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Gomes LHF, Marques AB, Dias ICDM, Gabeira SCDO, Barcelos TR, Guimarães MDO, Ferreira IR, Guida LC, Lucena SL, Rocha AD. Validation of Gene Expression Patterns for Oral Feeding Readiness: Transcriptional Analysis of Set of Genes in Neonatal Salivary Samples. Genes (Basel) 2024; 15:936. [PMID: 39062715 PMCID: PMC11275400 DOI: 10.3390/genes15070936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Neonatal health assessment is crucial for detecting and intervening in various disorders. Traditional gene expression analysis methods often require invasive procedures during sample collection, which may not be feasible or ideal for preterm infants. In recent years, saliva has emerged as a promising noninvasive biofluid for assessing gene expression. Another trend that has been growing is the use of "omics" technologies such as transcriptomics in the analysis of gene expression. The costs for carrying out these analyses and the difficulty of analysis make the detection of candidate genes necessary. These genes act as biomarkers for the maturation stages of the oral feeding issue. METHODOLOGY Salivary samples (n = 225) were prospectively collected from 45 preterm (<34 gestational age) infants from five predefined feeding stages and submitted to RT-qPCR. A better description of the targeted genes and results from RT-qPCR analyses were included. The six genes previously identified as predictive of feeding success were tested. The genes are AMPK, FOXP2, WNT3, NPHP4, NPY2R, and PLXNA1, along with two reference genes: GAPDH and 18S. RT-qPCR amplification enabled the analysis of the gene expression of AMPK, FOXP2, WNT3, NPHP4, NPY2R, and PLXNA1 in neonatal saliva. Expression results were correlated with the feeding status during sample collection. CONCLUSIONS In summary, the genes AMPK, FOXP2, WNT3, NPHP4, NPY2R, and PLXNA1 play critical roles in regulating oral feeding and the development of premature infants. Understanding the influence of these genes can provide valuable insights for improving nutritional care and support the development of these vulnerable babies. Evidence suggests that saliva-based gene expression analysis in newborns holds great promise for early detection and monitoring of disease and understanding developmental processes. More research and standardization of protocols are needed to fully explore the potential of saliva as a noninvasive biomarker in neonatal care.
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Affiliation(s)
- Leonardo Henrique Ferreira Gomes
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Andressa Brito Marques
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Isabel Cristina de Meireles Dias
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Sanny Cerqueira de O. Gabeira
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Tamara Rosa Barcelos
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Mariana de Oliveira Guimarães
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Igor Ribeiro Ferreira
- Rural and Remote Support Services, Department of Health, Integrated Cardiovascular Clinical Network SA, Adelaide, SA 5042, Australia
| | - Letícia Cunha Guida
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Sabrina Lopes Lucena
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
| | - Adriana Duarte Rocha
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil; (L.H.F.G.)
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2
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Faviez C, Chen X, Garcelon N, Zaidan M, Billot K, Petzold F, Faour H, Douillet M, Rozet JM, Cormier-Daire V, Attié-Bitach T, Lyonnet S, Saunier S, Burgun A. Objectivizing issues in the diagnosis of complex rare diseases: lessons learned from testing existing diagnosis support systems on ciliopathies. BMC Med Inform Decis Mak 2024; 24:134. [PMID: 38789985 PMCID: PMC11127295 DOI: 10.1186/s12911-024-02538-8] [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: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND There are approximately 8,000 different rare diseases that affect roughly 400 million people worldwide. Many of them suffer from delayed diagnosis. Ciliopathies are rare monogenic disorders characterized by a significant phenotypic and genetic heterogeneity that raises an important challenge for clinical diagnosis. Diagnosis support systems (DSS) applied to electronic health record (EHR) data may help identify undiagnosed patients, which is of paramount importance to improve patients' care. Our objective was to evaluate three online-accessible rare disease DSSs using phenotypes derived from EHRs for the diagnosis of ciliopathies. METHODS Two datasets of ciliopathy cases, either proven or suspected, and two datasets of controls were used to evaluate the DSSs. Patient phenotypes were automatically extracted from their EHRs and converted to Human Phenotype Ontology terms. We tested the ability of the DSSs to diagnose cases in contrast to controls based on Orphanet ontology. RESULTS A total of 79 cases and 38 controls were selected. Performances of the DSSs on ciliopathy real world data (best DSS with area under the ROC curve = 0.72) were not as good as published performances on the test set used in the DSS development phase. None of these systems obtained results which could be described as "expert-level". Patients with multisystemic symptoms were generally easier to diagnose than patients with isolated symptoms. Diseases easily confused with ciliopathy generally affected multiple organs and had overlapping phenotypes. Four challenges need to be considered to improve the performances: to make the DSSs interoperable with EHR systems, to validate the performances in real-life settings, to deal with data quality, and to leverage methods and resources for rare and complex diseases. CONCLUSION Our study provides insights into the complexities of diagnosing highly heterogenous rare diseases and offers lessons derived from evaluation existing DSSs in real-world settings. These insights are not only beneficial for ciliopathy diagnosis but also hold relevance for the enhancement of DSS for various complex rare disorders, by guiding the development of more clinically relevant rare disease DSSs, that could support early diagnosis and finally make more patients eligible for treatment.
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Affiliation(s)
- Carole Faviez
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France.
- HeKA, Inria Paris, Paris, F-75012, France.
- Universite Paris Cite, Paris, France.
| | - Xiaoyi Chen
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France
- HeKA, Inria Paris, Paris, F-75012, France
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Nicolas Garcelon
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France
- HeKA, Inria Paris, Paris, F-75012, France
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Mohamad Zaidan
- Service de Néphrologie, Dialyse et Transplantation, Hôpital Universitaire Bicêtre, Assistance Publique-Hôpitaux de Paris (AP-HP), Kremlin Bicêtre, F-94270, France
| | - Katy Billot
- Laboratory of Renal Hereditary Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
| | - Friederike Petzold
- Laboratory of Renal Hereditary Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Hassan Faour
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Maxime Douillet
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
| | - Valérie Cormier-Daire
- Reference Centre for Constitutional Bone Diseases, laboratory of Osteochondrodysplasia, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
| | - Tania Attié-Bitach
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
| | - Stanislas Lyonnet
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris Cité, Paris, F-75015, France
| | - Sophie Saunier
- Laboratory of Renal Hereditary Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
| | - Anita Burgun
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France
- HeKA, Inria Paris, Paris, F-75012, France
- Department of Medical Informatics, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
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Sekar T, Sebire NJ. Renal Pathology of Ciliopathies. Pediatr Dev Pathol 2024:10935266241242173. [PMID: 38616607 DOI: 10.1177/10935266241242173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Renal ciliopathies are a group of genetic disorders that affect the function of the primary cilium in the kidney, as well as other organs. Since primary cilia are important for regulation of cell signaling pathways, ciliary dysfunction results in a range of clinical manifestations, including renal failure, cyst formation, and hypertension. We summarize the current understanding of the pathophysiological and pathological features of renal ciliopathies in childhood, including autosomal dominant and recessive polycystic kidney disease, nephronophthisis, and Bardet-Biedl syndrome, as well as skeletal dysplasia associated renal ciliopathies. The genetic basis of these disorders is now well-established in many cases, with mutations in a large number of cilia-related genes such as PKD1, PKD2, BBS, MKS, and NPHP being responsible for the majority of cases. Renal ciliopathies are broadly characterized by development of interstitial fibrosis and formation of multiple renal cysts which gradually enlarge and replace normal renal tissue, with each condition demonstrating subtle differences in the degree, location, and age-related development of cysts and fibrosis. Presentation varies from prenatal diagnosis of congenital multisystem syndromes to an asymptomatic childhood with development of complications in later adulthood and therefore clinicopathological correlation is important, including increasing use of targeted genetic testing or whole genome sequencing, allowing greater understanding of genetic pathophysiological mechanisms.
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Affiliation(s)
- Thivya Sekar
- Histopathology Department, Level 3 CBL Labs, Great Ormond Street Hospital, London, UK
| | - Neil J Sebire
- Histopathology Department, Level 3 CBL Labs, Great Ormond Street Hospital, London, UK
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Che R, Wang C, Huang S, Zheng B, Li H, Cheng X, Zhao F, Ding G, Jia Z, Zhang A. The identification of a novel CCNQ gene tail extension variant contributing to syndactyly, telecanthus and anogenital and renal malformations syndrome. Clin Genet 2023; 103:179-189. [PMID: 36284407 DOI: 10.1111/cge.14255] [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: 04/25/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 01/07/2023]
Abstract
The "toe syndactyly, telecanthus and anogenital and renal malformations" (STAR) syndrome is a rare X-linked dominant inherited kidney ciliopathy caused by CCNQ gene mutations. Here, we investigated the genotype and phenotype in the first two twin sisters with a novel tail extension CCNQ variant in Asia. Genetic variants of the pedigree were screened using whole-exome sequence analysis and validated by direct Sanger sequencing. The genetic function was investigated through cultured cells and zebrafish embryos transfected with mutant. The proband is suffered from end-stage renal disease, telecanthus, scoliosis, anal atresia, bilateral hydronephrosis pyeloureter dilation and hearing loss, while her twin sister had milder phenotypes. A novel heterozygous variant c.502_518delinsA (p.Val168SerfsTer173) in CCNQ gene was identified in the twins and their asymptomatic mosaic mother. The concurrent deletion of 17 bases and insertion of one base variant led to the loss of 5 amino acids, subsequently caused a 96 more amino acids tail extension delaying the appearance of stop codon. The loss-of-function variant of CCNQ not only led to the impaired expression of cyclin M but also increased the binding affinity of CDK10-cyclin M complex, which is different from the previous study. The research expanded the genotypic and phenotypic spectrum of STAR syndrome.
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Affiliation(s)
- Ruochen Che
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Songming Huang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Huixia Li
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xueqin Cheng
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Fei Zhao
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Guixia Ding
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zhanjun Jia
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Aihua Zhang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
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5
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Gjerstad AC, Skrunes R, Tøndel C, Åsberg A, Leh S, Klingenberg C, Døllner H, Hammarstrøm C, Bjerre AK. Kidney biopsy diagnosis in childhood in the Norwegian Kidney Biopsy Registry and the long-term risk of kidney replacement therapy: a 25-year follow-up. Pediatr Nephrol 2023; 38:1249-1256. [PMID: 35994104 PMCID: PMC9925570 DOI: 10.1007/s00467-022-05706-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND There is scarce information on biopsy-verified kidney disease in childhood and its progression to chronic kidney disease stage 5 (CKD 5). This study aims to review biopsy findings in children, and to investigate risk of kidney replacement therapy (KRT). METHODS We conducted a retrospective long-term follow-up study of children included in the Norwegian Kidney Biopsy Registry (NKBR) and in the Norwegian Renal Registry (NRR) from 1988 to 2021. RESULTS In total, 575 children with a median (interquartile range, IQR) age of 10.7 (6.1 to 14.1) years were included, and median follow-up time (IQR) after kidney biopsy was 14.3 (range 8.9 to 21.6) years. The most common biopsy diagnoses were minimal change disease (MCD; n = 92), IgA vasculitis nephritis (IgAVN; n = 76), IgA nephropathy (n = 63), and focal and segmental glomerulosclerosis (FSGS; n = 47). In total, 118 (20.5%) of the biopsied children reached CKD 5, median (IQR) time to KRT 2.3 years (7 months to 8.4 years). Most frequently, nephronophthisis (NPHP; n = 16), FSGS (n = 30), IgA nephropathy (n = 9), and membranoproliferative glomerulonephritis (MPGN; n = 9) led to KRT. CONCLUSIONS The risk of KRT after a kidney biopsy diagnosis is highly dependent on the diagnosis. None of the children with MCD commenced KRT, while 63.8% with FSGS and 100% with NPHP reached KRT. Combining data from kidney biopsy registries with registries on KRT allows for detailed information concerning the risk for later CKD 5 after biopsy-verified kidney disease in childhood. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Ann Christin Gjerstad
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.
| | - Rannveig Skrunes
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Camilla Tøndel
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Anders Åsberg
- The Norwegian Renal Registry, Oslo University Hospital - Rikshospitalet, Oslo, Norway
- Department of Transplantation Medicine, Oslo University Hospital - Rikshospitalet, Oslo, Norway
- Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Claus Klingenberg
- Department of Pediatrics and Adolescence Medicine, University Hospital of North Norway, Tromsø, Norway
- Paediatric Research Group, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Henrik Døllner
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Children's Clinic, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Clara Hammarstrøm
- Department of Pathology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Anna Kristina Bjerre
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Higgins K, Moore BA, Berberovic Z, Adissu HA, Eskandarian M, Flenniken AM, Shao A, Imai DM, Clary D, Lanoue L, Newbigging S, Nutter LMJ, Adams DJ, Bosch F, Braun RE, Brown SDM, Dickinson ME, Dobbie M, Flicek P, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Chin HJG, Mammano F, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, Lloyd KCK, McKerlie C, Moshiri A. Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes. Sci Rep 2022; 12:20791. [PMID: 36456625 PMCID: PMC9715561 DOI: 10.1038/s41598-022-19710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/02/2022] [Indexed: 12/05/2022] Open
Abstract
We searched a database of single-gene knockout (KO) mice produced by the International Mouse Phenotyping Consortium (IMPC) to identify candidate ciliopathy genes. We first screened for phenotypes in mouse lines with both ocular and renal or reproductive trait abnormalities. The STRING protein interaction tool was used to identify interactions between known cilia gene products and those encoded by the genes in individual knockout mouse strains in order to generate a list of "candidate ciliopathy genes." From this list, 32 genes encoded proteins predicted to interact with known ciliopathy proteins. Of these, 25 had no previously described roles in ciliary pathobiology. Histological and morphological evidence of phenotypes found in ciliopathies in knockout mouse lines are presented as examples (genes Abi2, Wdr62, Ap4e1, Dync1li1, and Prkab1). Phenotyping data and descriptions generated on IMPC mouse line are useful for mechanistic studies, target discovery, rare disease diagnosis, and preclinical therapeutic development trials. Here we demonstrate the effective use of the IMPC phenotype data to uncover genes with no previous role in ciliary biology, which may be clinically relevant for identification of novel disease genes implicated in ciliopathies.
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Affiliation(s)
- Kendall Higgins
- The University of Miami Leonard M. Miller School of Medicine, Miami, FL, 33136, USA
| | - Bret A Moore
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, Gainesville, FL, 32608, USA
| | - Zorana Berberovic
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | | | - Mohammad Eskandarian
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Andy Shao
- University of Reno, Nevada, School of Medicine, Reno, NV, 89557, USA
| | - Denise M Imai
- Comparative Pathology Laboratory, U.C. Davis, Davis, 95616, USA
| | - Dave Clary
- Mouse Biology Program, U.C. Davis, Davis, CA, 95618, USA
| | - Louise Lanoue
- Mouse Biology Program, U.C. Davis, Davis, CA, 95618, USA
| | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fatima Bosch
- Centre of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | | | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Mary E Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael Dobbie
- Phenomics Australia, The Australian National University, 131 Garran Rd, Acton, Canberra, ACT, 2601, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | - Sanjeev Galande
- Indian Institutes of Science Education and Research, Dr. Homi Bhabha Rd, Ward No. 8, NCL Colony, Pashan, Pune, Maharashtra, 411008, India
| | - Anne Grobler
- Faculty of Health Sciences, PCDDP North-West University, North-West University Potchefstroom Campus 11 Hoffman Street, Potchefstroom, 2531, South Africa
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67400, Illkirch, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, Université of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Hsian-Jean Genie Chin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), 3F., No. 106, Sec. 2, Heping E. Rd., Da'an Dist., Taipei City, 106214, Taiwan (R.O.C.)
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via Ramarini, 00015, Monterotondo Scalo, Italy
| | - Chuan Qin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), Beijing, China
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Science, 5 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | | | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, IMG BIOCEV Building SO.02 Prumyslova 595, 252 50, Vestec, Czech Republic
| | - J-K Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul, 08826, South Korea
| | - Ying Xu
- CAM-SU Genomic Resource Center, Soochow University, Organization Planning of No. 1 Shizi Street, Suzhou, 215123, China
| | - K C Kent Lloyd
- Mouse Biology Program, U.C. Davis, Davis, CA, 95618, USA
- Department of Surgery, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA
| | - Colin McKerlie
- The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
- Department of Laboratory Medicine and Pathobiology, Hospital for Sick Children (SickKids), The Centre for Phenogenomics, Faculty of Medicine, University of Toronto, 25 Orde Street, Toronto, ON, M5T 3H7, USA.
| | - Ala Moshiri
- Department of Ophthalmology and Vision Science, School of Medicine, U.C. Davis Eye Center, 4860 Y. Street, Suite 2400, Sacramento, CA, 95817, USA.
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7
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Mascibroda LG, Shboul M, Elrod ND, Colleaux L, Hamamy H, Huang KL, Peart N, Singh MK, Lee H, Merriman B, Jodoin JN, Sitaram P, Lee LA, Fathalla R, Al-Rawashdeh B, Ababneh O, El-Khateeb M, Escande-Beillard N, Nelson SF, Wu Y, Tong L, Kenney LJ, Roy S, Russell WK, Amiel J, Reversade B, Wagner EJ. INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex. Nat Commun 2022; 13:6054. [PMID: 36229431 PMCID: PMC9559116 DOI: 10.1038/s41467-022-33547-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/22/2022] [Indexed: 12/24/2022] Open
Abstract
Oral-facial-digital (OFD) syndromes are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. Mutations within 12 cilia-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline variants in INTS13, a subunit of the Integrator complex. This multiprotein complex associates with RNA Polymerase II and cleaves nascent RNA to modulate gene expression. We determined that INTS13 utilizes its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline variants p.S652L and p.K668Nfs*9. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos leads to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions between components of the Integrator complex.
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Affiliation(s)
- Lauren G Mascibroda
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA
| | - Mohammad Shboul
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA
| | - Laurence Colleaux
- Inserm UMR 1163, Institut Imagine, 24 Boulevard du Montparnasse, 75015, Paris, France
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University Hospital, Geneva, Switzerland
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine Dentistry, Rochester, NY, 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine Dentistry, Rochester, NY, 14642, USA
| | - Natoya Peart
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA
| | - Moirangthem Kiran Singh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- 3billion, Inc., Seoul, South Korea
| | - Barry Merriman
- Department of Pathology and Laboratory Medicine, Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Jeanne N Jodoin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Poojitha Sitaram
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Laura A Lee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Raja Fathalla
- National Center for Diabetes, Endocrinology and Genetics, Amman, Jordan
| | - Baeth Al-Rawashdeh
- Faculty of Medicine, Hospital of the University of Jordan, University of Jordan, Amman, Jordan
| | - Osama Ababneh
- Faculty of Medicine, Hospital of the University of Jordan, University of Jordan, Amman, Jordan
| | | | - Nathalie Escande-Beillard
- Department of Medical Genetics, KOÇ University, Istanbul, Turkey
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Yixuan Wu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Linda J Kenney
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Department of Paediatrics, School of Medicine, NUS, Singapore, Singapore
- Department of Biological Sciences, Faculty of Science, NUS, Singapore, Singapore
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA
| | - Jeanne Amiel
- Service de Génétique, Institut Imagine, 24 Boulevard du Montparnasse, 75015, Paris, France
| | - Bruno Reversade
- Department of Medical Genetics, KOÇ University, Istanbul, Turkey.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Department of Paediatrics, School of Medicine, NUS, Singapore, Singapore.
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, 137673, Singapore.
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77550, USA.
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine Dentistry, Rochester, NY, 14642, USA.
- Center for RNA Biology, University of Rochester School of Medicine Dentistry, Rochester, NY, 14642, USA.
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8
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Pleeging R, Ibis F, Fan D, Sasso L, Eral H, Staufer U. Polymer nano manufacturing of a biomimicking surface for kidney stone crystallization studies. MICRO AND NANO ENGINEERING 2021. [DOI: 10.1016/j.mne.2021.100094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Brndiarova M, Mraz M, Kolkova Z, Cisarik F, Banovcin P. Sensenbrenner Syndrome Presenting with Severe Anorexia, Failure to Thrive, Chronic Kidney Disease and Angel-Shaped Middle Phalanges in Two Siblings. Mol Syndromol 2021; 12:263-267. [PMID: 34421506 DOI: 10.1159/000515645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/02/2021] [Indexed: 01/03/2023] Open
Abstract
Sensenbrenner syndrome is a very rare autosomal recessive disorder caused by variants in genes involved in the functional development of primary cilia. Typical clinical manifestations include craniofacial and skeletal abnormalities, hence the alternative name cranioectodermal dysplasia. Chronic kidney disease due to progressive tubulointerstitial nephritis (nephronophthisis) has been described in these patients. The authors present 2siblings with severe anorexia, failure to thrive, chronic kidney disease, and angel-shaped middle phalanges. Two previously described variants p.(Leu641*) and p.(Asp841Val) were identified in the WDR35 gene which is most commonly affected in this condition. Analysis of all coding exons of the GDF5 gene was normal. This is the first report of Sensenbrenner syndrome presenting with severe anorexia and failure to thrive at early age. Angel-shaped middle phalanges in the absence of the GDF5 variant may represent an overlapping phenotypic manifestation of ciliopathy.
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Affiliation(s)
- Miroslava Brndiarova
- Department of Paediatrics, Jessenius Faculty of Medicine of Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
| | - Martin Mraz
- Department of Paediatric and Adolescent Medicine, Children's University Hospital, Kosice, Slovakia
| | - Zuzana Kolkova
- Biomedical Center, Jessenius Faculty of Medicine of Comenius University in Bratislava, Bratislava, Slovakia
| | - Frantisek Cisarik
- Department of Genetics, University Hospital in Zilina, Zilina, Slovakia
| | - Peter Banovcin
- Department of Paediatrics, Jessenius Faculty of Medicine of Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
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10
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Molecular genetics of renal ciliopathies. Biochem Soc Trans 2021; 49:1205-1220. [PMID: 33960378 DOI: 10.1042/bst20200791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022]
Abstract
Renal ciliopathies are a heterogenous group of inherited disorders leading to an array of phenotypes that include cystic kidney disease and renal interstitial fibrosis leading to progressive chronic kidney disease and end-stage kidney disease. The renal tubules are lined with epithelial cells that possess primary cilia that project into the lumen and act as sensory and signalling organelles. Mutations in genes encoding ciliary proteins involved in the structure and function of primary cilia cause ciliopathy syndromes and affect many organ systems including the kidney. Recognised disease phenotypes associated with primary ciliopathies that have a strong renal component include autosomal dominant and recessive polycystic kidney disease and their various mimics, including atypical polycystic kidney disease and nephronophthisis. The molecular investigation of inherited renal ciliopathies often allows a precise diagnosis to be reached where renal histology and other investigations have been unhelpful and can help in determining kidney prognosis. With increasing molecular insights, it is now apparent that renal ciliopathies form a continuum of clinical phenotypes with disease entities that have been classically described as dominant or recessive at both extremes of the spectrum. Gene-dosage effects, hypomorphic alleles, modifier genes and digenic inheritance further contribute to the genetic complexity of these disorders. This review will focus on recent molecular genetic advances in the renal ciliopathy field with a focus on cystic kidney disease phenotypes and the genotypes that lead to them. We discuss recent novel insights into underlying disease mechanisms of renal ciliopathies that might be amenable to therapeutic intervention.
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11
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Brndiarova M, Kvassayova J, Vojtkova J, Igaz M, Buday T, Plevkova J. Changes of Motile Ciliary Phenotype in Patients with Primary Ciliopathies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1335:79-85. [PMID: 33687727 DOI: 10.1007/5584_2021_617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Primary ciliopathies are a group of disorders associated with abnormal formation and function of primary cilia. Many cilia-associated proteins found in primary cilia are also present in motile cilia. Such proteins are important for the ciliary base, such as the transition zone or basal bodies, and the intraflagellar transport. Their exact role in the respiratory motile cilia is unsettled. In this prospective clinical single-center study, we investigated the hypothesis that these proteins regulate the function of motile cilia. We addressed the issue by defining the motile cilia beat frequency in the respiratory tract of patients with primary ciliopathies accompanied by chronic kidney disease and comparing it in those without kidney involvement. Ciliary beat frequency in the nasal mucosa samples was evaluated by the ciliary analysis software LabVIEW. Both children and their parents with primary ciliopathies and kidney involvement had significantly lower median airway ciliary beat frequencies than those without kidney involvement who have normal ciliary motility. Further, the ciliary beat frequency is inversely associated with the serum creatinine level. These findings strongly suggest that kidney involvement in patients with primary ciliopathy may underlie the development of motile cilia dysfunction in the respiratory tract, potentially increasing respiratory morbidity.
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Affiliation(s)
- Miroslava Brndiarova
- Department of Pediatrics, Jessenius Faculty of Medicine and University Hospital, Comenius University in Bratislava, Martin, Slovakia.
| | - Julia Kvassayova
- Department of Pediatrics, Jessenius Faculty of Medicine and University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Jarmila Vojtkova
- Department of Pediatrics, Jessenius Faculty of Medicine and University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Matus Igaz
- Department of Pediatrics, Jessenius Faculty of Medicine and University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Tomas Buday
- Department of Pathophysiology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Jana Plevkova
- Department of Pathophysiology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
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12
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Santoni M, Piva F, Cimadamore A, Giulietti M, Battelli N, Montironi R, Cosmai L, Porta C. Exploring the Spectrum of Kidney Ciliopathies. Diagnostics (Basel) 2020; 10:E1099. [PMID: 33339422 PMCID: PMC7766105 DOI: 10.3390/diagnostics10121099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022] Open
Abstract
Ciliopathies are a group of multi-organ diseases caused by the disruption of the primary cilium. This event leads to a variety of kidney disorders, including nephronophthisis, renal cystic dysplasia, and renal cell carcinoma (RCC). Primary cilium contributes to the regulation of the cell cycle and protein homeostasis, that is, the balance between protein synthesis and degradation by acting on the ubiquitin-proteasome system, autophagy, and mTOR signaling. Many proteins are involved in renal ciliopathies. In particular, fibrocystin (PKHD1) is involved in autosomal recessive polycystic kidney disease (ARPKD), while polycystin-1 (PKD1) and polycystin-2 (PKD2) are implicated in autosomal dominant polycystic kidney disease (ADPKD). Moreover, primary cilia are associated with essential signaling pathways, such as Hedgehog, Wnt, and Platelet-Derived Growth Factor (PDGF). In this review, we focused on the ciliopathies associated with kidney diseases, exploring genes and signaling pathways associated with primary cilium and the potential role of cilia as therapeutic targets in renal disorders.
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Affiliation(s)
- Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (F.P.); (M.G.)
| | - Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy;
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (F.P.); (M.G.)
| | | | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy;
| | - Laura Cosmai
- Division of Nephrology and Dialysis, ASST Fatebenefratelli-Sacco, Fatebenefratelli Hospital, 20121 Milan, Italy;
| | - Camillo Porta
- Chair of Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari ‘A. Moro’, 70121 Bari, Italy;
- Division of Medical Oncology, A.O.U. ConsorzialePoliclinico di Bari, 70124 Bari, Italy
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13
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Fujii Y, Matsumura H, Shirasu A, Nakakura H, Yamazaki S, Morisada N, Iijima K, Ashida A. Genetic analysis diagnosed Bardet–Biedl syndrome in a patient with a clinical diagnosis of Senior–Løken syndrome. RENAL REPLACEMENT THERAPY 2020. [DOI: 10.1186/s41100-020-00294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Senior–Løken syndrome (SLS) and Bardet–Biedl syndrome (BBS) are ciliopathies. SLS is characterized by retinitis pigmentosa (RP) and familial nephronophthisis, leading to end-stage kidney disease, while BBS is characterized by six major symptoms: RP, polydactyly, obesity, genital abnormalities, learning difficulties, and renal defects. Ciliopathies have been diagnosed on a phenotypic basis, but diagnosis can now be established by genetic testing, using techniques such as next-generation sequencing. Here, we report a patient clinically diagnosed with SLS but diagnosed with BBS 13 years later using next-generation sequencing.
Case presentation
The patient was diagnosed with RP at the age of 6 years. She had some difficulty in social interactions and pre-obesity, but no polydactyly. At the age of 8 years, she was diagnosed with chronic kidney disease, anemia, and liver dysfunction. Kidney and liver biopsy revealed renal tubule cysts, tubule membrane disruption, and liver fibrosis. Therefore, SLS was diagnosed but no NPHP1 mutations were detected. Peritoneal dialysis was started at the age of 9 years, and she underwent kidney transplantation with a graft from her father at the age of 13 years. At the age of 21 years, she again underwent genetic testing for most of the mutations associated with ciliopathy. This revealed a homozygous frameshift mutation in intron 11 of SDCCAG8.
Conclusions
Mutations in SDCCAG8 are known to be causative of SLS and BBS without polydactyly. The fact that the patient had RP, some difficulty in social interactions, pre-obesity, juvenile nephronophthisis, liver fibrosis, bronchial asthma, and otitis media suggested BBS. However, some of these are not specific symptoms for BBS and she had few typical symptoms of BBS. Therefore, a definitive diagnosis of BBS was difficult without genetic analysis. Because many more patients with SDCCAG8 mutations have extrarenal manifestations like the current patient than standard nephronophthisis patients, careful monitoring of extrarenal manifestations is needed to improve patient management.
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Molecular dysregulation of ciliary polycystin-2 channels caused by variants in the TOP domain. Proc Natl Acad Sci U S A 2020; 117:10329-10338. [PMID: 32332171 PMCID: PMC7229662 DOI: 10.1073/pnas.1920777117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genetic variants in PKD2 which encodes for the polycystin-2 ion channel are responsible for many clinical cases of autosomal dominant polycystic kidney disease (ADPKD). Despite our strong understanding of the genetic basis of ADPKD, we do not know how most variants impact channel function. Polycystin-2 is found in organelle membranes, including the primary cilium-an antennae-like structure on the luminal side of the collecting duct. In this study, we focus on the structural and mechanistic regulation of polycystin-2 by its TOP domain-a site with unknown function that is commonly altered by missense variants. We use direct cilia electrophysiology, cryogenic electron microscopy, and superresolution imaging to determine that variants of the TOP domain finger 1 motif destabilizes the channel structure and impairs channel opening without altering cilia localization and channel assembly. Our findings support the channelopathy classification of PKD2 variants associated with ADPKD, where polycystin-2 channel dysregulation in the primary cilia may contribute to cystogenesis.
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Abo El Fotoh WMM, Al-Fiky AF. A Compound Heterozygous Mutation in the Ciliary Gene TTC21B Causes Nephronophthisis Type 12. J Pediatr Genet 2019; 9:198-202. [PMID: 32714622 DOI: 10.1055/s-0039-1700804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/25/2019] [Indexed: 12/31/2022]
Abstract
Nephronophthisis (NPHP) is one of the renal ciliopathies and is also a cystic renal disorder with an autosomal recessive inheritance, which usually progresses to end-stage renal disease (ESRD). It affects children, adolescents, and young adults. In approximately 15% of cases, the features of a ciliopathy syndrome, which include liver fibrosis, skeletal anomalies, retinal abnormalities, and neurodevelopmental delay, will be present. We describe a case of a 2-year-old male child with ESRD on hemodialysis and a family record of a similar condition (his brother). The clinical features of this child are succinctly summarized. The genetic study was conducted using whole exome sequencing. TTC21B mutational variants were detected in our patient who exhibited nephrotic-range proteinuria, focal segmental glomerulosclerosis, and tubulointerstitial lesions that evolved to ESRD. Compound heterozygous mutations, c.626c > t (p.P209L) in exon 6 and c.450 g > a (p.W150Ter) in exon 5, were uncovered. These findings are in line with the description of autosomal recessive NPHP type 12. Both clinical and pathological diagnoses of NPHP are critical, bearing in mind ESRD as well as its related extrarenal defining features. Identification of the pathogenic variants in the TTC21B gene assisted in the successful proof of the clinical diagnosis NPHP12 as well as providing information for formal suitable prenatal counseling.
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Affiliation(s)
| | - Amira Fathy Al-Fiky
- Department of Pediatrics, Faculty of Medicine, Menoufia University Hospitals, Menoufia, Egypt
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Corkins ME, Krneta-Stankic V, Kloc M, McCrea PD, Gladden AB, Miller RK. Divergent roles of the Wnt/PCP Formin Daam1 in renal ciliogenesis. PLoS One 2019; 14:e0221698. [PMID: 31469868 PMCID: PMC6716777 DOI: 10.1371/journal.pone.0221698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/13/2019] [Indexed: 12/16/2022] Open
Abstract
Kidneys are composed of numerous ciliated epithelial tubules called nephrons. Each nephron functions to reabsorb nutrients and concentrate waste products into urine. Defects in primary cilia are associated with abnormal formation of nephrons and cyst formation in a wide range of kidney disorders. Previous work in Xenopus laevis and zebrafish embryos established that loss of components that make up the Wnt/PCP pathway, Daam1 and ArhGEF19 (wGEF) perturb kidney tubulogenesis. Dishevelled, which activates both the canonical and non-canonical Wnt/PCP pathway, affect cilia formation in multiciliated cells. In this study, we investigated the role of the noncanoncial Wnt/PCP components Daam1 and ArhGEF19 (wGEF) in renal ciliogenesis utilizing polarized mammalian kidney epithelia cells (MDCKII and IMCD3) and Xenopus laevis embryonic kidney. We demonstrate that knockdown of Daam1 and ArhGEF19 in MDCKII and IMCD3 cells leads to loss of cilia, and Daam1's effect on ciliogenesis is mediated by the formin-activity of Daam1. Moreover, Daam1 co-localizes with the ciliary transport protein Ift88 and is present in cilia. Interestingly, knocking down Daam1 in Xenopus kidney does not lead to loss of cilia. These data suggests a new role for Daam1 in the formation of primary cilia.
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Affiliation(s)
- Mark E. Corkins
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, Texas, United States of America
| | - Vanja Krneta-Stankic
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genes and Development, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
| | - Malgorzata Kloc
- Houston Methodist, Research Institute, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Pierre D. McCrea
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Andrew B. Gladden
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Rachel K. Miller
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Biochemistry & Cell Biology, Houston, Texas, United States of America
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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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18
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Comparative transcriptomics of shear stress treated Pkd1−/− cells and pre-cystic kidneys reveals pathways involved in early polycystic kidney disease. Biomed Pharmacother 2018; 108:1123-1134. [DOI: 10.1016/j.biopha.2018.07.178] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023] Open
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19
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Shalata A, Lauhasurayotin S, Leibovitz Z, Li H, Hebert D, Dhanraj S, Hadid Y, Mahroum M, Bajar J, Egenburg S, Arad A, Shohat M, Haddad S, Bakry H, Moshiri H, Scherer SW, Tzur S, Dror Y. Biallelic mutations in EXOC3L2 cause a novel syndrome that affects the brain, kidney and blood. J Med Genet 2018; 56:340-346. [PMID: 30327448 DOI: 10.1136/jmedgenet-2018-105421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/18/2018] [Accepted: 08/17/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND Dandy-Walker malformation features agenesis/hypoplasia of the cerebellar vermis, cystic dilatation of the fourth ventricle and enlargement of posterior fossa. Although Dandy-Walker malformation is relatively common and several genes were linked to the syndrome, the genetic cause in the majority of cases is unknown. OBJECTIVE To identify the mutated gene responsible for Dandy-Walker malformation, kidney disease and bone marrow failure in four patients from two unrelated families. METHODS Medical assessment, sonographic, MRI and pathological studies were used to define phenotype. Chromosomal microarray analysis and whole-exome sequence were performed to unravel the genotype. RESULTS We report four subjects from two unrelated families with homozygous mutations in the Exocyst Complex Component 3-Like-2 gene (EXOC3L2).EXOC3L2 functions in trafficking of post-Golgi vesicles to the plasma membrane. In the first family a missense mutation in a highly conserved amino acid, p.Leu41Gln, was found in three fetuses; all had severe forms of Dandy-Walker malformation that was detectable by prenatal ultrasonography and confirmed by autopsy. In the second family, the affected child carried a nonsense mutation, p.Arg72*, and no detected protein. He had peritrigonal and cerebellar white matter abnormalities with enlargement of the ventricular trigones, developmental delay, pituitary hypoplasia, severe renal dysplasia and bone marrow failure. CONCLUSION We propose that biallelic EXOC3L2 mutations lead to a novel syndrome that affects hindbrain development, kidney and possibly the bone marrow.
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Affiliation(s)
- Adel Shalata
- Pediatrics and Medical Genetics and The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa, Israel
| | - Supanun Lauhasurayotin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/ Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Israel
| | - Zvi Leibovitz
- Obstetrics-Gynecology Ultrasound Unit, Bnai-Zion Medical Center and Rappaport Faculty of Medicine, The Technion, Haifa, Israel
| | - Hongbing Li
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/ Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Israel
| | - Diane Hebert
- Division of Nephrology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Santhosh Dhanraj
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/ Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Israel
| | - Yarin Hadid
- Pediatrics and Medical Genetics and The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa, Israel
| | - Mohammed Mahroum
- Pediatrics and Medical Genetics and The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa, Israel
| | - Jacob Bajar
- Department of Pathology, Bnai Zion Medical Center, Haifa, Israel
| | - Sandro Egenburg
- Department of Pathology, Bnai Zion Medical Center, Haifa, Israel
| | - Ayala Arad
- Department of Pathology, Bnai Zion Medical Center, Haifa, Israel
| | - Mordechai Shohat
- Sheba Cancer Research Center, Sackler School of Medicine, Tel Aviva University, Maccabi Genetic Institute, Tel Aviv, Israel
| | - Sami Haddad
- Ultrasound unit, Obstetrics-Gynecology Department, Baruch Padeh Peoria Hospital, Tiberias, Israel
| | - Hassan Bakry
- Obstetrics-Gynecology Ultrasound Unit, Bnai-Zion Medical Center and Rappaport Faculty of Medicine, The Technion, Haifa, Israel
| | - Houtan Moshiri
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shay Tzur
- Laboratory of Molecular Medicine, Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
- Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel
| | - Yigal Dror
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
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Zhang H, Su B, Liu X, Xiao H, Ding J, Yao Y. Mutations in TTC21B cause different phenotypes in two childhood cases in China. Nephrology (Carlton) 2018; 23:371-376. [PMID: 28124483 DOI: 10.1111/nep.13008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/17/2017] [Accepted: 01/22/2017] [Indexed: 12/22/2022]
Abstract
AIM The TTC21B gene is now known as causative of nephronophthisis-related ciliopathies (NPHP-RC). We reported two Chinese paediatric cases with end-stage renal disease and other phenotypes caused by the TTC21B gene mutations. METHODS The clinical features of Chinese paediatric cases with NPHP-RC were summarized. Mutation analysis of the TTC21B gene was performed using next-generation sequencing. RESULTS The two cases both had nephrotic proteinuria, renal failure, hypertension and abnormal liver function (or hepatic fibrosis). One case also presented situs inversus and short phalanges. They developed end-stage renal disease (ESRD) at 1 year old and 8 years old, respectively, when renal pathology both showed focal segmental glomerular sclerosis (FSGS) with tubulointerstitial lesions including interstitial fibrosis and atrophic tubules. Three novel disease-causing TTC21B mutations were identified. One case carried homozygous mutation c.2211 + 3A > G, while the other case carried compound heterozygous mutations c.1552 T > C (p.C518R) and c.1456dupA (p.R486KfsX22). CONCLUSION Mutations in TTC21B cause a range of ciliopathy phenotypes in humans. We identified 3 novel TTC21B mutations in two Chinese paediatric cases that both presented end-stage renal disease and other different features. This is the first TTC21B mutations ever reported in China.
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Affiliation(s)
- Hongwen Zhang
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Baige Su
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Xiaoyu Liu
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Huijie Xiao
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Yong Yao
- Department of Pediatric, Peking University First Hospital, Beijing, China
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21
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Bonsib SM. Urologic Diseases Germane to the Medical Renal Biopsy: Review of a Large Diagnostic Experience in the Context of the Renal Architecture and Its Environs. Adv Anat Pathol 2018; 25:333-352. [PMID: 30036201 PMCID: PMC6086223 DOI: 10.1097/pap.0000000000000199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The kidney is one of the most complicated organs in development and is susceptible to more types of diseases than other organs. The disease spectrum includes developmental and cystic diseases, involvement by systemic diseases, iatrogenic complications, ascending infections and urinary tract obstruction, and neoplastic diseases. The diagnosis of kidney disease is unique involving 2 subspecialties, urologic pathology and renal pathology. Both renal and urologic pathologists employ the renal biopsy as a diagnostic modality. However, urologic pathologists commonly have a generous specimen in the form of a nephrectomy or partial nephrectomy while a renal pathologist requires ancillary modalities of immunofluorescence and electron microscopy. The 2 subspecialties differ in the disease spectrum they diagnose. This separation is not absolute as diseases of one subspecialty not infrequently appear in the diagnostic materials of the other. The presence of medical renal diseases in a nephrectomy specimen is well described and recommendations for reporting these findings have been formalized. However, urologic diseases appearing in a medical renal biopsy have received less attention. This review attempts to fill that gap by first reviewing the perirenal anatomy to illustrate why inadvertent biopsy of adjacent organs occurs and determine its incidence in renal biopsies followed by a discussion of gross anatomic features relevant to the microscopic domain of the medical renal biopsy. Unsuspected neoplasms and renal cysts and cystic kidney diseases will then be discussed as they create a diagnostic challenge for the renal pathologist who often has limited training and experience in these diseases.
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22
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Metabolic Phenotyping of Anks3 Depletion in mIMCD-3 cells - a Putative Nephronophthisis Candidate. Sci Rep 2018; 8:9022. [PMID: 29899363 PMCID: PMC5998149 DOI: 10.1038/s41598-018-27389-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/01/2018] [Indexed: 11/08/2022] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive form of cystic kidney disease and the leading cause of hereditary kidney failure in children and young adults. Like other NPH proteins, the NPHP16/Anks6-interacting protein Anks3 has been identified to cause laterality defects in humans. However, the cellular functions of Anks3 remain enigmatic. We investigated the metabolic impact of Anks3 depletion in cultured murine inner medullary collecting duct cells via GC-MS profiling and LC-MS/MS analysis. Combined metabolomics successfully identified 155 metabolites; 48 metabolites were identified to be significantly altered by decreasing Anks3 levels. Especially, amino acid and purine/pyrimidine metabolism were affected by loss of Anks3. Branched-chain amino acids were identified to be significantly downregulated suggesting disrupted nutrient signalling. Tryptophan and 1-ribosyl-imidazolenicotinamide accumulated whereas NAD+ and NADP+ concentrations were diminished indicating disturbances within the tryptophan-niacin pathway. Most strikingly, nucleosides were reduced upon Anks3 depletion, while 5-methyluridine and 6-methyladenosine accumulated over time. Hence, elevated PARP1 and cleaved PARP1 levels could be detected. Furthermore, living cell number and viability was significantly declined. In combination, these results suggest that Anks3 may be involved in DNA damage responses by balancing the intracellular nucleoside pool.
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23
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Joseph N, Al-Jassar C, Johnson CM, Andreeva A, Barnabas DD, Freund SMV, Gergely F, van Breugel M. Disease-Associated Mutations in CEP120 Destabilize the Protein and Impair Ciliogenesis. Cell Rep 2018; 23:2805-2818. [PMID: 29847808 PMCID: PMC5990496 DOI: 10.1016/j.celrep.2018.04.100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/15/2018] [Accepted: 04/24/2018] [Indexed: 01/10/2023] Open
Abstract
Ciliopathies are a group of genetic disorders caused by a failure to form functional cilia. Due to a lack of structural information, it is currently poorly understood how ciliopathic mutations affect protein functionality to give rise to the underlying disease. Using X-ray crystallography, we show that the ciliopathy-associated centriolar protein CEP120 contains three C2 domains. The point mutations V194A and A199P, which cause Joubert syndrome (JS) and Jeune asphyxiating thoracic dystrophy (JATD), respectively, both reduce the thermostability of the second C2 domain by targeting residues that point toward its hydrophobic core. Genome-engineered cells homozygous for these mutations have largely normal centriole numbers but show reduced CEP120 levels, compromised recruitment of distal centriole markers, and deficient cilia formation. Our results provide insight into the disease mechanism of two ciliopathic mutations in CEP120, identify putative binding partners of CEP120 C2B, and suggest a complex genotype-phenotype relation of the CEP120 ciliopathy alleles.
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Affiliation(s)
- Nimesh Joseph
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Caezar Al-Jassar
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher M Johnson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Antonina Andreeva
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Deepak D Barnabas
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stefan M V Freund
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Mark van Breugel
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Faghihimehr A, Gharavi M, Mancuso M, Sreedher G. Fetal MR imaging in urogenital system anomalies. J Matern Fetal Neonatal Med 2018; 32:3487-3494. [DOI: 10.1080/14767058.2018.1465039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Mohammad Gharavi
- Department of Radiology, University of Maryland Medical Center, Baltimore, MD, USA
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25
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Renkema KY, Giles RH, Lilien MR, Beales PL, Roepman R, Oud MM, Arts HH, Knoers NVAM. The KOUNCIL Consortium: From Genetic Defects to Therapeutic Development for Nephronophthisis. Front Pediatr 2018; 6:131. [PMID: 29868523 PMCID: PMC5949343 DOI: 10.3389/fped.2018.00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/18/2018] [Indexed: 01/12/2023] Open
Abstract
Nephronophthisis (NPH) is the most common monogenic cause of renal failure in children. Treatment options are limited to dialysis and transplantation. Therapeutics to significantly delay or prevent end-stage renal disease (ESRD) in children are currently not available. In the Dutch-Anglo KOUNCIL (Kidney-Oriented UNderstanding of correcting CILiopathies) consortium, several groups and specialties united to perform scientific groundwork with the aim to develop genetic and therapeutic personalized care for NPH patients. At the start of this consortium, a genetic diagnosis for NPH was available for only 30-40% of patients, which improved to 50-60% during the course of the 4-year KOUNCIL project. Other major accomplishments of the consortium were (1) the establishment of a Dutch renal ciliopathy patient database with genotype and phenotype data; (2) composition of a proteomics-based integrated network of protein modules disrupted in NPH; (3) the development of non-invasive, urine-based assays that allow functional assessment of genomic variants in NPH and of therapeutic efficiency of drugs; and (4) chemical screening toward the identification of compounds that delay or prevent disease progression in NPH, which resulted in four potential medical interventions for NPH. In conclusion, the KOUNCIL consortium effectively channeled complementary approaches to broaden our understanding of NPH pathogenesis, resulted in 54 publications, improvement of genome diagnostics for NPH patients, awareness in the nephrology and clinical genetics communities for NPH, and new avenues for patient management.
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Affiliation(s)
- Kirsten Y Renkema
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Rachel H Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Marc R Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Philip L Beales
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ronald Roepman
- Department of Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Machteld M Oud
- Department of Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Heleen H Arts
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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26
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König JC, Titieni A, Konrad M. Network for Early Onset Cystic Kidney Diseases-A Comprehensive Multidisciplinary Approach to Hereditary Cystic Kidney Diseases in Childhood. Front Pediatr 2018; 6:24. [PMID: 29497606 PMCID: PMC5819567 DOI: 10.3389/fped.2018.00024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/25/2018] [Indexed: 12/16/2022] Open
Abstract
Hereditary cystic kidney diseases comprise a complex group of genetic disorders representing one of the most common causes of end-stage renal failure in childhood. The main representatives are autosomal recessive polycystic kidney disease, nephronophthisis, Bardet-Biedl syndrome, and hepatocyte nuclear factor-1beta nephropathy. Within the last years, genetic efforts have brought tremendous progress for the molecular understanding of hereditary cystic kidney diseases identifying more than 70 genes. Yet, genetic heterogeneity, phenotypic variability, a lack of reliable genotype-phenotype correlations and the absence of disease-specific biomarkers remain major challenges for physicians treating children with cystic kidney diseases. To tackle these challenges comprehensive scientific approaches are urgently needed that match the ongoing "revolution" in genetics and molecular biology with an improved efficacy of clinical data collection. Network for early onset cystic kidney diseases (NEOCYST) is a multidisciplinary, multicenter collaborative combining a detailed collection of clinical data with translational scientific approaches addressing the genetic, molecular, and functional background of hereditary cystic kidney diseases. Consisting of seven work packages, including an international registry as well as a biobank, NEOCYST is not only dedicated to current scientific questions, but also provides a platform for longitudinal clinical surveillance and provides precious sources for high-quality research projects and future clinical trials. Funded by the German Federal Government, the NEOCYST collaborative started in February 2016. Here, we would like to introduce the rationale, design, and objectives of the network followed by a short overview on the current state of progress.
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Affiliation(s)
- Jens Christian König
- Department of General Pediatrics, University Children's Hospital Münster, Münster, Germany
| | - Andrea Titieni
- Department of General Pediatrics, University Children's Hospital Münster, Münster, Germany
| | - Martin Konrad
- Department of General Pediatrics, University Children's Hospital Münster, Münster, Germany
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27
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Gehrig J, Pandey G, Westhoff JH. Zebrafish as a Model for Drug Screening in Genetic Kidney Diseases. Front Pediatr 2018; 6:183. [PMID: 30003073 PMCID: PMC6031734 DOI: 10.3389/fped.2018.00183] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
Genetic disorders account for a wide range of renal diseases emerging during childhood and adolescence. Due to the utilization of modern biochemical and biomedical techniques, the number of identified disease-associated genes is increasing rapidly. Modeling of congenital human disease in animals is key to our understanding of the biological mechanism underlying pathological processes and thus developing novel potential treatment options. The zebrafish (Danio rerio) has been established as a versatile small vertebrate organism that is widely used for studying human inherited diseases. Genetic accessibility in combination with elegant experimental methods in zebrafish permit modeling of human genetic diseases and dissecting the perturbation of underlying cellular networks and physiological processes. Beyond its utility for genetic analysis and pathophysiological and mechanistic studies, zebrafish embryos, and larvae are amenable for phenotypic screening approaches employing high-content and high-throughput experiments using automated microscopy. This includes large-scale chemical screening experiments using genetic models for searching for disease-modulating compounds. Phenotype-based approaches of drug discovery have been successfully performed in diverse zebrafish-based screening applications with various phenotypic readouts. As a result, these can lead to the identification of candidate substances that are further examined in preclinical and clinical trials. In this review, we discuss zebrafish models for inherited kidney disease as well as requirements and considerations for the technical realization of drug screening experiments in zebrafish.
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Affiliation(s)
- Jochen Gehrig
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
| | - Gunjan Pandey
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany.,Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Jens H Westhoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
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28
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Nestor JG, Groopman EE, Gharavi AG. Towards precision nephrology: the opportunities and challenges of genomic medicine. J Nephrol 2017; 31:47-60. [PMID: 29043570 DOI: 10.1007/s40620-017-0448-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/10/2017] [Indexed: 12/28/2022]
Abstract
The expansion of genomic medicine is furthering our understanding of many human diseases. This is well illustrated in the field of nephrology, through the characterization, discovery, and growing insight into various renal diseases through use of Next Generation Sequencing (NGS) technologies. This review will provide an overview of the diagnostic opportunities of using genetic testing in the clinical setting by describing notable discoveries regarding inherited forms of renal disease that have advanced the field and by highlighting some of the potential benefits of establishing a molecular diagnosis in a clinical practice. In addition, it will discuss some of the challenges associated with the expansion of genetic testing into the clinical setting, including clinical variant interpretation and return of genetic results.
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Affiliation(s)
- Jordan G Nestor
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Emily E Groopman
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA.
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29
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Frazier KS. Species Differences in Renal Development and Associated Developmental Nephrotoxicity. Birth Defects Res 2017; 109:1243-1256. [DOI: 10.1002/bdr2.1088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/14/2017] [Accepted: 06/20/2017] [Indexed: 12/19/2022]
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Abstract
The police brought a 65-year-old female patient to the EADU after being found 'roaming the streets' in an apparent state of confusion. This was her third admission under the same circumstances during the last 3 years. Neurological examination revealed (1) cognitive impairment, (2) oculomotor apraxia, (3) abnormal cancellation of vestibular ocular reflex, (4) mild ataxia and (5) mild hypotonia. Renal function was abnormal and liver function was normal. No retinal disturbance was found. The head CT on admission was normal for stroke and the lumbar puncture was negative for encephalitis. Her brain MRI showed 'molar tooth sign', suggestive of Joubert syndrome, which was confirmed by genetic testing showing anomalous NPHP1 gene.
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Affiliation(s)
- Carlo Canepa
- Department of Stroke and Neurology, James Paget University Hospital, Norwich, UK
| | - Ben Burton
- Stroke Services, James Paget University Hospitals NHS Foundation Trust, Great Yarmouth, Great Yarmouth, UK
| | - Abdul Muhith
- Stroke Services, James Paget University Hospitals NHS Foundation Trust, Great Yarmouth, Great Yarmouth, UK
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31
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Yoshikawa T, Kamei K, Nagata H, Saida K, Sato M, Ogura M, Ito S, Miyazaki O, Urushihara M, Kondo S, Sugawara N, Ishizuka K, Hamasaki Y, Shishido S, Morisada N, Iijima K, Nagata M, Yoshioka T, Ogata K, Ishikura K. Diversity of renal phenotypes in patients with WDR19
mutations: Two case reports. Nephrology (Carlton) 2017. [DOI: 10.1111/nep.12996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Takahisa Yoshikawa
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
| | - Koichi Kamei
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
| | - Hiroko Nagata
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
| | - Ken Saida
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
| | - Mai Sato
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
| | - Masao Ogura
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
| | - Shuichi Ito
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
- Department of Pediatrics, Graduate School of Medicine; Yokohama City University; Yokohama Japan
| | - Osamu Miyazaki
- Department of Radiology; National Center for Child Health and Development; Tokyo Japan
| | - Maki Urushihara
- Department of Pediatrics, Institute of Biomedical Sciences; Tokushima University Graduate School; Tokushima Japan
| | - Shuji Kondo
- Department of Pediatrics, Institute of Biomedical Sciences; Tokushima University Graduate School; Tokushima Japan
| | - Noriko Sugawara
- Department of Pediatric Nephrology; Tokyo Women's Medical University; Tokyo Japan
| | - Kiyonobu Ishizuka
- Department of Pediatric Nephrology; Tokyo Women's Medical University; Tokyo Japan
| | - Yuko Hamasaki
- Department of Pediatric Nephrology; Toho University Faculty of Medicine; Tokyo Japan
| | - Seiichiro Shishido
- Department of Pediatric Nephrology; Toho University Faculty of Medicine; Tokyo Japan
| | - Naoya Morisada
- Department of Pediatrics; Kobe University Graduate School of Medicine; Kobe Japan
- Department of Clinical Genetics; Hyogo Prefectural Kobe Children's Hospital; Kobe Japan
| | - Kazumoto Iijima
- Department of Pediatrics; Kobe University Graduate School of Medicine; Kobe Japan
| | - Michio Nagata
- Department of Kidney and Vascular Pathology, Faculty of Medicine; University of Tsukuba; Ibaraki Japan
| | - Takako Yoshioka
- Department of Pathology; National Center for Child Health and Development; Tokyo Japan
| | - Kentaro Ogata
- Department of Pathology; Federation of National Service Personnel Mutual Aid Associations, Tachikawa Hospital; Tokyo Japan
| | - Kenji Ishikura
- Division of Nephrology and Rheumatology; National Center for Child Health and Development; Tokyo Japan
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32
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Amiri FS, Kariminejad A. Juvenile nephronophthisis and dysthyroidism: a rare association. CEN Case Rep 2017; 6:98-104. [PMID: 28509138 DOI: 10.1007/s13730-017-0252-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/07/2017] [Indexed: 11/28/2022] Open
Abstract
Nephronophthisis, an autosomal recessive kidney disease, represents the most frequent genetic cause of end-stage kidney disease in the first three decades of life. A 27-year-old male was presented with gait imbalance, sever pruritus since 10 days prior time of admission. In past medical history, he had bilateral cataract, torsional nystagmus, and bilateral optic nerve atrophy since 2 years of age. He was also mentioned history of multinodular goiter with dysfunctional thyroid state since 2 years before admission. At admission bilateral blindness, torsional nystagmus, asymmetric thyromegaly with nodularity was found in physical examination. Laboratory tests showed elevated urea and creatinine (200, 10.7 mg/dl), hypomagnesemia (1.1 mEq/l), decreased thyroid stimulating hormone (<0.004 mIU/l). Ophthalmologist consultation confirmed retinitis pigmentosa. Renal sonography showed small-sized kidneys. Brain magnetic resonance imaging did not reveal molar tooth sign. Genetic testing performed and a large homozygous deletion at the NPHP1 gene locus was found. The patient was diagnosed with juvenile nephronophthisis and consideration of dysthyroidism as extrarenal manifestation of nephronophthisis is suggested in this case. Furthermore, loss of function mutation in SLC41A1 gene that leads to magnesium depletion must be noted in patients with suspected to nephronophthisis.
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Affiliation(s)
- Fateme Shamekhi Amiri
- Division of Nephrology, Imam khomeini hospital, Faculty of medicine, National University of Tehran Medical Sciences, Tehran, Iran.
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Mitchison HM, Valente EM. Motile and non-motile cilia in human pathology: from function to phenotypes. J Pathol 2017; 241:294-309. [PMID: 27859258 DOI: 10.1002/path.4843] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
Ciliopathies are inherited human disorders caused by both motile and non-motile cilia dysfunction that form an important and rapidly expanding disease category. Ciliopathies are complex conditions to diagnose, being multisystem disorders characterized by extensive genetic heterogeneity and clinical variability with high levels of lethality. There is marked phenotypic overlap among distinct ciliopathy syndromes that presents a major challenge for their recognition, diagnosis, and clinical management, in addition to posing an on-going task to develop the most appropriate family counselling. The impact of next-generation sequencing and high-throughput technologies in the last decade has significantly improved our understanding of the biological basis of ciliopathy disorders, enhancing our ability to determine the possible reasons for the extensive overlap in their symptoms and genetic aetiologies. Here, we review the diverse functions of cilia in human health and disease and discuss a growing shift away from the classical clinical definitions of ciliopathy syndromes to a more functional categorization. This approach arises from our improved understanding of this unique organelle, revealed through new genetic and cell biological insights into the discrete functioning of subcompartments of the cilium (basal body, transition zone, intraflagellar transport, motility). Mutations affecting these distinct ciliary protein modules can confer different genetic diseases and new clinical classifications are possible to define, according to the nature and extent of organ involvement. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Hannah M Mitchison
- Genetics and Genomic Medicine Programme, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Enza Maria Valente
- Department of Medicine and Surgery, University of Salerno, Salerno, Italy.,Neurogenetics Unit, IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano, 00143, Rome, Italy
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Walczak-Sztulpa J, Wawrocka A, Sobierajewicz A, Kuszel L, Zawadzki J, Grenda R, Swiader-Lesniak A, Kocyla-Karczmarewicz B, Wnuk A, Latos-Bielenska A, Chrzanowska KH. Intrafamilial phenotypic variability in a Polish family with Sensenbrenner syndrome and biallelic WDR35
mutations. Am J Med Genet A 2017; 173:1364-1368. [DOI: 10.1002/ajmg.a.38163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 12/31/2016] [Accepted: 01/06/2017] [Indexed: 11/06/2022]
Affiliation(s)
| | - Anna Wawrocka
- Department of Medical Genetics; Poznan University of Medical Sciences; Poznan Poland
| | - Agata Sobierajewicz
- Department of Medical Genetics; Poznan University of Medical Sciences; Poznan Poland
| | - Lukasz Kuszel
- Department of Medical Genetics; Poznan University of Medical Sciences; Poznan Poland
| | - Jan Zawadzki
- Department of Nephrology; Kidney Transplantation and Hypertension; The Children's Memorial Health Institute; Warsaw Poland
| | - Ryszard Grenda
- Department of Nephrology; Kidney Transplantation and Hypertension; The Children's Memorial Health Institute; Warsaw Poland
| | - Anna Swiader-Lesniak
- Department of Anthropology; The Children's Memorial Health Institute; Warsaw Poland
| | | | - Anna Wnuk
- Department of Diagnostic Imaging; The Children's Memorial Health Institute; Warsaw Poland
| | - Anna Latos-Bielenska
- Department of Medical Genetics; Poznan University of Medical Sciences; Poznan Poland
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Fluid shear stress-induced TGF-β/ALK5 signaling in renal epithelial cells is modulated by MEK1/2. Cell Mol Life Sci 2017; 74:2283-2298. [PMID: 28168444 PMCID: PMC5425503 DOI: 10.1007/s00018-017-2460-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/14/2022]
Abstract
Renal tubular epithelial cells are exposed to mechanical forces due to fluid flow shear stress within the lumen of the nephron. These cells respond by activation of mechano-sensors located at the plasma membrane or the primary cilium, having crucial roles in maintenance of cellular homeostasis and signaling. In this paper, we applied fluid shear stress to study TGF-β signaling in renal epithelial cells with and without expression of the Pkd1-gene, encoding a mechano-sensor mutated in polycystic kidney disease. TGF-β signaling modulates cell proliferation, differentiation, apoptosis, and fibrotic deposition, cellular programs that are altered in renal cystic epithelia. SMAD2/3-mediated signaling was activated by fluid flow, both in wild-type and Pkd1−/− cells. This was characterized by phosphorylation and nuclear accumulation of p-SMAD2/3, as well as altered expression of downstream target genes and epithelial-to-mesenchymal transition markers. This response was still present after cilia ablation. An inhibitor of upstream type-I-receptors, ALK4/ALK5/ALK7, as well as TGF-β-neutralizing antibodies effectively blocked SMAD2/3 activity. In contrast, an activin-ligand trap was ineffective, indicating that increased autocrine TGF-β signaling is involved. To study potential involvement of MAPK/ERK signaling, cells were treated with a MEK1/2 inhibitor. Surprisingly, fluid flow-induced expression of most SMAD2/3 targets was further enhanced upon MEK inhibition. We conclude that fluid shear stress induces autocrine TGF-β/ALK5-induced target gene expression in renal epithelial cells, which is partially restrained by MEK1/2-mediated signaling.
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Renal transplantation in Bardet-Biedl Syndrome. Pediatr Nephrol 2016; 31:2153-61. [PMID: 27245600 DOI: 10.1007/s00467-016-3415-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Renal anomalies are common in patients with Bardet-Biedl syndrome (BBS), a renal cystic ciliopathy with multi-systemic features. Renal transplantation is indicated in cases of end-stage renal disease (ESRD), but transplant centers may be hesitant to perform the necessary transplant in light of the multitude of metabolic comorbidities these patients often face with the potential to complicate outcomes. METHODS Data from the Clinical Registry Investigating BBS (CRIBBS) were used to investigate renal transplant outcomes in the largest BBS cohort described to date. RESULTS Of the 206 patients enrolled in the CRIBBS, 21 children (10.2 %; 16 girls, 5 boys; median age 8.4 years) had been diagnosed with ESRD. Renal transplantation was performed in 18 of these individuals between 1982 and 2015, including repeat transplantation in some cases, for a total of 22 kidneys. Overall graft survival was 81.6 % at 1 year post-transplantation, 75.7 % at 5 years, 59 % at 10 years, and 49.2 % at 25 years. Patient survival was 94.4 % at 1 year post-transplantation, 87.2 % at 8 years, and 79.3 % at 25 years. CONCLUSIONS At a median follow-up time of 97 months, relatively few complications of renal transplantation were reported in the patients of this study. However, body mass index was significantly elevated in transplanted individuals compared to non-transplanted individuals participating in CRIBBS at the most recent follow-up. Although the frequency of obesity and other manifestations of the metabolic syndrome warrant meticulous management in this high-risk population, favorable long-term outcomes suggest that renal transplantation is a viable option for patients with BBS and ESRD.
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Bertier G, Hétu M, Joly Y. Unsolved challenges of clinical whole-exome sequencing: a systematic literature review of end-users' views. BMC Med Genomics 2016; 9:52. [PMID: 27514372 PMCID: PMC4982236 DOI: 10.1186/s12920-016-0213-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/28/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically to inform patient care. The implementation of WES into healthcare poses significant organizational, regulatory, and ethical hurdles, which are widely discussed in the literature. METHODS In order to inform future policy decisions on the integration of WES into standard clinical practice, we performed a systematic literature review to identify the most important challenges directly reported by technology users. RESULTS Out of 2094 articles, we selected and analyzed 147 which reported a total of 23 different challenges linked to the production, analysis, reporting and sharing of patients' WES data. Interpretation of variants of unknown significance, incidental findings, and the cost and reimbursement of WES-based tests were the most reported challenges across all articles. CONCLUSIONS WES is already used in the clinical setting, and may soon be considered the standard of care for specific medical conditions. Yet, technology users are calling for certain standards and guidelines to be published before this technology replaces more focused approaches such as gene panels sequencing. In addition, a number of infrastructural adjustments will have to be made for clinics to store, process and analyze the amounts of data produced by WES.
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Affiliation(s)
- Gabrielle Bertier
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
- UMR 1027, Inserm, University of Toulouse III - Paul Sabatier, 37 allées Jules Guesde, F-31000 Toulouse, France
| | - Martin Hétu
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
| | - Yann Joly
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
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The expanding phenotypic spectra of kidney diseases: insights from genetic studies. Nat Rev Nephrol 2016; 12:472-83. [PMID: 27374918 DOI: 10.1038/nrneph.2016.87] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) has led to the identification of previously unrecognized phenotypes associated with classic kidney disease genes. In addition to improving diagnostics for genetically heterogeneous diseases and enabling a faster rate of gene discovery, NGS has enabled an expansion and redefinition of nephrogenetic disease categories. Findings from these studies raise the question of whether disease diagnoses should be made on clinical grounds, on genetic evidence or a combination thereof. Here, we discuss the major kidney disease-associated genes and gene categories for which NGS has expanded the phenotypic spectrum. For example, COL4A3-5 genes, which are classically associated with Alport syndrome, are now understood to also be involved in the aetiology of focal segmental glomerulosclerosis. DGKE, which is associated with nephrotic syndrome, is also mutated in patients with atypical haemolytic uraemic syndrome. We examine how a shared genetic background between diverse clinical phenotypes can provide insight into the function of genes and novel links with essential pathophysiological mechanisms. In addition, we consider genetic and epigenetic factors that contribute to the observed phenotypic heterogeneity of kidney diseases and discuss the challenges in the interpretation of genetic data. Finally, we discuss the implications of the expanding phenotypic spectra associated with kidney disease genes for clinical practice, genetic counselling and personalized care, and present our recommendations for the use of NGS-based tests in routine nephrology practice.
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Clinical utility gene card for: Meckel syndrome - update 2016. Eur J Hum Genet 2016; 24:ejhg201633. [PMID: 27094752 DOI: 10.1038/ejhg.2016.33] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 03/04/2016] [Accepted: 03/16/2016] [Indexed: 11/09/2022] Open
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Hakim S, Dyson JM, Feeney SJ, Davies EM, Sriratana A, Koenig MN, Plotnikova OV, Smyth IM, Ricardo SD, Hobbs RM, Mitchell CA. Inpp5e suppresses polycystic kidney disease via inhibition of PI3K/Akt-dependent mTORC1 signaling. Hum Mol Genet 2016; 25:2295-2313. [PMID: 27056978 DOI: 10.1093/hmg/ddw097] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/17/2016] [Indexed: 12/20/2022] Open
Abstract
Polycystic kidney disease (PKD) is a common cause of renal failure with few effective treatments. INPP5E is an inositol polyphosphate 5-phosphatase that dephosphorylates phosphoinositide 3-kinase (PI3K)-generated PI(3,4,5)P3 and is mutated in ciliopathy syndromes. Germline Inpp5e deletion is embryonically lethal, attributed to cilia stability defects, and is associated with polycystic kidneys. However, the molecular mechanisms responsible for PKD development upon Inpp5e loss remain unknown. Here, we show conditional inactivation of Inpp5e in mouse kidney epithelium results in severe PKD and renal failure, associated with a partial reduction in cilia number and hyperactivation of PI3K/Akt and downstream mammalian target of rapamycin complex 1 (mTORC1) signaling. Treatment with an mTORC1 inhibitor improved kidney morphology and function, but did not affect cilia number or length. Therefore, we identify Inpp5e as an essential inhibitor of the PI3K/Akt/mTORC1 signaling axis in renal epithelial cells, and demonstrate a critical role for Inpp5e-dependent mTORC1 regulation in PKD suppression.
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Affiliation(s)
- Sandra Hakim
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jennifer M Dyson
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sandra J Feeney
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Elizabeth M Davies
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Absorn Sriratana
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Monica N Koenig
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Olga V Plotnikova
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ian M Smyth
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia Development and Stem Cell program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sharon D Ricardo
- Development and Stem Cell program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Robin M Hobbs
- Development and Stem Cell program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Christina A Mitchell
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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Landolt L, Strauss P, Marti HP, Eikrem Ø. Next Generation Sequencing: A Tool for This Generation of Nephrologists. EUROPEAN MEDICAL JOURNAL 2016. [DOI: 10.33590/emj/10314001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The emergence of next generation sequencing (NGS) techniques has made the sequencing of whole genomes, transcriptomes, and epigenomes faster and more readily available than previous methods such as Sanger sequencing, which was developed in the 1970s. It is now 10 years since NGS began to revolutionise biological and medical research. Sequencing of RNA provides insights into up or downregulated gene expression patterns and therefore into molecular disease mechanisms. This can lead to the detection of new biomarkers that can be used as diagnostic tools in risk stratification, or even as new therapeutic targets. In nephrology, NGS plays a role in both basic and experimental research, but also in the clinical setting, whereby the diagnosis of innate genetic diseases such as ciliopathies or genetically moderated acquired diseases such as glomerulopathies has improved. NGS enables precise diagnosis and classification of common diseases of the kidneys and urinary tract, aids in both prognostic and predictive decision-making, and in the avoidance of unnecessary therapies. It also plays a role in the risk stratification of disease recurrence after transplantation. NGS is a robust method; however, the performance of NGS is dependent on the method of tissue storage, the extraction of DNA or RNA, and on the sequencing platform itself, as well as on the bioinformatic analyses performed, integration of clinical data, and comprehensive interpretation of the results. The aim of this article is to review and emphasise the importance of NGS as a tool for this generation of nephrologists.
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Affiliation(s)
- Lea Landolt
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Øystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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Grampa V, Delous M, Zaidan M, Odye G, Thomas S, Elkhartoufi N, Filhol E, Niel O, Silbermann F, Lebreton C, Collardeau-Frachon S, Rouvet I, Alessandri JL, Devisme L, Dieux-Coeslier A, Cordier MP, Capri Y, Khung-Savatovsky S, Sigaudy S, Salomon R, Antignac C, Gubler MC, Benmerah A, Terzi F, Attié-Bitach T, Jeanpierre C, Saunier S. Novel NEK8 Mutations Cause Severe Syndromic Renal Cystic Dysplasia through YAP Dysregulation. PLoS Genet 2016; 12:e1005894. [PMID: 26967905 PMCID: PMC4788435 DOI: 10.1371/journal.pgen.1005894] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/02/2016] [Indexed: 01/01/2023] Open
Abstract
Ciliopathies are a group of genetic multi-systemic disorders related to dysfunction of the primary cilium, a sensory organelle present at the cell surface that regulates key signaling pathways during development and tissue homeostasis. In order to identify novel genes whose mutations would cause severe developmental ciliopathies, >500 patients/fetuses were analyzed by a targeted high throughput sequencing approach allowing exome sequencing of >1200 ciliary genes. NEK8/NPHP9 mutations were identified in five cases with severe overlapping phenotypes including renal cystic dysplasia/hypodysplasia, situs inversus, cardiopathy with hypertrophic septum and bile duct paucity. These cases highlight a genotype-phenotype correlation, with missense and nonsense mutations associated with hypodysplasia and enlarged cystic organs, respectively. Functional analyses of NEK8 mutations in patient fibroblasts and mIMCD3 cells showed that these mutations differentially affect ciliogenesis, proliferation/apoptosis/DNA damage response, as well as epithelial morphogenesis. Notably, missense mutations exacerbated some of the defects due to NEK8 loss of function, highlighting their likely gain-of-function effect. We also showed that NEK8 missense and loss-of-function mutations differentially affect the regulation of the main Hippo signaling effector, YAP, as well as the expression of its target genes in patient fibroblasts and renal cells. YAP imbalance was also observed in enlarged spheroids of Nek8-invalidated renal epithelial cells grown in 3D culture, as well as in cystic kidneys of Jck mice. Moreover, co-injection of nek8 MO with WT or mutated NEK8-GFP RNA in zebrafish embryos led to shortened dorsally curved body axis, similar to embryos injected with human YAP RNA. Finally, treatment with Verteporfin, an inhibitor of YAP transcriptional activity, partially rescued the 3D spheroid defects of Nek8-invalidated cells and the abnormalities of NEK8-overexpressing zebrafish embryos. Altogether, our study demonstrates that NEK8 human mutations cause major organ developmental defects due to altered ciliogenesis and cell differentiation/proliferation through deregulation of the Hippo pathway. Genes mutated in ciliopathies encode proteins with various localizations and functions at the primary cilium. Here we report novel NEK8 mutations in patients with renal cystic hypodysplasia and associated ciliopathy defects. NEK8 belongs to a protein complex defining the Inversin compartment of the cilium. It is also a negative regulator of the Hippo signaling pathway that controls organ growth. We report genotype-phenotype correlation in the patients. We functionally demonstrate that the two types of mutations (missense versus nonsense) differentially affect ciliogenesis, cell apoptosis and epithelialisation. We also show that all the mutations lead to dysregulation of the Hippo pathway through nuclear YAP imbalance but that the nature of this imbalance is different according to the type of mutation. We confirm alteration of the Hippo pathway associated with Nek8 mutation in vivo in Jck mice. Remarkably, we show that morphogenesis defects observed in Nek8 knockdown epithelial cells or zebrafish embryos are rescued by Verteporfin, a specific inhibitor of YAP transcriptional activity, demonstrating the causative role of YAP dysregulation in the occurrence of these defects. Altogether, this study links NEK8 mutations to dysregulation of the Hippo pathway and provide molecular clues to understand the variability of the multiorgan defects in the patients.
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Affiliation(s)
- Valentina Grampa
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marion Delous
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Mohamad Zaidan
- INSERM U1151, CNRS UMR8253, Paris Descartes—Sorbonne Paris Cité University, Necker-Enfants Malades Institute, Mechanisms and Therapeutic Strategies of Chronic Kidney Diseases, Necker Hospital, Paris, France
| | - Gweltas Odye
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Sophie Thomas
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris, France
| | - Nadia Elkhartoufi
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris, France
- Department of Genetics, AP-HP, Necker Hospital, Paris, France
| | - Emilie Filhol
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Olivier Niel
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatric Nephrology, AP-HP, Robert Debré Hospital, Paris, France
| | - Flora Silbermann
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Corinne Lebreton
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Intestinal Immunity, Paris, France
| | | | - Isabelle Rouvet
- Cellular Biotechnology Department and Biobank, Hospices Civils de Lyon, CHU de Lyon, Lyon, France
| | | | - Louise Devisme
- Anatomopathological Department, CHRU Lille, University Hospital, Lille, France
| | | | - Marie-Pierre Cordier
- Department of Genetics, Femme Mère-Enfant Hospital, University of Lyon 1, Bron, France
| | - Yline Capri
- Department of Genetics, CHU Robert-Debré, Paris, France
| | | | - Sabine Sigaudy
- Multidisciplinary Department of Prenatal Diagnosis, La Timone Children’s Hospital, Marseille, France
| | - Rémi Salomon
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatric Nephrology, AP-HP, Necker Hospital, Paris, France
| | - Corinne Antignac
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Department of Genetics, AP-HP, Necker Hospital, Paris, France
| | - Marie-Claire Gubler
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Alexandre Benmerah
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Fabiola Terzi
- INSERM U1151, CNRS UMR8253, Paris Descartes—Sorbonne Paris Cité University, Necker-Enfants Malades Institute, Mechanisms and Therapeutic Strategies of Chronic Kidney Diseases, Necker Hospital, Paris, France
| | - Tania Attié-Bitach
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris, France
- Department of Histology-Embryology and Cytogenetics, AP-HP, Necker Hospital, Paris, France
| | - Cécile Jeanpierre
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Sophie Saunier
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- * E-mail:
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A Point Mutation in p190A RhoGAP Affects Ciliogenesis and Leads to Glomerulocystic Kidney Defects. PLoS Genet 2016; 12:e1005785. [PMID: 26859289 PMCID: PMC4747337 DOI: 10.1371/journal.pgen.1005785] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/12/2015] [Indexed: 01/09/2023] Open
Abstract
Rho family GTPases act as molecular switches regulating actin cytoskeleton dynamics. Attenuation of their signaling capacity is provided by GTPase-activating proteins (GAPs), including p190A, that promote the intrinsic GTPase activity of Rho proteins. In the current study we have performed a small-scale ENU mutagenesis screen and identified a novel loss of function allele of the p190A gene Arhgap35, which introduces a Leu1396 to Gln substitution in the GAP domain. This results in decreased GAP activity for the prototypical Rho-family members, RhoA and Rac1, likely due to disrupted ordering of the Rho binding surface. Consequently, Arhgap35-deficient animals exhibit hypoplastic and glomerulocystic kidneys. Investigation into the cystic phenotype shows that p190A is required for appropriate primary cilium formation in renal nephrons. P190A specifically localizes to the base of the cilia to permit axoneme elongation, which requires a functional GAP domain. Pharmacological manipulations further reveal that inhibition of either Rho kinase (ROCK) or F-actin polymerization is able to rescue the ciliogenesis defects observed upon loss of p190A activity. We propose a model in which p190A acts as a modulator of Rho GTPases in a localized area around the cilia to permit the dynamic actin rearrangement required for cilia elongation. Together, our results establish an unexpected link between Rho GTPase regulation, ciliogenesis and glomerulocystic kidney disease.
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Al-Hamed MH, Kurdi W, Alsahan N, Alabdullah Z, Abudraz R, Tulbah M, Alnemer M, Khan R, Al-Jurayb H, Alahmed A, Tahir AI, Khalil D, Edwards N, Al Abdulaziz B, Binhumaid FS, Majid S, Faquih T, El-Kalioby M, Abouelhoda M, Altassan N, Monies D, Meyer B, Sayer JA, Albaqumi M. Genetic spectrum of Saudi Arabian patients with antenatal cystic kidney disease and ciliopathy phenotypes using a targeted renal gene panel. J Med Genet 2016; 53:338-47. [PMID: 26862157 PMCID: PMC4853542 DOI: 10.1136/jmedgenet-2015-103469] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/04/2016] [Indexed: 12/24/2022]
Abstract
Background Inherited cystic kidney disorders are a common cause of end-stage renal disease. Over 50 ciliopathy genes, which encode proteins that influence the structure and function of the primary cilia, are implicated in cystic kidney disease. Methods To define the phenotype and genotype of cystic kidney disease in fetuses and neonates, we correlated antenatal ultrasound examination and postnatal renal ultrasound examination with targeted exon sequencing, using a renal gene panel. A cohort of 44 families in whom antenatal renal ultrasound scanning findings in affected cases included bilateral cystic kidney disease, echogenic kidneys or enlarged kidneys was investigated. Results In this cohort, disease phenotypes were severe with 36 cases of stillbirth or perinatal death. Extra renal malformations, including encephalocele, polydactyly and heart malformations, consistent with ciliopathy phenotypes, were frequently detected. Renal gene panel testing identified causative mutations in 21 out of 34 families (62%), where patient and parental DNA was available. In the remaining 10 families, where only parental DNA was available, 7 inferred causative mutations were found. Together, mutations were found in 12 different genes with a total of 13 novel pathogenic variants, including an inferred novel variant in NEK8. Mutations in CC2D2A were the most common cause of an antenatal cystic kidney disease and a suspected ciliopathy in our cohort. Conclusions In families with ciliopathy phenotypes, mutational analysis using a targeted renal gene panel allows a rapid molecular diagnosis and provides important information for patients, parents and their physicians.
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Affiliation(s)
- Mohamed H Al-Hamed
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Wesam Kurdi
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Nada Alsahan
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Zainab Alabdullah
- Obstetrics & Gynecology Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Rania Abudraz
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maha Tulbah
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maha Alnemer
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rubina Khan
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Haya Al-Jurayb
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ahmed Alahmed
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Asma I Tahir
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Dania Khalil
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Noel Edwards
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Basma Al Abdulaziz
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Faisal S Binhumaid
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Salma Majid
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Tariq Faquih
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Mohamed El-Kalioby
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Nada Altassan
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Dorota Monies
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Brian Meyer
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - John A Sayer
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Mamdouh Albaqumi
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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Knopp C, Rudnik-Schöneborn S, Eggermann T, Bergmann C, Begemann M, Schoner K, Zerres K, Ortiz Brüchle N. Syndromic ciliopathies: From single gene to multi gene analysis by SNP arrays and next generation sequencing. Mol Cell Probes 2015; 29:299-307. [DOI: 10.1016/j.mcp.2015.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/13/2015] [Accepted: 05/19/2015] [Indexed: 01/23/2023]
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Bakey Z, Bihoreau MT, Piedagnel R, Delestré L, Arnould C, de Villiers AD, Devuyst O, Hoffmann S, Ronco P, Gauguier D, Lelongt B. The SAM domain of ANKS6 has different interacting partners and mutations can induce different cystic phenotypes. Kidney Int 2015; 88:299-310. [PMID: 26039630 DOI: 10.1038/ki.2015.122] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/12/2015] [Accepted: 03/05/2015] [Indexed: 01/18/2023]
Abstract
The ankyrin repeat and sterile α motif (SAM) domain-containing six gene (Anks6) is a candidate for polycystic kidney disease (PKD). Originally identified in the PKD/Mhm(cy/+) rat model of PKD, the disease is caused by a mutation (R823W) in the SAM domain of the encoded protein. Recent studies support the etiological role of the ANKS6 SAM domain in human cystic diseases, but its function in kidney remains unknown. To investigate the role of ANKS6 in cyst formation, we screened an archive of N-ethyl-N-nitrosourea-treated mice and derived a strain carrying a missense mutation (I747N) within the SAM domain of ANKS6. This mutation is only six amino acids away from the PKD-causing mutation (R823W) in cy/+ rats. Evidence of renal cysts in these mice confirmed the crucial role of the SAM domain of ANKS6 in kidney function. Comparative phenotype analysis in cy/+ rats and our Anks6(I747N) mice further showed that the two models display noticeably different PKD phenotypes and that there is a defective interaction between ANKS6 with ANKS3 in the rat and between ANKS6 and BICC1 (bicaudal C homolog 1) in the mouse. Thus, our data demonstrate the importance of ANKS6 for kidney structure integrity and the essential mediating role of its SAM domain in the formation of protein complexes.
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Affiliation(s)
- Zeineb Bakey
- 1] Sorbonne Universités, UPMC Univ Paris 06, UMR_S1155, Paris, France [2] INSERM, UMR_S1155, Hôpital Tenon, Paris, France
| | | | - Rémi Piedagnel
- 1] Sorbonne Universités, UPMC Univ Paris 06, UMR_S1155, Paris, France [2] INSERM, UMR_S1155, Hôpital Tenon, Paris, France
| | - Laure Delestré
- 1] UPD University of Paris 05, Paris, France [2] INSERM, UMR_S1138, CRC, Paris, France
| | - Catherine Arnould
- 1] Sorbonne Universités, UPMC Univ Paris 06, UMR_S1155, Paris, France [2] INSERM, UMR_S1155, Hôpital Tenon, Paris, France
| | - Alexandre d'Hotman de Villiers
- 1] Sorbonne Universités, UPMC Univ Paris 06, UMR_S1155, Paris, France [2] INSERM, UMR_S1155, Hôpital Tenon, Paris, France
| | - Olivier Devuyst
- 1] UCL Medical School, Brussels, Belgium [2] University of Zurich, Zürich, Switzerland
| | - Sigrid Hoffmann
- Medical Research Center, University of Heidelberg, Mannheim, Germany
| | - Pierre Ronco
- 1] Sorbonne Universités, UPMC Univ Paris 06, UMR_S1155, Paris, France [2] INSERM, UMR_S1155, Hôpital Tenon, Paris, France [3] AP-HP, Hôpital Tenon, Paris, France
| | - Dominique Gauguier
- 1] UPD University of Paris 05, Paris, France [2] INSERM, UMR_S1138, CRC, Paris, France [3] Institute of Cardiometabolism and Nutrition, University Pierre & Marie Curie, Hospital Pitié Salpetrière, Paris, France
| | - Brigitte Lelongt
- 1] Sorbonne Universités, UPMC Univ Paris 06, UMR_S1155, Paris, France [2] INSERM, UMR_S1155, Hôpital Tenon, Paris, France
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Habbig S, Liebau MC. Ciliopathies - from rare inherited cystic kidney diseases to basic cellular function. Mol Cell Pediatr 2015; 2:8. [PMID: 26542298 PMCID: PMC4530564 DOI: 10.1186/s40348-015-0019-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/20/2015] [Indexed: 01/02/2023] Open
Abstract
Background Primary cilia are membrane-bound microtubule-based protuberances of the cell membrane projecting to the extracellular environment. While little attention was paid to this subcellular structure over a long time, recent research has highlighted multiple cellular functions of primary cilia and has brought cilia to the focus of medical and cell biological research. Findings Cilia are nowadays considered to be crucial cellular structures controlling diverse intracellular signaling cascades. Dysfunction of cilia leads to a pleiotropic group of diseases ranging from cystic kidney disease via neurologic disorders to metabolic phenotypes and cardiac malformations. According to the underlying cellular pathophysiology, these diverse disorders have been subsumed under the term “ciliopathies”. Conclusions The work on rare human ciliopathies has strongly deepened our genetic and cell biological understanding of multiple diseases and cellular events thus ultimately leading to clinical trials of novel therapeutic approaches. This review focuses on some of the important developments in ciliopathy research.
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Affiliation(s)
- Sandra Habbig
- Department of Pediatrics and Center for Molecular Medicine, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany. .,Department of Medicine II, Nephrology Research Laboratory University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany.
| | - Max Christoph Liebau
- Department of Pediatrics and Center for Molecular Medicine, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany. .,Department of Medicine II, Nephrology Research Laboratory University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany.
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Abstract
Inherited retinal degeneration (IRD) may occur in isolation or as part of a multi-systemic condition. Ocular manifestations may be the presenting symptom of a syndromic disease and can include retinitis pigmentosa, cone-rod dystrophy, or maculopathy. Alternatively, patients affected with syndromic disease may already have other systemic manifestations at the time retinal disease is diagnosed. Some of these systemic diseases can cause significant morbidity. Here, we review several of these syndromic IRDs and their underlying genetic causes. Early recognition and referral for systemic evaluation and surveillance may lead to early intervention and an improved outcome. Obtaining a molecular diagnosis can be beneficial in securing a definitive diagnosis, especially in cases with atypical presentations. A genetic diagnosis may also be informative with regard to prognosis and potential therapies. Effective management and rehabilitation for patients with syndromic retinal dystrophy requires a comprehensive genetic-based team approach involving patients, family members, ophthalmologists, primary care physicians, and geneticists.
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Affiliation(s)
- Xiang Q Werdich
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, Massachusetts , USA
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An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease. PLoS One 2015; 10:e0116680. [PMID: 25646624 PMCID: PMC4315576 DOI: 10.1371/journal.pone.0116680] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
Renal cysts are clinically and genetically heterogeneous conditions. Autosomal dominant polycystic kidney disease (ADPKD) is the most frequent life-threatening genetic disease and mainly caused by mutations in PKD1. The presence of six PKD1 pseudogenes and tremendous allelic heterogeneity make molecular genetic testing challenging requiring laborious locus-specific amplification. Increasing evidence suggests a major role for PKD1 in early and severe cases of ADPKD and some patients with a recessive form. Furthermore it is becoming obvious that clinical manifestations can be mimicked by mutations in a number of other genes with the necessity for broader genetic testing. We established and validated a sequence capture based NGS testing approach for all genes known for cystic and polycystic kidney disease including PKD1. Thereby, we demonstrate that the applied standard mapping algorithm specifically aligns reads to the PKD1 locus and overcomes the complication of unspecific capture of pseudogenes. Employing careful and experienced assessment of NGS data, the method is shown to be very specific and equally sensitive as established methods. An additional advantage over conventional Sanger sequencing is the detection of copy number variations (CNVs). Sophisticated bioinformatic read simulation increased the high analytical depth of the validation study and further demonstrated the strength of the approach. We further raise some awareness of limitations and pitfalls of common NGS workflows when applied in complex regions like PKD1 demonstrating that quality of NGS needs more than high coverage of the target region. By this, we propose a time- and cost-efficient diagnostic strategy for comprehensive molecular genetic testing of polycystic kidney disease which is highly automatable and will be of particular value when therapeutic options for PKD emerge and genetic testing is needed for larger numbers of patients.
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Chung EM, Conran RM, Schroeder JW, Rohena-Quinquilla IR, Rooks VJ. From the radiologic pathology archives: pediatric polycystic kidney disease and other ciliopathies: radiologic-pathologic correlation. Radiographics 2015; 34:155-78. [PMID: 24428289 DOI: 10.1148/rg.341135179] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetic defects of cilia cause a wide range of diseases, collectively known as ciliopathies. Primary, or nonmotile, cilia function as sensory organelles involved in the regulation of cell growth, differentiation, and homeostasis. Cilia are present in nearly every cell in the body and mutations of genes encoding ciliary proteins affect multiple organs, including the kidneys, liver, pancreas, retina, central nervous system (CNS), and skeletal system. Genetic mutations causing ciliary dysfunction result in a large number of heterogeneous phenotypes that can manifest with a variety of overlapping abnormalities in multiple organ systems. Renal manifestations of ciliopathies are the most common abnormalities and include collecting duct dilatation and cyst formation in autosomal recessive polycystic kidney disease (ARPKD), cyst formation anywhere in the nephron in autosomal dominant polycystic kidney disease (ADPKD), and tubulointerstitial fibrosis in nephronophthisis, as well as in several CNS and skeletal malformation syndromes. Hepatic disease is another common manifestation of ciliopathies, ranging from duct dilatation and cyst formation in ARPKD and ADPKD to periportal fibrosis in ARPKD and several malformation syndromes. The unifying molecular pathogenesis of this emerging class of disorders explains the overlap of abnormalities in disparate organ systems and links diseases of widely varied clinical features. It is important for radiologists to be able to recognize the multisystem manifestations of these syndromes, as imaging plays an important role in diagnosis and follow-up of affected patients.
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Affiliation(s)
- Ellen M Chung
- From the Department of Radiology and Radiological Sciences (E.M.C.) and Department of Pathology (R.M.C.), F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814; Pediatric Radiology Section, American Institute for Radiologic Pathology, Silver Spring, Md (E.M.C.); Department of Radiology, Walter Reed National Military Medical Center, Bethesda, Md (J.W.S., I.R.R.Q.); and Department of Radiology, Tripler Army Medical Center, Honolulu, Hawaii (V.J.R.)
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