia and internal abnormalities. To date, pathogenic variants in at least 30 genes, coding for different structural cilia proteins, are reported to cause skeletal ciliopathies. Here, we summarize genetic and phenotypic features of 34 affected individuals from 29 families with skeletal ciliopathies. Molecular diagnostic testing was performed using massively parallel sequencing (MPS) in combination with copy number variant (CNV) analyses and in silico filtering for variants in known skeletal ciliopathy genes. We identified biallelic disease-causing variants in seven genes: DYNC2H1, KIAA0753, WDR19, C2CD3, TTC21B, EVC, and EVC2. Four variants located in non-canonical splice sites of DYNC2H1, EVC, and KIAA0753 led to aberrant splicing that was shown by sequencing of cDNA. Furthermore, CNV analyses showed an intragenic deletion of DYNC2H1 in one individual and a 6.7 Mb de novo deletion on chromosome 1q24q25 in another. In five unsolved cases, MPS was performed in family setting. In one proband we identified a de novo variant in PRKACA and in another we found a homozygous intragenic deletion of IFT74, removing the first coding exon and leading to expression of a shorter message predicted to result in loss of 40 amino acids at the N-terminus. These findings establish IFT74 as a new skeletal ciliopathy gene. In conclusion, combined single nucleotide variant, CNV and cDNA analyses lead to a high yield of genetic diagnoses (90%) in a cohort of patients with skeletal ciliopathies.
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Affiliation(s)
- Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden.
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, and Mt. Sinai Hospital, Toronto, ON, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Atsuhiko Handa
- Department of Radiology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Marco Bartocci
- Department of Women's and Children's Health, Neonatology, Karolinska Institutet, Stockholm, Sweden
| | - Donald Basel
- Division of Medical Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ana Beleza-Meireles
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Peter Conner
- Department of Women's and Children's Health, Karolinska Institutet and Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Eisfeldt
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Brian Hon-Yin Chung
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong and Shenzhen Hospital, Futian District, Shenzhen, China.,Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Eva Horemuzova
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet and Paediatric Endocrinology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Hironobu Hyodo
- Department of Obstetrics and Gynecology, Tokyo Metropolitan Bokutoh Hospital, Kotobashi, Sumida-ku, Tokyo, Japan
| | - Liene Korņejeva
- Department of Prenatal Diagnostics, Riga Maternity Hospital, Riga, Latvia
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Angela E Lin
- Medical Genetics, MassGeneral Hospital for Children, Boston, MA, USA
| | - Måns Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Centre for Inherited Metabolic Diseases, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Shahida Moosa
- Medical Genetics, Tygerberg Hospital and Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Daniel Nilsson
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | - Naoko Ohashi-Fukuda
- Department of Obstetrics and Gynecology, Tokyo Metropolitan Bokutoh Hospital, Kotobashi, Sumida-ku, Tokyo, Japan
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Centre for Inherited Metabolic Diseases, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Rasa Traberg
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ulrika Voss
- Department of Pediatric Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Imaging, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, and Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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27
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Wu S, Li H, Wang L, Mak N, Wu X, Ge R, Sun F, Cheng CY. Motor Proteins and Spermatogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1288:131-159. [PMID: 34453735 DOI: 10.1007/978-3-030-77779-1_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Unlike the intermediate filament- and septin-based cytoskeletons which are apolar structures, the microtubule (MT) and actin cytoskeletons are polarized structures in mammalian cells and tissues including the testis, most notable in Sertoli cells. In the testis, these cytoskeletons that stretch across the epithelium of seminiferous tubules and lay perpendicular to the basement membrane of tunica propria serve as tracks for corresponding motor proteins to support cellular cargo transport. These cargoes include residual bodies, phagosomes, endocytic vesicles and most notably developing spermatocytes and haploid spermatids which lack the ultrastructures of motile cells (e.g., lamellipodia, filopodia). As such, these developing germ cells require the corresponding motor proteins to facilitate their transport across the seminiferous epithelium during the epithelial cycle of spermatogenesis. Due to the polarized natures of these cytoskeletons with distinctive plus (+) and minus (-) end, directional cargo transport can take place based on the use of corresponding actin- or MT-based motor proteins. These include the MT-based minus (-) end directed motor proteins: dyneins, and the plus (+) end directed motor proteins: kinesins, as well as the actin-based motor proteins: myosins, many of which are plus (+) end directed but a few are also minus (-) end directed motor proteins. Recent studies have shown that these motor proteins are essential to support spermatogenesis. In this review, we briefly summarize and evaluate these recent findings so that this information will serve as a helpful guide for future studies and for planning functional experiments to better understand their role mechanistically in supporting spermatogenesis.
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Affiliation(s)
- Siwen Wu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China.,The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA
| | - Huitao Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China.,The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA
| | - Lingling Wang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China.,The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu, China
| | - Nathan Mak
- The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA
| | - Xiaolong Wu
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu, China
| | - Renshan Ge
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China
| | - Fei Sun
- Sir Run Run Shaw Hospital (SRRSH), Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - C Yan Cheng
- Sir Run Run Shaw Hospital (SRRSH), Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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28
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Vig A, Poulter JA, Ottaviani D, Tavares E, Toropova K, Tracewska AM, Mollica A, Kang J, Kehelwathugoda O, Paton T, Maynes JT, Wheway G, Arno G, Khan KN, McKibbin M, Toomes C, Ali M, Di Scipio M, Li S, Ellingford J, Black G, Webster A, Rydzanicz M, Stawiński P, Płoski R, Vincent A, Cheetham ME, Inglehearn CF, Roberts A, Heon E. DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration. Genet Med 2020; 22:2041-2051. [PMID: 32753734 PMCID: PMC7708302 DOI: 10.1038/s41436-020-0915-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Determining the role of DYNC2H1 variants in nonsyndromic inherited retinal disease (IRD). METHODS Genome and exome sequencing were performed for five unrelated cases of IRD with no identified variant. In vitro assays were developed to validate the variants identified (fibroblast assay, induced pluripotent stem cell [iPSC] derived retinal organoids, and a dynein motility assay). RESULTS Four novel DYNC2H1 variants (V1, g.103327020_103327021dup; V2, g.103055779A>T; V3, g.103112272C>G; V4, g.103070104A>C) and one previously reported variant (V5, g.103339363T>G) were identified. In proband 1 (V1/V2), V1 was predicted to introduce a premature termination codon (PTC), whereas V2 disrupted the exon 41 splice donor site causing incomplete skipping of exon 41. V1 and V2 impaired dynein-2 motility in vitro and perturbed IFT88 distribution within cilia. V3, homozygous in probands 2-4, is predicted to cause a PTC in a retina-predominant transcript. Analysis of retinal organoids showed that this new transcript expression increased with organoid differentiation. V4, a novel missense variant, was in trans with V5, previously associated with Jeune asphyxiating thoracic dystrophy (JATD). CONCLUSION The DYNC2H1 variants discussed herein were either hypomorphic or affecting a retina-predominant transcript and caused nonsyndromic IRD. Dynein variants, specifically DYNC2H1 variants are reported as a cause of non syndromic IRD.
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Affiliation(s)
- Anjali Vig
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, The University of Toronto, Toronto, Canada
| | - James A Poulter
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | | | - Erika Tavares
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Katerina Toropova
- Department of Biological Sciences, Birbeck, University of London, London, UK
| | - Anna Maria Tracewska
- DNA Analysis Unit, ŁUKASIEWICZ Research Network-PORT Polish Center for Technology Development, Wrocław, Poland
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Antonio Mollica
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jasmine Kang
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | | | - Tara Paton
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Jason T Maynes
- Department of Anesthesia and Pain Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | - Kamron N Khan
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Martin McKibbin
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Carmel Toomes
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Manir Ali
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Matteo Di Scipio
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Shuning Li
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jamie Ellingford
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicines and health, The University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
| | - Graeme Black
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicines and health, The University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew Webster
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | | | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Ajoy Vincent
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, The University of Toronto, Toronto, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Anthony Roberts
- Department of Biological Sciences, Birbeck, University of London, London, UK.
| | - Elise Heon
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.
- Institute of Medical Science, The University of Toronto, Toronto, Canada.
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.
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29
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Solaguren-Beascoa M, Bujakowska KM, Méjécase C, Emmenegger L, Orhan E, Neuillé M, Mohand-Saïd S, Condroyer C, Lancelot ME, Michiels C, Demontant V, Antonio A, Letexier M, Saraiva JP, Lonjou C, Carpentier W, Léveillard T, Pierce EA, Dollfus H, Sahel JA, Bhattacharya SS, Audo I, Zeitz C. WDR34, a candidate gene for non-syndromic rod-cone dystrophy. Clin Genet 2020; 99:298-302. [PMID: 33124039 DOI: 10.1111/cge.13872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/01/2020] [Accepted: 10/26/2020] [Indexed: 01/30/2023]
Abstract
Rod-cone dystrophy (RCD), also called retinitis pigmentosa, is characterized by rod followed by cone photoreceptor degeneration, leading to gradual visual loss. Mutations in over 65 genes have been associated with non-syndromic RCD explaining 60% to 70% of cases, with novel gene defects possibly accounting for the unsolved cases. Homozygosity mapping and whole-exome sequencing applied to a case of autosomal recessive non-syndromic RCD from a consanguineous union identified a homozygous variant in WDR34. Mutations in WDR34 have been previously associated with severe ciliopathy syndromes possibly associated with a retinal dystrophy. This is the first report of a homozygous mutation in WDR34 associated with non-syndromic RCD.
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Affiliation(s)
- Maria Solaguren-Beascoa
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Kinga M Bujakowska
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, USA
| | - Cécile Méjécase
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Lisa Emmenegger
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Elise Orhan
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marion Neuillé
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Saddek Mohand-Saïd
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France
| | - Christel Condroyer
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marie-Elise Lancelot
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Christelle Michiels
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Vanessa Demontant
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | | | - Christine Lonjou
- Plateforme Post-Génomique P3S, Hôpital Pitié Salpêtrière, Paris, France
| | - Wassila Carpentier
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Plateforme Post-Génomique P3S, Hôpital Pitié Salpêtrière, Paris, France
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Eric A Pierce
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, USA
| | - Hélène Dollfus
- Centre de Référence Pour les Affections Rares en Génétique Ophtalmologique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Laboratoire UMRS_1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France
| | - José-Alain Sahel
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine University, Pittsburgh, USA.,Académie des Sciences-Institut de France, Paris, France
| | - Shomi S Bhattacharya
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,UCL-Institute of Ophthalmology, London, UK.,Department of Cellular Therapy and Regenerative Medicine, Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Isabelle Audo
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France.,UCL-Institute of Ophthalmology, London, UK
| | - Christina Zeitz
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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30
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Abstract
Motile cilia are highly complex hair-like organelles of epithelial cells lining the surface of various organ systems. Genetic mutations (usually with autosomal recessive inheritance) that impair ciliary beating cause a variety of motile ciliopathies, a heterogeneous group of rare disorders. The pathogenetic mechanisms, clinical symptoms and severity of the disease depend on the specific affected genes and the tissues in which they are expressed. Defects in the ependymal cilia can result in hydrocephalus, defects in the cilia in the fallopian tubes or in sperm flagella can cause female and male subfertility, respectively, and malfunctional motile monocilia of the left-right organizer during early embryonic development can lead to laterality defects such as situs inversus and heterotaxy. If mucociliary clearance in the respiratory epithelium is severely impaired, the disorder is referred to as primary ciliary dyskinesia, the most common motile ciliopathy. No single test can confirm a diagnosis of motile ciliopathy, which is based on a combination of tests including nasal nitric oxide measurement, transmission electron microscopy, immunofluorescence and genetic analyses, and high-speed video microscopy. With the exception of azithromycin, there is no evidence-based treatment for primary ciliary dyskinesia; therapies aim at relieving symptoms and reducing the effects of reduced ciliary motility.
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31
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Adamo L, Kassif E, Jacobson JM, Achiron R. Prenatal Diagnosis of Jeune Syndrome by Whole-Exome Sequencing in a Case With Mild Skeletal Changes. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2020; 39:1869-1871. [PMID: 32154601 DOI: 10.1002/jum.15266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Affiliation(s)
- Laura Adamo
- Prenatal Diagnostic Unit, Department of Obstetrics and Gynecology, Sheba Medical Center, Ramat Gan, Israel
| | - Eran Kassif
- Prenatal Diagnostic Unit, Department of Obstetrics and Gynecology, Sheba Medical Center, Ramat Gan, Israel
| | - Jeffrey M Jacobson
- Department of Diagnostic Imaging, Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Reuven Achiron
- Prenatal Diagnostic Unit, Department of Obstetrics and Gynecology, Sheba Medical Center, Ramat Gan, Israel
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32
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Vuolo L, Stevenson NL, Mukhopadhyay AG, Roberts AJ, Stephens DJ. Cytoplasmic dynein-2 at a glance. J Cell Sci 2020; 133:133/6/jcs240614. [DOI: 10.1242/jcs.240614] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT
Cytoplasmic dynein-2 is a motor protein complex that drives the movement of cargoes along microtubules within cilia, facilitating the assembly of these organelles on the surface of nearly all mammalian cells. Dynein-2 is crucial for ciliary function, as evidenced by deleterious mutations in patients with skeletal abnormalities. Long-standing questions include how the dynein-2 complex is assembled, regulated, and switched between active and inactive states. A combination of model organisms, in vitro cell biology, live-cell imaging, structural biology and biochemistry has advanced our understanding of the dynein-2 motor. In this Cell Science at a Glance article and the accompanying poster, we discuss the current understanding of dynein-2 and its roles in ciliary assembly and function.
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Affiliation(s)
- Laura Vuolo
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Nicola L. Stevenson
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Aakash G. Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London WC1E 7HX, UK
| | - Anthony J. Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London WC1E 7HX, UK
| | - David J. Stephens
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
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33
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Čechová A, Baxová A, Zeman J, Lambert L, Honzík T, Leiská A, Čunát V, Tesařová M. Attenuated Type of Asphyxiating Thoracic Dysplasia due to Mutations in DYNC2H1 Gene. Prague Med Rep 2020; 120:124-130. [PMID: 31935347 DOI: 10.14712/23362936.2019.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Asphyxiating thoracic dysplasia (ATD) represents a heterogeneous group of skeletal dysplasias with short ribs, narrow chest and reduced thoracic capacity. Mutations in several genes including IFT80, DYNC2H1, TTC21B and WDR19 have been found in patients with ATD. Both severe and milder course of the disease were described in correlation with secondary involvement of lung's function. Two children with attenuated form of ATD are described. Their anthropometric parameters for birth weight, length and head circumference were normal but narrow thorax was observed in both of them in early infancy with chest circumference < -3 SD (standard deviation) in comparison to age related controls. The postnatal adaptation and development of both children was uneventful except for mild tachypnoea in one of them which persisted till the age of 6 months. In both children, radiographs revealed narrow upper half of the chest with shorter ribs and atypical configuration of pelvis with horizontally running acetabula and coarse internal edges typical for ATD. Molecular analyses using whole exome sequencing in one family revealed that the patient is compound heterozygote in DYNC2H1 gene for a frame-shift mutation c.4458delT resulting in premature stop-codon p.Phe1486Leufs*11 and a missense mutation c.9044A>G (p.Asp3015Gly). The second family refused the DNA analysis. Regular monitoring of anthropometric parameters during childhood is of big importance both in health and disease. In addition, measurement of the chest circumference should be included, at least at birth and during infancy.
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Affiliation(s)
- Anna Čechová
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Alice Baxová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jiří Zeman
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Lukáš Lambert
- Department of Radiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Tomáš Honzík
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Alena Leiská
- Department of Radiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Václav Čunát
- The Institute for the Care of Mother and Child, Prague, Czech Republic
| | - Markéta Tesařová
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
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34
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Pazour GJ, Quarmby L, Smith AO, Desai PB, Schmidts M. Cilia in cystic kidney and other diseases. Cell Signal 2019; 69:109519. [PMID: 31881326 DOI: 10.1016/j.cellsig.2019.109519] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/21/2019] [Accepted: 12/21/2019] [Indexed: 12/23/2022]
Abstract
Epithelial cells lining the ducts and tubules of the kidney nephron and collecting duct have a single non-motile cilium projecting from their surface into the lumen of the tubule. These organelles were long considered vestigial remnants left as a result of evolution from a ciliated ancestor, but we now recognize them as critical sensory antennae. In the kidney, the polycystins and fibrocystin, products of the major human polycystic kidney disease genes, localize to this organelle. The polycystins and fibrocystin, through an unknown mechanism, monitor the diameter of the kidney tubules and regulate the proliferation and differentiation of the cells lining the tubule. When the polycystins, fibrocystin or cilia themselves are defective, the cell perceives this as a pro-proliferative signal, which leads to tubule dilation and cystic disease. In addition to critical roles in preventing cyst formation in the kidney, cilia are also important in cystic and fibrotic diseases of the liver and pancreas, and ciliary defects lead to a variety of developmental abnormalities that cause structural birth defects in most organs.
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Affiliation(s)
- Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, United States of America.
| | - Lynne Quarmby
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
| | - Abigail O Smith
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, United States of America
| | - Paurav B Desai
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, United States of America
| | - Miriam Schmidts
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79112 Freiburg, Germany.
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35
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Liang N, Jiang X, Zeng L, Li Z, Liang D, Wu L. 28 novel mutations identified from 33 Chinese patients with cilia-related kidney disorders. Clin Chim Acta 2019; 501:207-215. [PMID: 31730820 DOI: 10.1016/j.cca.2019.10.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/03/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Cilia play an important role in cellular signaling pathways. Defective ciliary function causes a variety of disorders involve retina, skeleton, liver, kidney or others. Cilia-related kidney disorders are characterized by cystic renal disease, nephronophthisis and renal failure in general. METHODS In this study, we collected 33 families clinically suspected of cilia-related kidney disorders. Capture-based next-generation sequencing (NGS) of 88 related genes, Sanger sequencing, pedigree analysis and functional study were performed to analyze their genetic cause. RESULTS 40 mutations in PKD1, PKD2, PKHD1, DYNC2H1 and TMEM67 genes were identified from 27 of 33 affected families. 70% (28/40) of the mutations were first found in patients. We reported a very early-onset autosomal dominant polycystic kidney disease (ADPKD) family caused by a novel heterozygous PKD1 mutation; another fetus with DYNC2H1 compound heterozygous missense mutations showed mainly kidney dysplasia instead of skeletal abnormalities; and a novel PKD1 mutation, c.12445-3C > G, was confirmed to cause two wrong splicing modes. As for previously reported mutations, such as PKD1, c.6395 T > G (p.F2132C) and c.6868G > T (p.D2290Y), we had new and different findings. CONCLUSION The findings provided new references for genotype-phenotype analyses and broadened the mutation spectrum of detected genes, which were significantly valuable for prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Nana Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Xuanyu Jiang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Lanlan Zeng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China.
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China.
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36
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Affiliation(s)
- Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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37
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Parisi MA. The molecular genetics of Joubert syndrome and related ciliopathies: The challenges of genetic and phenotypic heterogeneity. ACTA ACUST UNITED AC 2019; 4:25-49. [PMID: 31763177 PMCID: PMC6864416 DOI: 10.3233/trd-190041] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Joubert syndrome (JS; MIM PS213300) is a rare, typically autosomal recessive disorder characterized by cerebellar vermis hypoplasia and a distinctive malformation of the cerebellum and brainstem identified as the “molar tooth sign” on brain MRI. Other universal features include hypotonia with later ataxia and intellectual disability/developmental delay, with additional features consisting of oculomotor apraxia and abnormal respiratory pattern. Notably, other, more variable features include renal cystic disease, typically nephronophthisis, retinal dystrophy, and congenital hepatic fibrosis; skeletal changes such as polydactyly and findings consistent with short-rib skeletal dysplasias are also seen in many subjects. These pleiotropic features are typical of a number of disorders of the primary cilium, and make the identification of causal genes challenging given the significant overlap between JS and other ciliopathy conditions such as nephronophthisis and Meckel, Bardet-Biedl, and COACH syndromes. This review will describe the features of JS, characterize the 35 known genes associated with the condition, and describe some of the genetic conundrums of JS, such as the heterogeneity of founder effects, lack of genotype-phenotype correlations, and role of genetic modifiers. Finally, aspects of JS and related ciliopathies that may pave the way for development of therapeutic interventions, including gene therapy, will be described.
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Affiliation(s)
- Melissa A Parisi
- Chief, Intellectual & Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
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Fujita A, Higashijima T, Shirozu H, Masuda H, Sonoda M, Tohyama J, Kato M, Nakashima M, Tsurusaki Y, Mitsuhashi S, Mizuguchi T, Takata A, Miyatake S, Miyake N, Fukuda M, Kameyama S, Saitsu H, Matsumoto N. Pathogenic variants of DYNC2H1, KIAA0556, and PTPN11 associated with hypothalamic hamartoma. Neurology 2019; 93:e237-e251. [PMID: 31197031 DOI: 10.1212/wnl.0000000000007774] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/04/2019] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE Intensive genetic analysis was performed to reveal comprehensive molecular insights into hypothalamic hamartoma (HH). METHODS Thirty-eight individuals with HH were investigated by whole exome sequencing, target capture-based deep sequencing, or single nucleotide polymorphism (SNP) array using DNA extracted from blood leukocytes or HH samples. RESULTS We identified a germline variant of KIAA0556, which encodes a ciliary protein, and 2 somatic variants of PTPN11, which forms part of the RAS/mitogen-activated protein kinase (MAPK) pathway, as well as variants in known genes associated with HH. An SNP array identified (among 3 patients) one germline copy-neutral loss of heterozygosity (cnLOH) at 6p22.3-p21.31 and 2 somatic cnLOH; one at 11q12.2-q25 that included DYNC2H1, which encodes a ciliary motor protein, and the other at 17p13.3-p11.2. A germline heterozygous variant and an identical somatic variant of DYNC2H1 arising from cnLOH at 11q12.2-q25 were confirmed in one patient (whose HH tissue, therefore, contains biallelic variants of DYNC2H1). Furthermore, a combination of a germline and a somatic DYNC2H1 variant was detected in another patient. CONCLUSIONS Overall, our cohort identified germline/somatic alterations in 34% (13/38) of patients with HH. Disruption of the Shh signaling pathway associated with cilia or the RAS/MAPK pathway may lead to the development of HH.
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Affiliation(s)
- Atsushi Fujita
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takefumi Higashijima
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Shirozu
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Masuda
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Masaki Sonoda
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Jun Tohyama
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mitsuhiro Kato
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mitsuko Nakashima
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshinori Tsurusaki
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Satomi Mitsuhashi
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takeshi Mizuguchi
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Atsushi Takata
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Satoko Miyatake
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriko Miyake
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Masafumi Fukuda
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Shigeki Kameyama
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hirotomo Saitsu
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan
| | - Naomichi Matsumoto
- From the Departments of Human Genetics (A.F., S. Mitsuhashi, T.M., A.T., S. Miyatake, N. Miyake, N. Matsumoto) and Neurosurgery (M.S.), Yokohama City University Graduate School of Medicine; Departments of Functional Neurosurgery (T.H., H. Shirozu, H.M., M.F., S.K.) and Child Neurology (J.T.), Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital Niigata, Japan; Department of Pediatrics and Neurology (M.S.), Wayne State University, Children's Hospital of Michigan, Detroit Medical Center; Department of Pediatrics (M.K.), Showa University School of Medicine, Tokyo; Department of Biochemistry (M.N., H. Saitsu), Hamamatsu University School of Medicine; and Clinical Research Institute (Y.T.), Kanagawa Children's Medical Center, Yokohama, Japan.
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39
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King A, Hoch NC, McGregor NE, Sims NA, Smyth IM, Heierhorst J. Dynll1 is essential for development and promotes endochondral bone formation by regulating intraflagellar dynein function in primary cilia. Hum Mol Genet 2019; 28:2573-2588. [DOI: 10.1093/hmg/ddz083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/18/2019] [Accepted: 04/15/2019] [Indexed: 01/15/2023] Open
Abstract
AbstractMutations in subunits of the cilia-specific cytoplasmic dynein-2 (CD2) complex cause short-rib thoracic dystrophy syndromes (SRTDs), characterized by impaired bone growth and life-threatening perinatal respiratory complications. Different SRTD mutations result in varying disease severities. It remains unresolved whether this reflects the extent of retained hypomorphic protein functions or relative importance of the affected subunits for the activity of the CD2 holoenzyme. To define the contribution of the LC8-type dynein light chain subunit to the CD2 complex, we have generated Dynll1-deficient mouse strains, including the first-ever conditional knockout (KO) mutant for any CD2 subunit. Germline Dynll1 KO mice exhibit a severe ciliopathy-like phenotype similar to mice lacking another CD2 subunit, Dync2li1. Limb mesoderm-specific loss of Dynll1 results in severe bone shortening similar to human SRTD patients. Mechanistically, loss of Dynll1 leads to a partial depletion of other SRTD-related CD2 subunits, severely impaired retrograde intra-flagellar transport, significant thickening of primary cilia and cilia signaling defects. Interestingly, phenotypes of Dynll1-deficient mice are very similar to entirely cilia-deficient Kif3a/Ift88-null mice, except that they never present with polydactyly and retain relatively higher signaling outputs in parts of the hedgehog pathway. Compared to complete loss of Dynll1, maintaining very low DYNLL1 levels in mice lacking the Dynll1-transcription factor ASCIZ (ATMIN) results in significantly attenuated phenotypes and improved CD2 protein levels. The results suggest that primary cilia can maintain some functionality in the absence of intact CD2 complexes and provide a viable animal model for the analysis of the underlying bone development defects of SRTDs.
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Affiliation(s)
- Ashleigh King
- St. Vincent’s Institute of Medical Research
- Department of Medicine at St. Vincent’s Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, Victoria, Australia
| | | | | | - Natalie A Sims
- St. Vincent’s Institute of Medical Research
- Department of Medicine at St. Vincent’s Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, Victoria, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jörg Heierhorst
- St. Vincent’s Institute of Medical Research
- Department of Medicine at St. Vincent’s Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, Victoria, Australia
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40
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Wheway G, Mitchison HM. Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project. Front Genet 2019; 10:127. [PMID: 30915099 PMCID: PMC6421331 DOI: 10.3389/fgene.2019.00127] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/05/2019] [Indexed: 01/11/2023] Open
Abstract
Cilia are highly specialized cellular organelles that serve multiple functions in human development and health. Their central importance in the body is demonstrated by the occurrence of a diverse range of developmental disorders that arise from defects of cilia structure and function, caused by a range of different inherited mutations found in more than 150 different genes. Genetic analysis has rapidly advanced our understanding of the cell biological basis of ciliopathies over the past two decades, with more recent technological advances in genomics rapidly accelerating this progress. The 100,000 Genomes Project was launched in 2012 in the UK to improve diagnosis and future care for individuals affected by rare diseases like ciliopathies, through whole genome sequencing (WGS). In this review we discuss the potential promise and medical impact of WGS for ciliopathies and report on current progress of the 100,000 Genomes Project, reviewing the medical, technical and ethical challenges and opportunities that new, large scale initiatives such as this can offer.
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Affiliation(s)
- Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Hannah M. Mitchison
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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41
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Wehrle A, Witkos TM, Unger S, Schneider J, Follit JA, Hermann J, Welting T, Fano V, Hietala M, Vatanavicharn N, Schoner K, Spranger J, Schmidts M, Zabel B, Pazour GJ, Bloch-Zupan A, Nishimura G, Superti-Furga A, Lowe M, Lausch E. Hypomorphic mutations of TRIP11 cause odontochondrodysplasia. JCI Insight 2019; 4:124701. [PMID: 30728324 PMCID: PMC6413787 DOI: 10.1172/jci.insight.124701] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/20/2018] [Indexed: 12/24/2022] Open
Abstract
Odontochondrodysplasia (ODCD) is an unresolved genetic disorder of skeletal and dental development. Here, we show that ODCD is caused by hypomorphic TRIP11 mutations, and we identify ODCD as the nonlethal counterpart to achondrogenesis 1A (ACG1A), the known null phenotype in humans. TRIP11 encodes Golgi-associated microtubule-binding protein 210 (GMAP-210), an essential tether protein of the Golgi apparatus that physically interacts with intraflagellar transport 20 (IFT20), a component of the ciliary intraflagellar transport complex B. This association and extraskeletal disease manifestations in ODCD point to a cilium-dependent pathogenesis. However, our functional studies in patient-derived primary cells clearly support a Golgi-based disease mechanism. In spite of reduced abundance, residual GMAP variants maintain partial Golgi integrity, normal global protein secretion, and subcellular distribution of IFT20 in ODCD. These functions are lost when GMAP-210 is completely abrogated in ACG1A. However, a similar defect in chondrocyte maturation is observed in both disorders, which produces a cellular achondrogenesis phenotype of different severity, ensuing from aberrant glycan processing and impaired extracellular matrix proteoglycan secretion by the Golgi apparatus. Bi-allelic mutations of TRIP11 cause a spectrum of skeletal phenotypes whose severity is primarily based on impaired secretory trafficking and aberrant glycan processing.
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Affiliation(s)
- Anika Wehrle
- Department of Pediatrics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tomasz M Witkos
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Sheila Unger
- Division of Genetic Medicine, University of Lausanne, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Judith Schneider
- Department of Pediatrics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - John A Follit
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Johannes Hermann
- Department of Pediatrics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tim Welting
- Laboratory for Experimental Orthopedics, Department of Orthopaedic Surgery, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Virginia Fano
- Hospital de Pediatria JP Garrahan, Buenos Aires, Argentina
| | - Marja Hietala
- Medical Biochemistry and Genetics, University of Turku, Turku, Finland
| | | | - Katharina Schoner
- Institute of Pathology, Philipps-University Marburg, Marburg, Germany
| | - Jürgen Spranger
- Department of Pediatrics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Schmidts
- Department of Pediatrics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernhard Zabel
- Department of Pediatrics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Agnes Bloch-Zupan
- Centre de Référence des Manifestations Odontologiques des Maladies Rares, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpitaux Universitaires de Strasbourg (HUS), Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Université de Strasbourg, Faculté de Chirurgie Dentaire, Institute of Advanced Studies, USIAS, Strasbourg, France.,HUS, Pôle de Médecine et Chirurgie Bucco-dentaires Hôpital Civil, Centre de référence des maladies rares orales et dentaires, O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network ERN CRANIO, Strasbourg, France.,Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CERBM, INSERM U1258, CNRS- UMR7104, Illkirch, France
| | - Gen Nishimura
- Department of Radiology and Medical Imaging, Tokyo Metropolitan Kiyose Children's Hospital, Kiyose, Japan
| | - Andrea Superti-Furga
- Division of Genetic Medicine, University of Lausanne, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Martin Lowe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Ekkehart Lausch
- Department of Pediatrics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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42
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Marchuk DS, Crooks K, Strande N, Kaiser-Rogers K, Milko LV, Brandt A, Arreola A, Tilley CR, Bizon C, Vora NL, Wilhelmsen KC, Evans JP, Berg JS. Increasing the diagnostic yield of exome sequencing by copy number variant analysis. PLoS One 2018; 13:e0209185. [PMID: 30557390 PMCID: PMC6296659 DOI: 10.1371/journal.pone.0209185] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/01/2018] [Indexed: 01/17/2023] Open
Abstract
As whole exome sequencing (WES) becomes more widely used in the clinical realm, a wealth of unanalyzed information will be routinely generated. Using WES read depth data to predict copy number variation (CNV) could extend the diagnostic utility of this previously underutilized data by providing clinically important information such as previously unsuspected deletions or duplications. We evaluated ExomeDepth, a free R package, in addition to an aneuploidy prediction method, to detect CNVs in WES data. First, in a blinded pilot study, five out of five genomic alterations were correctly identified from clinical samples with previously defined chromosomal gains or losses, including submicroscopic deletions, duplications, and chromosomal trisomy. We then examined CNV calls among 53 patients participating in the NCGENES research study and undergoing WES, who had existing clinical chromosomal microarray (CMA) data that could be used for validation. For unique CNVs that overlap well with WES coverage regions, sensitivity was 89% for deletions and 65% for duplications. While specificity of the algorithm calls remains a concern, this is less of an issue at high threshold filtering levels. When applied to all 672 patients from the exome sequencing study, ExomeDepth identified eleven diagnostically relevant CNVs ranging in size from a two exon deletion to whole chromosome duplications, as well as numerous other CNVs with varying clinical significance. This opportunistic analysis of WES data yields an additional 1.6% of patients in this study with pathogenic or likely pathogenic CNVs that are clinically relevant to their phenotype as well as clinically relevant secondary findings. Finally, we demonstrate the potential value of copy number analysis in cases where a single heterozygous likely or known pathogenic single nucleotide alteration is identified in a gene associated with an autosomal recessive condition.
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Affiliation(s)
- Daniel S. Marchuk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kristy Crooks
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Natasha Strande
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kathleen Kaiser-Rogers
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, United Sates of America
| | - Laura V. Milko
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Alicia Brandt
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Alexandra Arreola
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Christian R. Tilley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, United States of America
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kirk C. Wilhelmsen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, United States of America
| | - James P. Evans
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- * E-mail:
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Jensen VL, Lambacher NJ, Li C, Mohan S, Williams CL, Inglis PN, Yoder BK, Blacque OE, Leroux MR. Role for intraflagellar transport in building a functional transition zone. EMBO Rep 2018; 19:e45862. [PMID: 30429209 PMCID: PMC6280794 DOI: 10.15252/embr.201845862] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 10/22/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
Genetic disorders caused by cilia dysfunction, termed ciliopathies, frequently involve the intraflagellar transport (IFT) system. Mutations in IFT subunits-including IFT-dynein motor DYNC2H1-impair ciliary structures and Hedgehog signalling, typically leading to "skeletal" ciliopathies such as Jeune asphyxiating thoracic dystrophy. Intriguingly, IFT gene mutations also cause eye, kidney and brain ciliopathies often linked to defects in the transition zone (TZ), a ciliary gate implicated in Hedgehog signalling. Here, we identify a C. elegans temperature-sensitive (ts) IFT-dynein mutant (che-3; human DYNC2H1) and use it to show a role for retrograde IFT in anterograde transport and ciliary maintenance. Unexpectedly, correct TZ assembly and gating function for periciliary proteins also require IFT-dynein. Using the reversibility of the novel ts-IFT-dynein, we show that restoring IFT in adults (post-developmentally) reverses defects in ciliary structure, TZ protein localisation and ciliary gating. Notably, this ability to reverse TZ defects declines as animals age. Together, our findings reveal a previously unknown role for IFT in TZ assembly in metazoans, providing new insights into the pathomechanism and potential phenotypic overlap between IFT- and TZ-associated ciliopathies.
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Affiliation(s)
- Victor L Jensen
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Nils J Lambacher
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Swetha Mohan
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Corey L Williams
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham Medical School, Birmingham, AL, USA
| | - Peter N Inglis
- Department of Biology, Kwantlen Polytechnic University, Surrey, BC, Canada
| | - Bradley K Yoder
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham Medical School, Birmingham, AL, USA
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
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Lin H, Guo S, Dutcher SK. RPGRIP1L helps to establish the ciliary gate for entry of proteins. J Cell Sci 2018; 131:jcs220905. [PMID: 30237221 PMCID: PMC6215392 DOI: 10.1242/jcs.220905] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
Mutations in transition zone genes change the composition of the ciliary proteome. We isolated new mutations in RPGRIP1L (denotated as RPG1 in algae) that affect the localization of the transition zone protein NPHP4 in the model organism Chlamydomonas reinhardtii NPHP4 localization is not affected in multiple new intraflagellar transport (IFT) mutants. We compared the proteome of cilia from wild-type and mutants that affect the transition zone (RPGRIP1L) or IFT (IFT172 and DHC1b) by mass spectrometry. The rpg1-1 mutant cilia show the most dramatic increase in cytoplasmic proteins. These nonciliary proteins function in translation, membrane remodeling, ATP production and as chaperonins. These proteins are excluded in isolated cilia from fla11-1 (IFT172) and fla24-1 (DHC1b). Our data support the idea that RPGRIP1L, but not IFT proteins, acts as part of the gate for cytoplasmic proteins. The rpg1-1 cilia lack only a few proteins, which suggests that RPGRIP1L only has a minor role of in the retention of ciliary proteins. The fla11-1 mutant shows the greatest loss/reduction of proteins, and one-third of these proteins have a transmembrane domain. Hence, IFT172 may play a role in the retention of proteins.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Suyang Guo
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA
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Vuolo L, Stevenson NL, Heesom KJ, Stephens DJ. Dynein-2 intermediate chains play crucial but distinct roles in primary cilia formation and function. eLife 2018; 7:39655. [PMID: 30320547 PMCID: PMC6211827 DOI: 10.7554/elife.39655] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/14/2018] [Indexed: 12/16/2022] Open
Abstract
The dynein-2 microtubule motor is the retrograde motor for intraflagellar transport. Mutations in dynein-2 components cause skeletal ciliopathies, notably Jeune syndrome. Dynein-2 contains a heterodimer of two non-identical intermediate chains, WDR34 and WDR60. Here, we use knockout cell lines to demonstrate that each intermediate chain has a distinct role in cilium function. Using quantitative proteomics, we show that WDR34 KO cells can assemble a dynein-2 motor complex that binds IFT proteins yet fails to extend an axoneme, indicating complex function is stalled. In contrast, WDR60 KO cells do extend axonemes but show reduced assembly of dynein-2 and binding to IFT proteins. Both proteins are required to maintain a functional transition zone and for efficient bidirectional intraflagellar transport. Our results indicate that the subunit asymmetry within the dynein-2 complex is matched with a functional asymmetry between the dynein-2 intermediate chains. Furthermore, this work reveals that loss of function of dynein-2 leads to defects in transition zone architecture, as well as intraflagellar transport. Almost all cells in the human body are covered in tiny hair-like structures known as primary cilia. These structures act as antennae to receive signals from outside the cell that regulate how the body grows and develops. The cell has to deliver new proteins and other molecules to precise locations within its cilia to ensure that they work properly. Each cilium is separated from the rest of the cell by a selective barrier known as the transition zone, which controls the movement of molecules to and from the rest of the cell. Dynein-2 is a motor protein that moves other proteins and cell materials within cilia. It includes two subunits known as WDR34 and WDR60. The genes that produce these subunits are mutated in Jeune and short rib polydactyly syndromes that primarily affect how the skeleton forms. However, little is known about the roles the individual subunits play within the motor protein. Vuolo et al. used a gene editing technique called CRISPR-Cas9 to remove one or both of the genes encoding the dynein-2 subunits from human cells. The experiments show that the two subunits have very different roles in cilia. WDR34 is required for cells to build a cilium whereas WDR60 is not. Instead, WDR60 is needed to move proteins and other materials within an established cilium. Unexpectedly, the experiments suggest that dynein-2 is also required to maintain the transition zone. This work provides the foundations for future studies on the role of dynein-2 in building and maintaining the structure of cilia. This could ultimately help to develop new treatments to reduce the symptoms of Jeune syndrome and other diseases caused by defects in cilia.
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Affiliation(s)
- Laura Vuolo
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Nicola L Stevenson
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Kate J Heesom
- Proteomics Facility, Faculty of Biomedical Sciences, University of Bristol, Bristol, United Kingdom
| | - David J Stephens
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, United Kingdom
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Chen CP, Ko TM, Chang TY, Chern SR, Chen SW, Lai ST, Chuang TY, Wang W. Prenatal diagnosis of short-rib polydactyly syndrome type III or short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3) associated with compound heterozygous mutations in DYNC2H1 in a fetus. Taiwan J Obstet Gynecol 2018; 57:123-127. [PMID: 29458881 DOI: 10.1016/j.tjog.2017.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE We present the perinatal imaging findings and molecular genetic analysis in a fetus with short-rib polydactyly syndrome (SRPS) type III or short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3). CASE REPORT A 29-year-old, primigravid woman was referred for genetic counseling at 15 weeks of gestation because of abnormal ultrasound findings of short limbs, a narrow chest and bilateral polydactyly of the hands and feet, consistent with a diagnosis of SRPS type III. Chorionic villus sampling was performed, and targeted next-generation sequencing (NGS) was applied to analyze a panel of 25 genes including CEP120, DYNC2H1, DYNC2LI1, EVC, EVC2, FGFR2, FGFR3, HOXD10, IFT122, IFT140, IFT172, IFT52, IFT80, KIAA0586, NEK1, PAPSS2, SLC26A2, SOX9, TCTEX1D2, TCTN3, TTC21B, WDR19, WDR34, WDR35 and WDR60. The NGS analysis identified novel mutations in the DYNC2H1 gene. The fetus was compound heterozygous for a missense mutation c.8077G > T (p.Asp2693Tyr) of paternal origin in DYNC2H1 and a frameshift mutation c.11741_11742delTT (p.Phe3914X) of maternal origin in DYNC2H1. The fetus had a karyotype of 46,XY, and postnatally manifested characteristic SRPS type III phenotype. CONCLUSION Targeted NGS is useful in genetic diagnosis of fetal skeletal dysplasia and SRPS, and the information acquired is helpful in genetic counseling.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | | | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shih-Ting Lai
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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Chen B, Niu J, Kreuzer J, Zheng B, Jarugumilli GK, Haas W, Wu X. Auto-fatty acylation of transcription factor RFX3 regulates ciliogenesis. Proc Natl Acad Sci U S A 2018; 115:E8403-E8412. [PMID: 30127002 PMCID: PMC6130365 DOI: 10.1073/pnas.1800949115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Defects in cilia have been associated with an expanding human disease spectrum known as ciliopathies. Regulatory Factor X 3 (RFX3) is one of the major transcription factors required for ciliogenesis and cilia functions. In addition, RFX3 regulates pancreatic islet cell differentiation and mature β-cell functions. However, how RFX3 protein is regulated at the posttranslational level remains poorly understood. Using chemical reporters of protein fatty acylation and mass spectrometry analysis, here we show that RFX3 transcriptional activity is regulated by S-fatty acylation at a highly conserved cysteine residue in the dimerization domain. Surprisingly, RFX3 undergoes enzyme-independent, "self-catalyzed" auto-fatty acylation and displays preferences for 18-carbon stearic acid and oleic acid. The fatty acylation-deficient mutant of RFX3 shows decreased homodimerization; fails to promote ciliary gene expression, ciliogenesis, and elongation; and impairs Hedgehog signaling. Our findings reveal a regulation of RFX3 transcription factor and link fatty acid metabolism and protein lipidation to the regulation of ciliogenesis.
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Affiliation(s)
- Baoen Chen
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Jixiao Niu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Baohui Zheng
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Gopala K Jarugumilli
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129;
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Mellis R, Chandler N, Chitty LS. Next-generation sequencing and the impact on prenatal diagnosis. Expert Rev Mol Diagn 2018; 18:689-699. [PMID: 29962246 DOI: 10.1080/14737159.2018.1493924] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION The advent of affordable and rapid next-generation sequencing has been transformative for prenatal diagnosis. Sequencing of cell-free DNA in maternal plasma has enabled the development of not only a highly sensitive screening test for fetal aneuploidies, but now definitive noninvasive prenatal diagnosis for monogenic disorders at an early gestation. Sequencing of fetal exomes offers broad diagnostic capability for pregnancies with unexpected fetal anomalies, improving the yield and accuracy of diagnoses and allowing better counseling for parents. The challenge now is to translate these approaches into mainstream use in the clinic. Areas covered: Here, the authors review the current literature to describe the technologies available and how these have evolved. The opportunities and challenges at hand, including considerations for service delivery, counseling, and development of ethical guidelines, are discussed. Expert commentary: As technology continues to advance, future developments may be toward noninvasive fetal whole exome or whole genome sequencing and a universal method for noninvasive prenatal diagnosis without the need to sequence both parents or an affected proband. Expansion of cell-free fetal DNA analysis to include the transcriptome and the methylome is likely to yield clinical benefits for monitoring other pregnancy-related pathologies such as preeclampsia and intrauterine growth restriction.
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Affiliation(s)
- Rhiannon Mellis
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK
| | - Natalie Chandler
- b North Thames NHS Regional Genetics Service , Great Ormond Street NHS Foundation Trust , London , UK
| | - Lyn S Chitty
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK.,c Genetics and Genomic Medicine , UCL Great Ormond Street Institute of Child Health , London , UK
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Neurocristopathies: New insights 150 years after the neural crest discovery. Dev Biol 2018; 444 Suppl 1:S110-S143. [PMID: 29802835 DOI: 10.1016/j.ydbio.2018.05.013] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/12/2022]
Abstract
The neural crest (NC) is a transient, multipotent and migratory cell population that generates an astonishingly diverse array of cell types during vertebrate development. These cells, which originate from the ectoderm in a region lateral to the neural plate in the neural fold, give rise to neurons, glia, melanocytes, chondrocytes, smooth muscle cells, odontoblasts and neuroendocrine cells, among others. Neurocristopathies (NCP) are a class of pathologies occurring in vertebrates, especially in humans that result from the abnormal specification, migration, differentiation or death of neural crest cells during embryonic development. Various pigment, skin, thyroid and hearing disorders, craniofacial and heart abnormalities, malfunctions of the digestive tract and tumors can also be considered as neurocristopathies. In this review we revisit the current classification and propose a new way to classify NCP based on the embryonic origin of the affected tissues, on recent findings regarding the molecular mechanisms that drive NC formation, and on the increased complexity of current molecular embryology techniques.
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50
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Oud MM, Latour BL, Bakey Z, Letteboer SJ, Lugtenberg D, Wu KM, Cornelissen EAM, Yntema HG, Schmidts M, Roepman R, Bongers EMHF. Cellular ciliary phenotyping indicates pathogenicity of novel variants in IFT140 and confirms a Mainzer-Saldino syndrome diagnosis. Cilia 2018; 7:1. [PMID: 30479745 PMCID: PMC6247778 DOI: 10.1186/s13630-018-0055-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 01/27/2018] [Indexed: 11/14/2022] Open
Abstract
Background Mainzer–Saldino syndrome (MZSDS) is a skeletal ciliopathy and part of the short-rib thoracic dysplasia (SRTD) group of ciliary disorders. The main characteristics of MZSDS are short limbs, mild narrow thorax, blindness, and renal failure. Thus far, variants in two genes are associated with MZSDS: IFT140, and IFT172. In this study, we describe a 1-year-old girl presenting with mild skeletal abnormalities, Leber congenital amaurosis, and bilateral hearing difficulties. For establishing an accurate diagnosis, we combined clinical, molecular, and functional analyses. Methods We performed diagnostic whole-exome sequencing (WES) analysis to determine the genetic cause of the disease and analyzed two gene panels, containing all currently known genes in vision disorders, and in hearing impairment. Upon detection of the likely causative variants, ciliary phenotyping was performed in patient urine-derived renal epithelial cells (URECs) and rescue experiments were performed in CRISPR/Cas9-derived Ift140 knock out cells to determine the pathogenicity of the detected variants in vitro. Cilium morphology, cilium length, and intraflagellar transport (IFT) were evaluated by immunocytochemistry. Results Diagnostic WES revealed two novel compound heterozygous variants in IFT140, encoding IFT140. Thorough investigation of WES data did not reveal any variants in candidate genes associated with hearing impairment. Patient-derived URECs revealed an accumulation of IFT-B protein IFT88 at the ciliary tip in 41% of the cells indicative of impaired retrograde IFT, while this was absent in cilia from control URECs. Furthermore, transfection of CRISPR/Cas9-derived Ift140 knock out cells with an IFT140 construct containing the patient mutation p.Tyr923Asp resulted in a significantly higher percentage of IFT88 tip accumulation than transfection with the wild-type IFT140 construct. Conclusions By combining the clinical, genetic, and functional data from this study, we could conclude that the patient has SRTD9, also called Mainzer–Saldino syndrome, caused by variants in IFT140. We suggest the possibility that variants in IFT140 may underlie hearing impairment. Moreover, we show that urine provides an excellent source to obtain patient-derived cells in a non-invasive manner to study the pathogenicity of variants detected by genetic testing. Electronic supplementary material The online version of this article (10.1186/s13630-018-0055-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Machteld M Oud
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,2Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO-Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Brooke L Latour
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,2Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO-Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Zeineb Bakey
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,2Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO-Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Stef J Letteboer
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,2Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO-Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Dorien Lugtenberg
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ka Man Wu
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,2Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO-Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Helger G Yntema
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,4Donders Centre for Neuroscience, Radboud University Medical Center, PO-Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Miriam Schmidts
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,2Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO-Box 9101, 6500 HB, Nijmegen, The Netherlands.,Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Medical Faculty, Freiburg, Germany
| | - Ronald Roepman
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands.,2Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO-Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ernie M H F Bongers
- 1Department of Human Genetics (855), Radboud University Medical Centre, PO-Box 9101, 6500 HB Nijmegen, The Netherlands
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