1
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Pantel D, Mertens ND, Schneider R, Hölzel S, Kari JA, Desoky SE, Shalaby MA, Lim TY, Sanna-Cherchi S, Shril S, Hildebrandt F. Copy number variation analysis in 138 families with steroid-resistant nephrotic syndrome identifies causal homozygous deletions in PLCE1 and NPHS2 in two families. Pediatr Nephrol 2024; 39:455-461. [PMID: 37670083 PMCID: PMC10979458 DOI: 10.1007/s00467-023-06134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/06/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
BACKGROUND Steroid-resistant nephrotic syndrome (SRNS) is the second most common cause of kidney failure in children and adults under the age of 20 years. Previously, we were able to detect by exome sequencing (ES) a known monogenic cause of SRNS in 25-30% of affected families. However, ES falls short of detecting copy number variants (CNV). Therefore, we hypothesized that causal CNVs could be detected in a large SRNS cohort. METHODS We performed genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on a cohort of 138 SRNS families, in whom we previously did not identify a genetic cause through ES. We evaluated ES and CNV data for variants in 60 known SRNS genes and in 13 genes in which variants are known to cause a phenocopy of SRNS. We applied previously published, predefined criteria for CNV evaluation. RESULTS We detected a novel CNV in two genes in 2 out of 138 families (1.5%). The 9,673 bp homozygous deletion in PLCE1 and the 6,790 bp homozygous deletion in NPHS2 were confirmed across the breakpoints by PCR and Sanger sequencing. CONCLUSIONS We confirmed that CNV analysis can identify the genetic cause in SRNS families that remained unsolved after ES. Though the rate of detected CNVs is minor, CNV analysis can be used when there are no other genetic causes identified. Causative CNVs are less common in SRNS than in other monogenic kidney diseases, such as congenital anomalies of the kidneys and urinary tract, where the detection rate was 5.3%. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Dalia Pantel
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Nils D Mertens
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Ronen Schneider
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Selina Hölzel
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Jameela A Kari
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohamed A Shalaby
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA.
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2
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Riedhammer KM, Ćomić J, Tasic V, Putnik J, Abazi-Emini N, Paripovic A, Stajic N, Meitinger T, Nushi-Stavileci V, Berutti R, Braunisch MC, Hoefele J. Exome sequencing in individuals with congenital anomalies of the kidney and urinary tract (CAKUT): a single-center experience. Eur J Hum Genet 2023; 31:674-680. [PMID: 36922632 PMCID: PMC10250376 DOI: 10.1038/s41431-023-01331-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Individuals with congenital anomalies of the kidney and urinary tract (CAKUT) show a broad spectrum of malformations. CAKUT can occur in an isolated fashion or as part of a syndromic disorder and can lead to end-stage kidney failure. A monogenic cause can be identified in ~12% of affected individuals. This study investigated a single-center CAKUT cohort analyzed by exome sequencing (ES). Emphasis was placed on the question whether diagnostic yield differs between certain CAKUT phenotypes (e.g., bilateral kidney affection, unilateral kidney affection or only urinary tract affection). 86 unrelated individuals with CAKUT were categorized according to their phenotype and analyzed by ES to identify a monogenic cause. Prioritized variants were rated according to the recommendations of the American College of Medical Genetics and Genomics and the Association for Clinical Genomic Science. Diagnostic yields of different phenotypic categories were compared. Clinical data were collected using a standardized questionnaire. In the study cohort, 7/86 individuals had a (likely) pathogenic variant in the genes PAX2, PBX1, EYA1, or SALL1. Additionally, in one individual, a 17q12 deletion syndrome (including HNF1B) was detected. 64 individuals had a kidney affection, which was bilateral in 36. All solved cases (8/86, 9%) had bilateral kidney affection (diagnostic yield in subcohort: 8/36, 22%). Although the diagnostic yield in CAKUT cohorts is low, our single-center experience argues, that, in individuals with bilateral kidney affection, monogenic burden is higher than in those with unilateral kidney or only urinary tract affection.
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Affiliation(s)
- Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Jasmina Ćomić
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Velibor Tasic
- University Children's Hospital, Medical Faculty of Skopje, Skopje, North Macedonia
| | - Jovana Putnik
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Nora Abazi-Emini
- University Children's Hospital, Medical Faculty of Skopje, Skopje, North Macedonia
| | - Aleksandra Paripovic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Natasa Stajic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | | | - Riccardo Berutti
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias C Braunisch
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany.
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3
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Koslow M, Zhu P, McCabe C, Xu X, Lin X. Kidney transcriptome and cystic kidney disease genes in zebrafish. Front Physiol 2023; 14:1184025. [PMID: 37256068 PMCID: PMC10226271 DOI: 10.3389/fphys.2023.1184025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/20/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction: Polycystic kidney disease (PKD) is a condition where fluid filled cysts form on the kidney which leads to overall renal failure. Zebrafish has been recently adapted to study polycystic kidney disease, because of its powerful embryology and genetics. However, there are concerns on the conservation of this lower vertebrate in modeling polycystic kidney disease. Methods: Here, we aim to assess the molecular conservation of zebrafish by searching homologues polycystic kidney disease genes and carrying transcriptome studies in this animal. Results and Discussion: We found that out of 82 human cystic kidney disease genes, 81 have corresponding zebrafish homologs. While 75 of the genes have a single homologue, only 6 of these genes have two homologs. Comparison of the expression level of the transcripts enabled us to identify one homolog over the other homolog with >70% predominance, which would be prioritized for future experimental studies. Prompted by sexual dimorphism in human and rodent kidneys, we studied transcriptome between different sexes and noted significant differences in male vs. female zebrafish, indicating that sex dimorphism also occurs in zebrafish. Comparison between zebrafish and mouse identified 10% shared genes and 38% shared signaling pathways. String analysis revealed a cluster of genes differentially expressed in male vs. female zebrafish kidneys. In summary, this report demonstrated remarkable molecular conservation, supporting zebrafish as a useful animal model for cystic kidney disease.
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Affiliation(s)
- Matthew Koslow
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Ping Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Chantal McCabe
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Xueying Lin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
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4
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Airik M, Arbore H, Childs E, Huynh AB, Phua YL, Chen CW, Aird K, Bharathi S, Zhang B, Conlon P, Kmoch S, Kidd K, Bleyer AJ, Vockley J, Goetzman E, Wipf P, Airik R. Mitochondrial ROS Triggers KIN Pathogenesis in FAN1-Deficient Kidneys. Antioxidants (Basel) 2023; 12:900. [PMID: 37107275 PMCID: PMC10135478 DOI: 10.3390/antiox12040900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Karyomegalic interstitial nephritis (KIN) is a genetic adult-onset chronic kidney disease (CKD) characterized by genomic instability and mitotic abnormalities in the tubular epithelial cells. KIN is caused by recessive mutations in the FAN1 DNA repair enzyme. However, the endogenous source of DNA damage in FAN1/KIN kidneys has not been identified. Here we show, using FAN1-deficient human renal tubular epithelial cells (hRTECs) and FAN1-null mice as a model of KIN, that FAN1 kidney pathophysiology is triggered by hypersensitivity to endogenous reactive oxygen species (ROS), which cause chronic oxidative and double-strand DNA damage in the kidney tubular epithelial cells, accompanied by an intrinsic failure to repair DNA damage. Furthermore, persistent oxidative stress in FAN1-deficient RTECs and FAN1 kidneys caused mitochondrial deficiencies in oxidative phosphorylation and fatty acid oxidation. The administration of subclinical, low-dose cisplatin increased oxidative stress and aggravated mitochondrial dysfunction in FAN1-deficient kidneys, thereby exacerbating KIN pathophysiology. In contrast, treatment of FAN1 mice with a mitochondria-targeted ROS scavenger, JP4-039, attenuated oxidative stress and accumulation of DNA damage, mitigated tubular injury, and preserved kidney function in cisplatin-treated FAN1-null mice, demonstrating that endogenous oxygen stress is an important source of DNA damage in FAN1-deficient kidneys and a driver of KIN pathogenesis. Our findings indicate that therapeutic modulation of kidney oxidative stress may be a promising avenue to mitigate FAN1/KIN kidney pathophysiology and disease progression in patients.
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Affiliation(s)
- Merlin Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Haley Arbore
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Elizabeth Childs
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Amy B. Huynh
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Yu Leng Phua
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi Wei Chen
- Department of Pharmacology & Chemical Biology and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Katherine Aird
- Department of Pharmacology & Chemical Biology and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sivakama Bharathi
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Bob Zhang
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Peter Conlon
- Nephrology Department, Beaumont Hospital, D09 V2N0 Dublin, Ireland
| | - Stanislav Kmoch
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Kendrah Kidd
- Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | | | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Eric Goetzman
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rannar Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15224, USA
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5
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Kohl S, Liebau MC. Fetal and Perinatal Nephrology: Small but Mighty. KIDNEY360 2023; 4:291-293. [PMID: 36996292 PMCID: PMC10103224 DOI: 10.34067/kid.0000000000000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Affiliation(s)
- Stefan Kohl
- Department of Pediatrics and Center for Family Health, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Max C. Liebau
- Department of Pediatrics and Center for Family Health, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC) and Center for Rare Diseases, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
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6
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Kohl S, Avni FE, Boor P, Capone V, Clapp WL, De Palma D, Harris T, Heidet L, Hilger AC, Liapis H, Lilien M, Manzoni G, Montini G, Negrisolo S, Pierrat MJ, Raes A, Reutter H, Schreuder MF, Weber S, Winyard PJD, Woolf AS, Schaefer F, Liebau MC. Definition, diagnosis and clinical management of non-obstructive kidney dysplasia: a consensus statement by the ERKNet Working Group on Kidney Malformations. Nephrol Dial Transplant 2022; 37:2351-2362. [PMID: 35772019 PMCID: PMC9681917 DOI: 10.1093/ndt/gfac207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 12/31/2022] Open
Abstract
Kidney dysplasia is one of the most frequent causes of chronic kidney failure in children. While dysplasia is a histological diagnosis, the term 'kidney dysplasia' is frequently used in daily clinical life without histopathological confirmation. Clinical parameters of kidney dysplasia have not been clearly defined, leading to imprecise communication amongst healthcare professionals and patients. This lack of consensus hampers precise disease understanding and the development of specific therapies. Based on a structured literature search, we here suggest a common basis for clinical, imaging, genetic, pathological and basic science aspects of non-obstructive kidney dysplasia associated with functional kidney impairment. We propose to accept hallmark sonographic findings as surrogate parameters defining a clinical diagnosis of dysplastic kidneys. We suggest differentiated clinical follow-up plans for children with kidney dysplasia and summarize established monogenic causes for non-obstructive kidney dysplasia. Finally, we point out and discuss research gaps in the field.
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Affiliation(s)
- Stefan Kohl
- Department of Pediatrics, University Hospital of Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Fred E Avni
- Department of Pediatric Imaging, Jeanne de Flandre Hospital, Lille University Hospitals, Lille Cedex, France
| | - Peter Boor
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany,Medical Clinic II (Nephrology and Immunology), University Hospital RWTH Aachen, Aachen, Germany
| | - Valentina Capone
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - William L Clapp
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Diego De Palma
- Nuclear Medicine Unit, Circolo Hospital and Macchi Foundation, ASST-settelaghi, Varese, Italy
| | - Tess Harris
- The Polycystic Kidney Disease Charity, London, UK
| | - Laurence Heidet
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France,APHP, Service de Néphrologie Pédiatrique, Centre de Référence MARHEA, Hôpital universitaire Necker-Enfants malades, Paris, France
| | - Alina C Hilger
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany,Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Erlangen, Germany
| | - Helen Liapis
- Nephrology Center, Ludwig Maximilian University (LMU), Munich, Germany
| | - Marc Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gianantonio Manzoni
- Pediatric Urology Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy,Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
| | - Susanna Negrisolo
- Laboratory of Immunopathology and Molecular Biology of the Kidney, Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Marie-Jeanne Pierrat
- Federation of European Patient Groups affected by Rare/Genetic Kidney Diseases (FEDERG), Brussels, Belgium
| | - Ann Raes
- Department of Pediatric Nephrology and Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Heiko Reutter
- Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Erlangen, Germany,Division of Neonatology and Pediatric Intensive Care Medicine, Department of Pediatric and Adolescent Medicine, Friedrich-Alexander-Universitat Erlangen-Nürnberg, Erlangen, Germany
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Stefanie Weber
- Department of Pediatric Nephrology, Marburg Kidney Research Center, Philipps University, Marburg, Germany
| | - Paul J D Winyard
- University College London Great Ormond Street, Institute of Child Health, London, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK,Royal Manchester Children's Hospital, Manchester University National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Franz Schaefer
- Division of Pediatric Nephrology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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7
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Sakakibara N, Nozu K, Yamamura T, Horinouchi T, Nagano C, Ye MJ, Ishiko S, Aoto Y, Rossanti R, Hamada R, Okamoto N, Shima Y, Nakanishi K, Matsuo M, Iijima K, Morisada N. Comprehensive genetic analysis using next-generation sequencing for the diagnosis of nephronophthisis-related ciliopathies in the Japanese population. J Hum Genet 2022; 67:427-440. [PMID: 35140360 DOI: 10.1038/s10038-022-01020-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/09/2022]
Abstract
Nephronophthisis is an autosomal-recessive kidney disease that is caused by abnormalities in primary cilia. Nephronophthisis-related ciliopathies (NPHP-RCs) are a common cause of end-stage kidney disease (ESKD) in children and adolescents. NPHP-RCs are often accompanied by extrarenal manifestations, including intellectual disability, retinitis pigmentosa, or polydactyly. Although more than 100 causative genes have been identified, its diagnosis is difficult because the clinical features of each mutation often overlap. From September 2010 to August 2021, we performed genetic analysis, including next-generation sequencing (NGS), in 574 probands with kidney dysfunction and retrospectively studied cases genetically diagnosed with NPHP-RCs. RESULTS: We detected mutations related to NPHP-RCs in 93 patients from 83 families. Members of 60 families were diagnosed using NGS, and the mutations and the corresponding number of families are as follows: NPHP1 (24), NPHP3 (10), OFD1 (7), WDR35 (5), SDCCAG8 (4), BBS10 (3), TMEM67 (3), WDR19 (3), BBS1 (2), BBS2 (2), IFT122 (2), IFT140 (2), IQCB1 (2), MKKS (2), SCLT1 (2), TTC21B (2), ALMS1 (1), ANKS6 (1), BBS4 (1), BBS12 (1), CC2D2A (1), DYNC2H1 (1), IFT172 (1), and MAPKBP1 (1). A total of 39 cases (41.9%) progressed to ESKD at the time of genetic analysis, whereas 58 cases (62.3%) showed extrarenal manifestations, the most common being developmental delay, intellectual disability, and autism spectrum disorder in 44 patients. Comprehensive genetic analysis using NGS is useful for diagnosing patients with NPHP-RCs.
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Affiliation(s)
- Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ming Juan Ye
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Riku Hamada
- Department of Nephrology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Koichi Nakanishi
- Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.,Hospital Director, Hyogo Prefectural Kobe Children's Hospital, Kobe, 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.
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8
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Primary coenzyme Q10 nephropathy, a potentially treatable form of steroid-resistant nephrotic syndrome. Pediatr Nephrol 2021; 36:3515-3527. [PMID: 33479824 PMCID: PMC8295399 DOI: 10.1007/s00467-020-04914-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/28/2020] [Accepted: 12/31/2020] [Indexed: 12/18/2022]
Abstract
Steroid-resistant nephrotic syndrome (SRNS) is a genetically heterogeneous kidney disease that is the second most frequent cause of kidney failure in the first 2 decades of life. Despite the identification of mutations in more than 39 genes as causing SRNS, and the localization of its pathogenesis to glomerular podocytes, the disease mechanisms of SRNS remain poorly understood and no universally safe and effective therapy exists to treat patients with this condition. Recently, genetic research has identified a subgroup of SRNS patients whose kidney pathology is caused by primary coenzyme Q10 (CoQ10) deficiency due to recessive mutations in genes that encode proteins in the CoQ10 biosynthesis pathway. Clinical and preclinical studies show that primary CoQ10 deficiency may be responsive to treatment with CoQ10 supplements bypassing the biosynthesis defects. Coenzyme Q10 is an essential component of the mitochondrial respiratory chain, where it transports electrons from complexes I and II to complex III. Studies in yeast and mammalian model systems have recently identified the molecular functions of the individual CoQ10 biosynthesis complex proteins, validated these findings, and provided an impetus for developing therapeutic compounds to replenish CoQ10 levels in the tissues/organs and thus prevent the destruction of tissues due to mitochondrial OXPHOS deficiencies. In this review, we will summarize the clinical findings of the kidney pathophysiology of primary CoQ10 deficiencies and discuss recent advances in the development of therapies to counter CoQ10 deficiency in tissues.
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9
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El-Dessouky SH, Hosny H, Elarab AE, Issa MY. Prenatal presentation of Walker–Warburg syndrome with a POMT2 mutation: an extended fetal phenotype. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00093-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Walker–Warburg syndrome (WWS) is a rare, lethal, genetically, and clinically heterogeneous congenital muscular dystrophy resulting from defective glycosylation of α-dystroglycan (α-DG) and is associated with both cranial and ocular malformations. Prenatal detection of posterior fossa anomalies in association with hydrocephalus are nonspecific, however, an additional finding of eye anomalies are typical for WWS. The purpose of this report is to elucidate the pattern of associated malformations in a fetus with WWS born to 3rd degree consanguineously married couple. Additionally, the fetal ultrasonography revealed congenital heart disease, clenched hands, and talipes equinovarus; these findings have not been previously reported and represent an expansion of prenatal spectrum associated with WWS.
Case presentation
We report on a specific sonographic pattern of congenital anomalies including hydrocephalus, agenesis of corpus callosum, and Dandy–Walker malformation. Ocular abnormalities include microphthalmia, cataract, and an echoic structure suggestive of persistent primary vitreous. Other features include congenital heart disease, unilateral multicystic kidney, and previously unreported findings of bilateral clenched hands and talipes equinovarus. The molecular analysis detected a homozygous splicing mutation, c.924-2A>C, in the POMT2 gene; this variant segregated with the phenotype.
Conclusion
WWS syndrome has characteristic prenatal ultrasound findings which can improve the prenatal identification of this condition and help in guiding the molecular diagnosis and counseling. The detection of bilateral clenched hands and talipes equinovarus is a novel finding that further expands the phenotypic spectrum of WWS.
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10
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Becherucci F, Landini S, Cirillo L, Mazzinghi B, Romagnani P. Look Alike, Sound Alike: Phenocopies in Steroid-Resistant Nephrotic Syndrome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E8363. [PMID: 33198123 PMCID: PMC7696007 DOI: 10.3390/ijerph17228363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022]
Abstract
Steroid-resistant nephrotic syndrome (SRNS) is a clinical picture defined by the lack of response to standard steroid treatment, frequently progressing toward end-stage kidney disease. The genetic basis of SRNS has been thoroughly explored since the end of the 1990s and especially with the advent of next-generation sequencing. Genetic forms represent about 30% of cases of SRNS. However, recent evidence supports the hypothesis that "phenocopies" could account for a non-negligible fraction of SRNS patients who are currently classified as non-genetic, paving the way for a more comprehensive understanding of the genetic background of the disease. The identification of phenocopies is mandatory in order to provide patients with appropriate clinical management and to inform therapy. Extended genetic testing including phenocopy genes, coupled with reverse phenotyping, is recommended for all young patients with SRNS to avoid unnecessary and potentially harmful diagnostic procedures and treatment, and for the reclassification of the disease. The aim of this work is to review the main steps of the evolution of genetic testing in SRNS, demonstrating how a paradigm shifting from "forward" to "reverse" genetics could significantly improve the identification of the molecular mechanisms of the disease, as well as the overall clinical management of affected patients.
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Affiliation(s)
- Francesca Becherucci
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
| | - Samuela Landini
- Department of Biomedical, Experimental and Clinical Science “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy;
| | - Luigi Cirillo
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
- Department of Biomedical, Experimental and Clinical Science “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy;
| | - Benedetta Mazzinghi
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
| | - Paola Romagnani
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
- Department of Biomedical, Experimental and Clinical Science “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy;
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11
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Groopman EE, Povysil G, Goldstein DB, Gharavi AG. Rare genetic causes of complex kidney and urological diseases. Nat Rev Nephrol 2020; 16:641-656. [PMID: 32807983 PMCID: PMC7772719 DOI: 10.1038/s41581-020-0325-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 02/08/2023]
Abstract
Although often considered a single-entity, chronic kidney disease (CKD) comprises many pathophysiologically distinct disorders that result in persistently abnormal kidney structure and/or function, and encompass both monogenic and polygenic aetiologies. Rare inherited forms of CKD frequently span diverse phenotypes, reflecting genetic phenomena including pleiotropy, incomplete penetrance and variable expressivity. Use of chromosomal microarray and massively parallel sequencing technologies has revealed that genomic disorders and monogenic aetiologies contribute meaningfully to seemingly complex forms of CKD across different clinically defined subgroups and are characterized by high genetic and phenotypic heterogeneity. Investigations of prevalent genomic disorders in CKD have integrated genetic, bioinformatic and functional studies to pinpoint the genetic drivers underlying their renal and extra-renal manifestations, revealing both monogenic and polygenic mechanisms. Similarly, massively parallel sequencing-based analyses have identified gene- and allele-level variation that contribute to the clinically diverse phenotypes observed for many monogenic forms of nephropathy. Genome-wide sequencing studies suggest that dual genetic diagnoses are found in at least 5% of patients in whom a genetic cause of disease is identified, highlighting the fact that complex phenotypes can also arise from multilocus variation. A multifaceted approach that incorporates genetic and phenotypic data from large, diverse cohorts will help to elucidate the complex relationships between genotype and phenotype for different forms of CKD, supporting personalized medicine for individuals with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York, NY, USA.
- Center for Precision Medicine and Genomics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
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12
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Ahram DF, Aggarwal VS, Sanna-Cherchi S. Phenocopies, Phenotypic Expansion, and Coincidental Diagnoses: Time to Abandon Targeted Gene Panels? Am J Kidney Dis 2020; 76:451-453. [PMID: 32807573 DOI: 10.1053/j.ajkd.2020.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/09/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Dina F Ahram
- Division of Nephrology, Columbia University, New York, NY; Department of Pathology & Cell Biology, Columbia University, New York, NY
| | - Vimla S Aggarwal
- Department of Pathology & Cell Biology, Columbia University, New York, NY
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13
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Phenotype expansion of heterozygous FOXC1 pathogenic variants toward involvement of congenital anomalies of the kidneys and urinary tract (CAKUT). Genet Med 2020; 22:1673-1681. [PMID: 32475988 DOI: 10.1038/s41436-020-0844-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney disease in childhood and adolescence. We aim to identify novel monogenic causes of CAKUT. METHODS Exome sequencing was performed in 550 CAKUT-affected families. RESULTS We discovered seven FOXC1 heterozygous likely pathogenic variants within eight CAKUT families. These variants are either never reported, or present in <5 alleles in the gnomAD database with ~141,456 controls. FOXC1 is a causal gene for Axenfeld-Rieger syndrome type 3 and anterior segment dysgenesis 3. Pathogenic variants in FOXC1 have not been detected in patients with CAKUT yet. Interestingly, mouse models for Foxc1 show severe CAKUT phenotypes with incomplete penetrance and variable expressivity. The FOXC1 variants are enriched in the CAKUT cohort compared with the control. Genotype-phenotype correlations showed that Axenfeld-Rieger syndrome or anterior segment dysgenesis can be caused by both truncating and missense pathogenic variants, and the missense variants are located at the forkhead domain. In contrast, for CAKUT, there is no truncating pathogenic variant, and all variants except one are located outside the forkhead domain. CONCLUSION We thereby expanded the phenotype of FOXC1 pathogenic variants toward involvement of CAKUT, which can potentially be explained by allelism.
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14
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Kampf LL, Schneider R, Gerstner L, Thünauer R, Chen M, Helmstädter M, Amar A, Onuchic-Whitford AC, Loza Munarriz R, Berdeli A, Müller D, Schrezenmeier E, Budde K, Mane S, Laricchia KM, Rehm HL, MacArthur DG, Lifton RP, Walz G, Römer W, Bergmann C, Hildebrandt F, Hermle T. TBC1D8B Mutations Implicate RAB11-Dependent Vesicular Trafficking in the Pathogenesis of Nephrotic Syndrome. J Am Soc Nephrol 2019; 30:2338-2353. [PMID: 31732614 DOI: 10.1681/asn.2019040414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Mutations in about 50 genes have been identified as monogenic causes of nephrotic syndrome, a frequent cause of CKD. These genes delineated the pathogenetic pathways and rendered significant insight into podocyte biology. METHODS We used whole-exome sequencing to identify novel monogenic causes of steroid-resistant nephrotic syndrome (SRNS). We analyzed the functional significance of an SRNS-associated gene in vitro and in podocyte-like Drosophila nephrocytes. RESULTS We identified hemizygous missense mutations in the gene TBC1D8B in five families with nephrotic syndrome. Coimmunoprecipitation assays indicated interactions between TBC1D8B and active forms of RAB11. Silencing TBC1D8B in HEK293T cells increased basal autophagy and exocytosis, two cellular functions that are independently regulated by RAB11. This suggests that TBC1D8B plays a regulatory role by inhibiting endogenous RAB11. Coimmunoprecipitation assays showed TBC1D8B also interacts with the slit diaphragm protein nephrin, and colocalizes with it in immortalized cell lines. Overexpressed murine Tbc1d8b with patient-derived mutations had lower affinity for endogenous RAB11 and nephrin compared with wild-type Tbc1d8b protein. Knockdown of Tbc1d8b in Drosophila impaired function of the podocyte-like nephrocytes, and caused mistrafficking of Sns, the Drosophila ortholog of nephrin. Expression of Rab11 RNAi in nephrocytes entailed defective delivery of slit diaphragm protein to the membrane, whereas RAB11 overexpression revealed a partial phenotypic overlap to Tbc1d8b loss of function. CONCLUSIONS Novel mutations in TBC1D8B are monogenic causes of SRNS. This gene inhibits RAB11. Our findings suggest that RAB11-dependent vesicular nephrin trafficking plays a role in the pathogenesis of nephrotic syndrome.
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Affiliation(s)
- Lina L Kampf
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Ronen Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lea Gerstner
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Roland Thünauer
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Freiburg, Germany.,Advanced Light and Fluorescence Microscopy Facility, Centre for Structural Systems Biology (CSSB) and University of Hamburg, Hamburg, Germany
| | - Mengmeng Chen
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Martin Helmstädter
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Ali Amar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ana C Onuchic-Whitford
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Afig Berdeli
- Department of Pediatrics, Molecular Medicine Laboratory, Ege University, Izmir, Turkey
| | - Dominik Müller
- Department of Pediatric Nephrology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Eva Schrezenmeier
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Kristen M Laricchia
- Broad Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge
| | - Heidi L Rehm
- Broad Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge
| | - Daniel G MacArthur
- Broad Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Gerd Walz
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Winfried Römer
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Carsten Bergmann
- Center for Human Genetics, Mainz, Germany.,Center for Human Genetics, Bioscientia, Ingelheim, Germany; and.,Department of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts;
| | - Tobias Hermle
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany;
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15
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COL4A1 mutations as a potential novel cause of autosomal dominant CAKUT in humans. Hum Genet 2019; 138:1105-1115. [PMID: 31230195 DOI: 10.1007/s00439-019-02042-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/18/2019] [Indexed: 01/03/2023]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney disease (~ 45%) that manifests before 30 years of age. The genetic locus containing COL4A1 (13q33-34) has been implicated in vesicoureteral reflux (VUR), but mutations in COL4A1 have not been reported in CAKUT. We hypothesized that COL4A1 mutations cause CAKUT in humans. We performed whole exome sequencing (WES) in 550 families with CAKUT. As negative control cohorts we used WES sequencing data from patients with nephronophthisis (NPHP) with no genetic cause identified (n = 257) and with nephrotic syndrome (NS) due to monogenic causes (n = 100). We identified a not previously reported heterozygous missense variant in COL4A1 in three siblings with isolated VUR. When examining 549 families with CAKUT, we identified nine additional different heterozygous missense mutations in COL4A1 in 11 individuals from 11 unrelated families with CAKUT, while no COL4A1 mutations were identified in a control cohort with NPHP and only one in the cohort with NS. Most individuals (12/14) had isolated CAKUT with no extrarenal features. The predominant phenotype was VUR (9/14). There were no clinical features of the COL4A1-related disorders (e.g., HANAC syndrome, porencephaly, tortuosity of retinal arteries). Whereas COL4A1-related disorders are typically caused by glycine substitutions in the collagenous domain (84.4% of variants), only one variant in our cohort is a glycine substitution within the collagenous domain (1/10). We identified heterozygous COL4A1 mutations as a potential novel autosomal dominant cause of CAKUT that is allelic to the established COL4A1-related disorders and predominantly caused by non-glycine substitutions.
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16
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Monogenic causes of chronic kidney disease in adults. Kidney Int 2019; 95:914-928. [PMID: 30773290 DOI: 10.1016/j.kint.2018.10.031] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/10/2018] [Accepted: 10/19/2018] [Indexed: 12/18/2022]
Abstract
Approximately 500 monogenic causes of chronic kidney disease (CKD) have been identified, mainly in pediatric populations. The frequency of monogenic causes among adults with CKD has been less extensively studied. To determine the likelihood of detecting monogenic causes of CKD in adults presenting to nephrology services in Ireland, we conducted whole exome sequencing (WES) in a multi-centre cohort of 114 families including 138 affected individuals with CKD. Affected adults were recruited from 78 families with a positive family history, 16 families with extra-renal features, and 20 families with neither a family history nor extra-renal features. We detected a pathogenic mutation in a known CKD gene in 42 of 114 families (37%). A monogenic cause was identified in 36% of affected families with a positive family history of CKD, 69% of those with extra-renal features, and only 15% of those without a family history or extra-renal features. There was no difference in the rate of genetic diagnosis in individuals with childhood versus adult onset CKD. Among the 42 families in whom a monogenic cause was identified, WES confirmed the clinical diagnosis in 17 (40%), corrected the clinical diagnosis in 9 (22%), and established a diagnosis for the first time in 16 families referred with CKD of unknown etiology (38%). In this multi-centre study of adults with CKD, a molecular genetic diagnosis was established in over one-third of families. In the evolving era of precision medicine, WES may be an important tool to identify the cause of CKD in adults.
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17
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Mann N, Braun DA, Amann K, Tan W, Shril S, Connaughton DM, Nakayama M, Schneider R, Kitzler TM, van der Ven AT, Chen J, Ityel H, Vivante A, Majmundar AJ, Daga A, Warejko JK, Lovric S, Ashraf S, Jobst-Schwan T, Widmeier E, Hugo H, Mane SM, Spaneas L, Somers MJG, Ferguson MA, Traum AZ, Stein DR, Baum MA, Daouk GH, Lifton RP, Manzi S, Vakili K, Kim HB, Rodig NM, Hildebrandt F. Whole-Exome Sequencing Enables a Precision Medicine Approach for Kidney Transplant Recipients. J Am Soc Nephrol 2019; 30:201-215. [PMID: 30655312 DOI: 10.1681/asn.2018060575] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) finds a CKD-related mutation in approximately 20% of patients presenting with CKD before 25 years of age. Although provision of a molecular diagnosis could have important implications for clinical management, evidence is lacking on the diagnostic yield and clinical utility of WES for pediatric renal transplant recipients. METHODS To determine the diagnostic yield of WES in pediatric kidney transplant recipients, we recruited 104 patients who had received a transplant at Boston Children's Hospital from 2007 through 2017, performed WES, and analyzed results for likely deleterious variants in approximately 400 genes known to cause CKD. RESULTS By WES, we identified a genetic cause of CKD in 34 out of 104 (32.7%) transplant recipients. The likelihood of detecting a molecular genetic diagnosis was highest for patients with urinary stone disease (three out of three individuals), followed by renal cystic ciliopathies (seven out of nine individuals), steroid-resistant nephrotic syndrome (nine out of 21 individuals), congenital anomalies of the kidney and urinary tract (ten out of 55 individuals), and chronic glomerulonephritis (one out of seven individuals). WES also yielded a molecular diagnosis for four out of nine individuals with ESRD of unknown etiology. The WES-related molecular genetic diagnosis had implications for clinical care for five patients. CONCLUSIONS Nearly one third of pediatric renal transplant recipients had a genetic cause of their kidney disease identified by WES. Knowledge of this genetic information can help guide management of both transplant patients and potential living related donors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut; and
| | | | | | | | | | | | | | | | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut; and.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Shannon Manzi
- Department of Genetics and Genomics, Department of Pharmacy, and
| | - Khashayar Vakili
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heung Bae Kim
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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18
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Mutations of ADAMTS9 Cause Nephronophthisis-Related Ciliopathy. Am J Hum Genet 2019; 104:45-54. [PMID: 30609407 DOI: 10.1016/j.ajhg.2018.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023] Open
Abstract
Nephronophthisis-related ciliopathies (NPHP-RCs) are a group of inherited diseases that are associated with defects in primary cilium structure and function. To identify genes mutated in NPHP-RC, we performed homozygosity mapping and whole-exome sequencing for >100 individuals, some of whom were single affected individuals born to consanguineous parents and some of whom were siblings of indexes who were also affected by NPHP-RC. We then performed high-throughput exon sequencing in a worldwide cohort of 800 additional families affected by NPHP-RC. We identified two ADAMTS9 mutations (c.4575_4576del [p.Gln1525Hisfs∗60] and c.194C>G [p.Thr65Arg]) that appear to cause NPHP-RC. Although ADAMTS9 is known to be a secreted extracellular metalloproteinase, we found that ADAMTS9 localized near the basal bodies of primary cilia in the cytoplasm. Heterologously expressed wild-type ADAMTS9, in contrast to mutant proteins detected in individuals with NPHP-RC, localized to the vicinity of the basal body. Loss of ADAMTS9 resulted in shortened cilia and defective sonic hedgehog signaling. Knockout of Adamts9 in IMCD3 cells, followed by spheroid induction, resulted in defective lumen formation, which was rescued by an overexpression of wild-type, but not of mutant, ADAMTS9. Knockdown of adamts9 in zebrafish recapitulated NPHP-RC phenotypes, including renal cysts and hydrocephalus. These findings suggest that the identified mutations in ADAMTS9 cause NPHP-RC and that ADAMTS9 is required for the formation and function of primary cilia.
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19
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Chen F, Sun SZ, Tang HX, Li RP, Wang W, Liu K, DU YK. [Joubert syndrome caused by INPP5E mutations: report of a family]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2018; 20:861-863. [PMID: 30369365 PMCID: PMC7389035 DOI: 10.7499/j.issn.1008-8830.2018.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Fang Chen
- Department of Neurology, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
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20
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Chen F, Sun SZ, Tang HX, Li RP, Wang W, Liu K, DU YK. [Joubert syndrome caused by INPP5E mutations: report of a family]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2018; 20:861-863. [PMID: 30369365 PMCID: PMC7389035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/01/2018] [Indexed: 08/01/2024]
Affiliation(s)
- Fang Chen
- Department of Neurology, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
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21
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van der Ven AT, Connaughton DM, Ityel H, Mann N, Nakayama M, Chen J, Vivante A, Hwang DY, Schulz J, Braun DA, Schmidt JM, Schapiro D, Schneider R, Warejko JK, Daga A, Majmundar AJ, Tan W, Jobst-Schwan T, Hermle T, Widmeier E, Ashraf S, Amar A, Hoogstraaten CA, Hugo H, Kitzler TM, Kause F, Kolvenbach CM, Dai R, Spaneas L, Amann K, Stein DR, Baum MA, Somers MJG, Rodig NM, Ferguson MA, Traum AZ, Daouk GH, Bogdanović R, Stajić N, Soliman NA, Kari JA, El Desoky S, Fathy HM, Milosevic D, Al-Saffar M, Awad HS, Eid LA, Selvin A, Senguttuvan P, Sanna-Cherchi S, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Wilson MW, Mane SM, Lifton RP, Lee RS, Bauer SB, Lu W, Reutter HM, Tasic V, Shril S, Hildebrandt F. Whole-Exome Sequencing Identifies Causative Mutations in Families with Congenital Anomalies of the Kidney and Urinary Tract. J Am Soc Nephrol 2018; 29:2348-2361. [PMID: 30143558 PMCID: PMC6115658 DOI: 10.1681/asn.2017121265] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/11/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) are the most prevalent cause of kidney disease in the first three decades of life. Previous gene panel studies showed monogenic causation in up to 12% of patients with CAKUT. METHODS We applied whole-exome sequencing to analyze the genotypes of individuals from 232 families with CAKUT, evaluating for mutations in single genes known to cause human CAKUT and genes known to cause CAKUT in mice. In consanguineous or multiplex families, we additionally performed a search for novel monogenic causes of CAKUT. RESULTS In 29 families (13%), we detected a causative mutation in a known gene for isolated or syndromic CAKUT that sufficiently explained the patient's CAKUT phenotype. In three families (1%), we detected a mutation in a gene reported to cause a phenocopy of CAKUT. In 15 of 155 families with isolated CAKUT, we detected deleterious mutations in syndromic CAKUT genes. Our additional search for novel monogenic causes of CAKUT in consanguineous and multiplex families revealed a potential single, novel monogenic CAKUT gene in 19 of 232 families (8%). CONCLUSIONS We identified monogenic mutations in a known human CAKUT gene or CAKUT phenocopy gene as the cause of disease in 14% of the CAKUT families in this study. Whole-exome sequencing provides an etiologic diagnosis in a high fraction of patients with CAKUT and will provide a new basis for the mechanistic understanding of CAKUT.
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Affiliation(s)
- Amelie T van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dervla M Connaughton
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hadas Ityel
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nina Mann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Makiko Nakayama
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julian Schulz
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ali Amar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charlotte A Hoogstraaten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hannah Hugo
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Thomas M Kitzler
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Franziska Kause
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Caroline M Kolvenbach
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rufeng Dai
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Spaneas
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kassaundra Amann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Deborah R Stein
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michelle A Baum
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael J G Somers
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nancy M Rodig
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael A Ferguson
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Avram Z Traum
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ghaleb H Daouk
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Radovan Bogdanović
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Natasa Stajić
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Cairo University, Egypt
- Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Jameela A Kari
- Department of Pediatrics and
- Pediatric Nephrology Center of Excellence, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics and
- Pediatric Nephrology Center of Excellence, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Danko Milosevic
- University of Zagreb School of Medicine, University Hospital Center Zagreb, Zagreb, Croatia
| | - Muna Al-Saffar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Kidney Center Of Excellence, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Kidney Center Of Excellence, Dubai Hospital, Dubai, United Arab Emirates
| | - Aravind Selvin
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, The Tamil Nadu Dr. M.G.R. Medical University, Chennai, Tamil Nadu, India
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta's Multi-Specialty Hospital, Chennai, Tamil Nadu, India
| | | | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Rockefeller University, New York, New York
| | - Richard S Lee
- Department of Urology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Weining Lu
- Renal Section, Department of Medicine and Pathology, Boston University Medical Center, Boston, Massachusetts
| | - Heiko M Reutter
- Institute of Human Genetics and
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; and
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts;
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22
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A kidney-disease gene panel allows a comprehensive genetic diagnosis of cystic and glomerular inherited kidney diseases. Kidney Int 2018; 94:363-371. [DOI: 10.1016/j.kint.2018.02.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/09/2018] [Accepted: 02/15/2018] [Indexed: 12/14/2022]
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23
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Molinari E, Decker E, Mabillard H, Tellez J, Srivastava S, Raman S, Wood K, Kempf C, Alkanderi S, Ramsbottom SA, Miles CG, Johnson CA, Hildebrandt F, Bergmann C, Sayer JA. Human urine-derived renal epithelial cells provide insights into kidney-specific alternate splicing variants. Eur J Hum Genet 2018; 26:1791-1796. [PMID: 30002499 PMCID: PMC6244279 DOI: 10.1038/s41431-018-0212-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 01/07/2023] Open
Abstract
The majority of multi-exon genes undergo alternative splicing to produce different mRNA transcripts and this may occur in a tissue-specific manner. Assessment of mRNA transcripts isolated from blood samples may sometimes be unhelpful in determining the affect on function of putative splice-site variants affecting kidney-specific mRNA transcripts. Here we present data demonstrating the power of using human urine-derived renal epithelial cells (hUREC) as a source of kidney RNA. We report clinical and molecular genetic data from three affected cases from two families all with end-stage renal disease by 15 years of age. In both families, heterozygous variants which are predicted to effect function in NPHP3 were found on one allele, in combination with a synonymous SNV (c.2154C>T; p.Phe718=), 18 base pairs from the exon–intron boundary within exon 15 of NPHP3. The only mRNA transcript amplified from wild-type whole blood showed complete splicing out of exon 15. Urine samples obtained from control subjects and the father of family 2, who carried the synonymous SNV variant, were therefore used to culture hUREC and allowed us to obtain kidney-specific mRNA. Control kidney mRNA showed retention of exon 15, while the mRNA from the patient’s father confirmed evidence of a heterozygous alternate splicing of exon 15 of NPHP3. Analysis of RNA derived from hUREC allows for a comparison of kidney-specific and whole-blood RNA transcripts and for assessment of the effect on function of putative splice variants leading to end-stage kidney disease.
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Affiliation(s)
- Elisa Molinari
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - Eva Decker
- Center for Human Genetics, Bioscientia, Ingelheim, Germany
| | - Holly Mabillard
- Renal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE7 7DN, UK
| | - James Tellez
- Northern Genetic Service, Newcastle upon Tyne NHS Foundation Trust, Newcastle, NE1 3BZ, UK
| | - Shalabh Srivastava
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - Shreya Raman
- Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Katrina Wood
- Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Caroline Kempf
- Department of Pediatric Nephrology, Charité University Hospital, Berlin, Germany
| | - Sumaya Alkanderi
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - Simon A Ramsbottom
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - Colin G Miles
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - Colin A Johnson
- Faculty of Medicine & Health, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, LS9 7TF, UK
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carsten Bergmann
- Center for Human Genetics, Bioscientia, Ingelheim, Germany.,Department of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK. .,Renal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE7 7DN, UK.
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24
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Luo F, Tao YH. Nephronophthisis: A review of genotype-phenotype correlation. Nephrology (Carlton) 2018; 23:904-911. [PMID: 29717526 PMCID: PMC6175366 DOI: 10.1111/nep.13393] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2018] [Indexed: 12/13/2022]
Abstract
Nephronophthisis is an autosomal recessive cystic kidney disease and one of the most common genetic disorders causing end‐stage renal disease in children. Nephronophthisis is a genetically heterogenous disorder with more than 25 identified genes. In 10%–20% of cases, there are additional features of a ciliopathy syndrome, such as retinal defects, liver fibrosis, skeletal abnormalities, and brain developmental disorders. This review provides an update of the recent advances in the clinical features and related gene mutations of nephronophthisis, and novel approaches for therapy in nephronophthisis patients may be needed. Nephronophthisis (NPHP) is a renal ciliopathy affecting children and young adults. This review gives an update on the recent advances in the clinical features and related gene mutations of NPHP.
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Affiliation(s)
- Fenglan Luo
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, China.,Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry Education, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yu-Hong Tao
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, China
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25
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Gulati A, Somlo S. Whole exome sequencing: a state-of-the-art approach for defining (and exploring!) genetic landscapes in pediatric nephrology. Pediatr Nephrol 2018; 33:745-761. [PMID: 28660367 DOI: 10.1007/s00467-017-3698-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/04/2017] [Accepted: 05/09/2017] [Indexed: 12/30/2022]
Abstract
The genesis of whole exome sequencing as a powerful tool for detailing the protein coding sequence of the human genome was conceptualized based on the availability of next-generation sequencing technology and knowledge of the human reference genome. The field of pediatric nephrology enriched with molecularly unsolved phenotypes is allowing the clinical and research application of whole exome sequencing to enable novel gene discovery and provide amendment of phenotypic misclassification. Recent studies in the field have informed us that newer high-throughput sequencing techniques are likely to be of high yield when applied in conjunction with conventional genomic approaches such as linkage analysis and other strategies used to focus subsequent analysis. They have also emphasized the need for the validation of novel genetic findings in large collaborative cohorts and the production of robust corroborative biological data. The well-structured application of comprehensive genomic testing in clinical and research arenas will hopefully continue to advance patient care and precision medicine, but does call for attention to be paid to its integrated challenges.
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Affiliation(s)
- Ashima Gulati
- Division of Nephrology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA.
| | - Stefan Somlo
- Departments of Internal Medicine and Genetics, Yale University School of Medicine, New Haven, CT, USA
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26
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Warejko JK, Schueler M, Vivante A, Tan W, Daga A, Lawson JA, Braun DA, Shril S, Amann K, Somers MJG, Rodig NM, Baum MA, Daouk G, Traum AZ, Kim HB, Vakili K, Porras D, Lock J, Rivkin MJ, Chaudry G, Smoot LB, Singh MN, Smith ER, Mane SM, Lifton RP, Stein DR, Ferguson MA, Hildebrandt F. Whole Exome Sequencing Reveals a Monogenic Cause of Disease in ≈43% of 35 Families With Midaortic Syndrome. Hypertension 2018; 71:691-699. [PMID: 29483232 PMCID: PMC5843550 DOI: 10.1161/hypertensionaha.117.10296] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/06/2017] [Accepted: 01/18/2018] [Indexed: 11/16/2022]
Abstract
Midaortic syndrome (MAS) is a rare cause of severe childhood hypertension characterized by narrowing of the abdominal aorta in children and is associated with extensive vascular disease. It may occur as part of a genetic syndrome, such as neurofibromatosis, or as consequence of a pathological inflammatory disease. However, most cases are considered idiopathic. We hypothesized that in a high percentage of these patients, a monogenic cause of disease may be detected by evaluating whole exome sequencing data for mutations in 1 of 38 candidate genes previously described to cause vasculopathy. We studied a cohort of 36 individuals from 35 different families with MAS by exome sequencing. In 15 of 35 families (42.9%), we detected likely causal dominant mutations. In 15 of 35 (42.9%) families with MAS, whole exome sequencing revealed a mutation in one of the genes previously associated with vascular disease (NF1, JAG1, ELN, GATA6, and RNF213). Ten of the 15 mutations have not previously been reported. This is the first report of ELN, RNF213, or GATA6 mutations in individuals with MAS. Mutations were detected in NF1 (6/15 families), JAG1 (4/15 families), ELN (3/15 families), and one family each for GATA6 and RNF213 Eight individuals had syndromic disease and 7 individuals had isolated MAS. Whole exome sequencing can provide conclusive molecular genetic diagnosis in a high fraction of individuals with syndromic or isolated MAS. Establishing an etiologic diagnosis may reveal genotype/phenotype correlations for MAS in the future and should, therefore, be performed routinely in MAS.
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Affiliation(s)
- Jillian K Warejko
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Markus Schueler
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Asaf Vivante
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Weizhen Tan
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Ankana Daga
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Jennifer A Lawson
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Daniela A Braun
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Shirlee Shril
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Kassaundra Amann
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael J G Somers
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Nancy M Rodig
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michelle A Baum
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Ghaleb Daouk
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Avram Z Traum
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Heung Bae Kim
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Khashayar Vakili
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Diego Porras
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - James Lock
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael J Rivkin
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Gulraiz Chaudry
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Leslie B Smoot
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael N Singh
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Edward R Smith
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Shrikant M Mane
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Richard P Lifton
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Deborah R Stein
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael A Ferguson
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Friedhelm Hildebrandt
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.).
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Abstract
Technologies such as next-generation sequencing and chromosomal microarray have advanced the understanding of the molecular pathogenesis of a variety of renal disorders. Genetic findings are increasingly used to inform the clinical management of many nephropathies, enabling targeted disease surveillance, choice of therapy, and family counselling. Genetic analysis has excellent diagnostic utility in paediatric nephrology, as illustrated by sequencing studies of patients with congenital anomalies of the kidney and urinary tract and steroid-resistant nephrotic syndrome. Although additional investigation is needed, pilot studies suggest that genetic testing can also provide similar diagnostic insight among adult patients. Reaching a genetic diagnosis first involves choosing the appropriate testing modality, as guided by the clinical presentation of the patient and the number of potential genes associated with the suspected nephropathy. Genome-wide sequencing increases diagnostic sensitivity relative to targeted panels, but holds the challenges of identifying causal variants in the vast amount of data generated and interpreting secondary findings. In order to realize the promise of genomic medicine for kidney disease, many technical, logistical, and ethical questions that accompany the implementation of genetic testing in nephrology must be addressed. The creation of evidence-based guidelines for the utilization and implementation of genetic testing in nephrology will help to translate genetic knowledge into improved clinical outcomes for patients with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
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Warejko JK, Tan W, Daga A, Schapiro D, Lawson JA, Shril S, Lovric S, Ashraf S, Rao J, Hermle T, Jobst-Schwan T, Widmeier E, Majmundar AJ, Schneider R, Gee HY, Schmidt JM, Vivante A, van der Ven AT, Ityel H, Chen J, Sadowski CE, Kohl S, Pabst WL, Nakayama M, Somers MJG, Rodig NM, Daouk G, Baum M, Stein DR, Ferguson MA, Traum AZ, Soliman NA, Kari JA, El Desoky S, Fathy H, Zenker M, Bakkaloglu SA, Müller D, Noyan A, Ozaltin F, Cadnapaphornchai MA, Hashmi S, Hopcian J, Kopp JB, Benador N, Bockenhauer D, Bogdanovic R, Stajić N, Chernin G, Ettenger R, Fehrenbach H, Kemper M, Munarriz RL, Podracka L, Büscher R, Serdaroglu E, Tasic V, Mane S, Lifton RP, Braun DA, Hildebrandt F. Whole Exome Sequencing of Patients with Steroid-Resistant Nephrotic Syndrome. Clin J Am Soc Nephrol 2018; 13:53-62. [PMID: 29127259 PMCID: PMC5753307 DOI: 10.2215/cjn.04120417] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/12/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND OBJECTIVES Steroid-resistant nephrotic syndrome overwhelmingly progresses to ESRD. More than 30 monogenic genes have been identified to cause steroid-resistant nephrotic syndrome. We previously detected causative mutations using targeted panel sequencing in 30% of patients with steroid-resistant nephrotic syndrome. Panel sequencing has a number of limitations when compared with whole exome sequencing. We employed whole exome sequencing to detect monogenic causes of steroid-resistant nephrotic syndrome in an international cohort of 300 families. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Three hundred thirty-five individuals with steroid-resistant nephrotic syndrome from 300 families were recruited from April of 1998 to June of 2016. Age of onset was restricted to <25 years of age. Exome data were evaluated for 33 known monogenic steroid-resistant nephrotic syndrome genes. RESULTS In 74 of 300 families (25%), we identified a causative mutation in one of 20 genes known to cause steroid-resistant nephrotic syndrome. In 11 families (3.7%), we detected a mutation in a gene that causes a phenocopy of steroid-resistant nephrotic syndrome. This is consistent with our previously published identification of mutations using a panel approach. We detected a causative mutation in a known steroid-resistant nephrotic syndrome gene in 38% of consanguineous families and in 13% of nonconsanguineous families, and 48% of children with congenital nephrotic syndrome. A total of 68 different mutations were detected in 20 of 33 steroid-resistant nephrotic syndrome genes. Fifteen of these mutations were novel. NPHS1, PLCE1, NPHS2, and SMARCAL1 were the most common genes in which we detected a mutation. In another 28% of families, we detected mutations in one or more candidate genes for steroid-resistant nephrotic syndrome. CONCLUSIONS Whole exome sequencing is a sensitive approach toward diagnosis of monogenic causes of steroid-resistant nephrotic syndrome. A molecular genetic diagnosis of steroid-resistant nephrotic syndrome may have important consequences for the management of treatment and kidney transplantation in steroid-resistant nephrotic syndrome.
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Affiliation(s)
- Jillian K Warejko
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
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29
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Daga A, Majmundar AJ, Braun DA, Gee HY, Lawson JA, Shril S, Jobst-Schwan T, Vivante A, Schapiro D, Tan W, Warejko JK, Widmeier E, Nelson CP, Fathy HM, Gucev Z, Soliman NA, Hashmi S, Halbritter J, Halty M, Kari JA, El-Desoky S, Ferguson MA, Somers MJG, Traum AZ, Stein DR, Daouk GH, Rodig NM, Katz A, Hanna C, Schwaderer AL, Sayer JA, Wassner AJ, Mane S, Lifton RP, Milosevic D, Tasic V, Baum MA, Hildebrandt F. Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis. Kidney Int 2017; 93:204-213. [PMID: 28893421 DOI: 10.1016/j.kint.2017.06.025] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/05/2017] [Accepted: 06/30/2017] [Indexed: 01/07/2023]
Abstract
The incidence of nephrolithiasis continues to rise. Previously, we showed that a monogenic cause could be detected in 11.4% of individuals with adult-onset nephrolithiasis or nephrocalcinosis and in 16.7-20.8% of individuals with onset before 18 years of age, using gene panel sequencing of 30 genes known to cause nephrolithiasis/nephrocalcinosis. To overcome the limitations of panel sequencing, we utilized whole exome sequencing in 51 families, who presented before age 25 years with at least one renal stone or with a renal ultrasound finding of nephrocalcinosis to identify the underlying molecular genetic cause of disease. In 15 of 51 families, we detected a monogenic causative mutation by whole exome sequencing. A mutation in seven recessive genes (AGXT, ATP6V1B1, CLDN16, CLDN19, GRHPR, SLC3A1, SLC12A1), in one dominant gene (SLC9A3R1), and in one gene (SLC34A1) with both recessive and dominant inheritance was detected. Seven of the 19 different mutations were not previously described as disease-causing. In one family, a causative mutation in one of 117 genes that may represent phenocopies of nephrolithiasis-causing genes was detected. In nine of 15 families, the genetic diagnosis may have specific implications for stone management and prevention. Several factors that correlated with the higher detection rate in our cohort were younger age at onset of nephrolithiasis/nephrocalcinosis, presence of multiple affected members in a family, and presence of consanguinity. Thus, we established whole exome sequencing as an efficient approach toward a molecular genetic diagnosis in individuals with nephrolithiasis/nephrocalcinosis who manifest before age 25 years.
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Affiliation(s)
- Ankana Daga
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amar J Majmundar
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniela A Braun
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Department of Pharmacology, Brain Korea 21 Program for Leading Universities and Students Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Jennifer A Lawson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tilman Jobst-Schwan
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Asaf Vivante
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Schapiro
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Weizhen Tan
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K Warejko
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Caleb P Nelson
- Department of Urology and General Pediatrics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanan M Fathy
- Pediatric Nephrology Unit, Alexandria University, Alexandria, Egypt
| | - Zoran Gucev
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt; Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Seema Hashmi
- Department of Pediatric Nephrology, Sindh Institute of Urology and Transplantation, Karachi, Pakistan
| | - Jan Halbritter
- Division of Endocrinology and Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany
| | - Margarita Halty
- School of Medicine, Department of Pediatrics, Centro Hospitalario Pereira Rossell, Montevideo, Uruguay
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence and Pediatrics Department, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Sherif El-Desoky
- Pediatric Nephrology Center of Excellence and Pediatrics Department, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Michael A Ferguson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J G Somers
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Avram Z Traum
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Deborah R Stein
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ghaleb H Daouk
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nancy M Rodig
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Avi Katz
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christian Hanna
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew L Schwaderer
- Division of Nephrology, Department of Pediatrics, Nationwide Children's Hospital/The Ohio State University, Columbus, Ohio, USA
| | - John A Sayer
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Ari J Wassner
- Division of Endocrinology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Danko Milosevic
- Department of Pediatric Nephrology, Dialysis and Transplantation, Clinical Hospital Center Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Michelle A Baum
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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30
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Mallett AJ, McCarthy HJ, Ho G, Holman K, Farnsworth E, Patel C, Fletcher JT, Mallawaarachchi A, Quinlan C, Bennetts B, Alexander SI. Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Kidney Int 2017; 92:1493-1506. [PMID: 28844315 DOI: 10.1016/j.kint.2017.06.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes.
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Affiliation(s)
- Andrew J Mallett
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia; Faculty of Medicine, University of Queensland, Brisbane, Australia; KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia.
| | - Hugh J McCarthy
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gladys Ho
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Katherine Holman
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Elizabeth Farnsworth
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Jeffery T Fletcher
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatrics, The Canberra Hospital, Canberra, Australia
| | - Amali Mallawaarachchi
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Clinical Genetics, Liverpool Hospital, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatric Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Bruce Bennetts
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia; Centre for Kidney Research, University of Sydney, Sydney, Australia.
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31
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Nabhan MM, ElKhateeb N, Braun DA, Eun S, Saleem SN, YungGee H, Hildebrandt F, Soliman NA. Cystic kidneys in fetal Walker-Warburg syndrome with POMT2 mutation: Intrafamilial phenotypic variability in four siblings and review of literature. Am J Med Genet A 2017; 173:2697-2702. [PMID: 28815891 DOI: 10.1002/ajmg.a.38393] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 11/11/2022]
Abstract
Walker-Warburg syndrome (WWS) is a severe form of congenital muscular dystrophy secondary to α-dystroglycanopathy with muscle, brain, and eye abnormalities often leading to death in the first weeks of life. It is transmitted in an autosomal recessive pattern, and has been linked to at least 15 different genes; including protein O-mannosyltransferase 1 (POMT1), protein O-mannosyltransferase 2 (POMT2), protein O-mannose beta-1,2-N acetylglucosaminyltransferase (POMGNT1), fukutin (FKTN), isoprenoid synthase domain-containing protein (ISPD), and other genes. We report on a consanguineous family with four consecutive siblings affected by this condition with lethal outcome in three (still birth), and termination of the fourth pregnancy based on antenatal MRI identification of brain and kidney anomalies that heralded proper and deep clinical phenotyping. The diagnosis of WWS was suggested based on the unique collective phenotype comprising brain anomalies in the form of lissencephaly, subcortical/subependymal heterotopia, and cerebellar hypoplasia shared by all four siblings; microphthalmia in one sibling; and large cystic kidneys in the fetus and another sibling. Other unshared neurological abnormalities included hydrocephalus and Dandy-Walker malformation. Whole exome sequencing of the fetus revealed a highly conserved missense mutation in POMT2 that is known to cause WWS with brain and eye anomalies.In conclusion, the heterogeneous clinical presentation in the four affected conceptions with POMT2 mutation expands the current clinical spectrum of POMT2-associated WWS to include large cystic kidneys; and confirms intra-familial variability in terms of brain, kidney, and eye anomalies.
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Affiliation(s)
- Marwa M Nabhan
- Department of Pediatrics, Centre of Pediatric Nephrology & Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Nour ElKhateeb
- Department of Pediatrics, Centre of Pediatric Neurology & Metabolic diseases, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sungho Eun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sahar N Saleem
- Department of Radiology, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Heon YungGee
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Neveen A Soliman
- Department of Pediatrics, Centre of Pediatric Nephrology & Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
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32
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Ars E, Torra R. Rare diseases, rare presentations: recognizing atypical inherited kidney disease phenotypes in the age of genomics. Clin Kidney J 2017; 10:586-593. [PMID: 28980669 PMCID: PMC5622904 DOI: 10.1093/ckj/sfx051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/03/2017] [Indexed: 12/11/2022] Open
Abstract
A significant percentage of adults (10%) and children (20%) on renal replacement therapy have an inherited kidney disease (IKD). The new genomic era, ushered in by the next generation sequencing techniques, has contributed to the identification of new genes and facilitated the genetic diagnosis of the highly heterogeneous IKDs. Consequently, it has also allowed the reclassification of diseases and has broadened the phenotypic spectrum of many classical IKDs. Various genetic, epigenetic and environmental factors may explain ‘atypical’ phenotypes. In this article, we examine different mechanisms that may contribute to phenotypic variability and also provide case examples that illustrate them. The aim of the article is to raise awareness, among nephrologists and geneticists, of rare presentations that IKDs may show, to facilitate diagnosis.
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Affiliation(s)
- Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Roser Torra
- Inherited Kidney Disorders, Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
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33
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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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34
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Abstract
Nephronophthisis-related ciliopathies (NPHP-RC) are a group of inherited diseases that affect genes encoding proteins that localize to primary cilia or centrosomes. With few exceptions, ciliopathies are inherited in an autosomal recessive manner, and affected individuals manifest early during childhood or adolescence. NPHP-RC are genetically very heterogeneous, and, currently, mutations in more than 90 genes have been described as single-gene causes. The phenotypes of NPHP-RC are very diverse, and include cystic-fibrotic kidney disease, brain developmental defects, retinal degeneration, skeletal deformities, facial dimorphism, and, in some cases, laterality defects, and congenital heart disease. Mutations in the same gene can give rise to diverse phenotypes depending on the mutated allele. At the same time, there is broad phenotypic overlap between different monogenic genes. The identification of monogenic causes of ciliopathies has furthered the understanding of molecular mechanism and cellular pathways involved in the pathogenesis.
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35
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The genetic and clinical spectrum of a large cohort of patients with distal renal tubular acidosis. Kidney Int 2017; 91:1243-1255. [PMID: 28233610 DOI: 10.1016/j.kint.2016.12.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 11/24/2022]
Abstract
Primary distal renal tubular acidosis is a rare genetic disease. Mutations in SLC4A1, ATP6V0A4, and ATP6V1B1 genes have been described as the cause of the disease, transmitted as either an autosomal dominant or recessive trait. Particular clinical features, such as sensorineural hearing loss, have been mainly described in association with mutations in one gene instead of the others. Nevertheless, the diagnosis of distal renal tubular acidosis is essentially based on clinical and laboratory findings, and the series of patients described so far are usually represented by small cohorts. Therefore, a strict genotype-phenotype correlation is still lacking, and questions about whether clinical and laboratory data should direct the genetic analysis remain open. Here, we applied next-generation sequencing in 89 patients with a clinical diagnosis of distal renal tubular acidosis, analyzing the prevalence of genetic defects in SLC4A1, ATP6V0A4, and ATP6V1B1 genes and the clinical phenotype. A genetic cause was determined in 71.9% of cases. In our group of sporadic cases, clinical features, including sensorineural hearing loss, are not specific indicators of the causal underlying gene. Mutations in the ATP6V0A4 gene are quite as frequent as mutations in ATP6V1B1 in patients with recessive disease. Chronic kidney disease was frequent in patients with a long history of the disease. Thus, our results suggest that when distal renal tubular acidosis is suspected, complete genetic testing could be considered, irrespective of the clinical phenotype of the patient.
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36
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Lovric S, Goncalves S, Gee HY, Oskouian B, Srinivas H, Choi WI, Shril S, Ashraf S, Tan W, Rao J, Airik M, Schapiro D, Braun DA, Sadowski CE, Widmeier E, Jobst-Schwan T, Schmidt JM, Girik V, Capitani G, Suh JH, Lachaussée N, Arrondel C, Patat J, Gribouval O, Furlano M, Boyer O, Schmitt A, Vuiblet V, Hashmi S, Wilcken R, Bernier FP, Innes AM, Parboosingh JS, Lamont RE, Midgley JP, Wright N, Majewski J, Zenker M, Schaefer F, Kuss N, Greil J, Giese T, Schwarz K, Catheline V, Schanze D, Franke I, Sznajer Y, Truant AS, Adams B, Désir J, Biemann R, Pei Y, Ars E, Lloberas N, Madrid A, Dharnidharka VR, Connolly AM, Willing MC, Cooper MA, Lifton RP, Simons M, Riezman H, Antignac C, Saba JD, Hildebrandt F. Mutations in sphingosine-1-phosphate lyase cause nephrosis with ichthyosis and adrenal insufficiency. J Clin Invest 2017; 127:912-928. [PMID: 28165339 DOI: 10.1172/jci89626] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/12/2016] [Indexed: 12/24/2022] Open
Abstract
Steroid-resistant nephrotic syndrome (SRNS) causes 15% of chronic kidney disease cases. A mutation in 1 of over 40 monogenic genes can be detected in approximately 30% of individuals with SRNS whose symptoms manifest before 25 years of age. However, in many patients, the genetic etiology remains unknown. Here, we have performed whole exome sequencing to identify recessive causes of SRNS. In 7 families with SRNS and facultative ichthyosis, adrenal insufficiency, immunodeficiency, and neurological defects, we identified 9 different recessive mutations in SGPL1, which encodes sphingosine-1-phosphate (S1P) lyase. All mutations resulted in reduced or absent SGPL1 protein and/or enzyme activity. Overexpression of cDNA representing SGPL1 mutations resulted in subcellular mislocalization of SGPL1. Furthermore, expression of WT human SGPL1 rescued growth of SGPL1-deficient dpl1Δ yeast strains, whereas expression of disease-associated variants did not. Immunofluorescence revealed SGPL1 expression in mouse podocytes and mesangial cells. Knockdown of Sgpl1 in rat mesangial cells inhibited cell migration, which was partially rescued by VPC23109, an S1P receptor antagonist. In Drosophila, Sply mutants, which lack SGPL1, displayed a phenotype reminiscent of nephrotic syndrome in nephrocytes. WT Sply, but not the disease-associated variants, rescued this phenotype. Together, these results indicate that SGPL1 mutations cause a syndromic form of SRNS.
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37
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Braun DA, Schueler M, Halbritter J, Gee HY, Porath JD, Lawson JA, Airik R, Shril S, Allen SJ, Stein D, Al Kindy A, Beck BB, Cengiz N, Moorani KN, Ozaltin F, Hashmi S, Sayer JA, Bockenhauer D, Soliman NA, Otto EA, Lifton RP, Hildebrandt F. Whole exome sequencing identifies causative mutations in the majority of consanguineous or familial cases with childhood-onset increased renal echogenicity. Kidney Int 2017; 89:468-475. [PMID: 26489029 PMCID: PMC4840095 DOI: 10.1038/ki.2015.317] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/10/2015] [Accepted: 08/20/2015] [Indexed: 12/16/2022]
Abstract
Chronically increased echogenicity on renal ultrasound is a sensitive early finding of chronic kidney disease that can be detected before manifestation of other symptoms. Increased echogenicity, however, is not specific for a certain etiology of chronic kidney disease. Here, we performed whole exome sequencing in 79 consanguineous or familial cases of suspected nephronophthisis in order to determine the underlying molecular disease cause. In 50 cases, there was a causative mutation in a known monogenic disease gene. In 32 of these cases whole exome sequencing confirmed the diagnosis of a nephronophthisis-related ciliopathy. In 8 cases it revealed the diagnosis of a renal tubulopathy. The remaining 10 cases were identified as Alport syndrome (4), autosomal-recessive polycystic kidney disease (2), congenital anomalies of the kidney and urinary tract (3), and APECED syndrome (1). In 5 families, in whom mutations in known monogenic genes were excluded, we applied homozygosity mapping for variant filtering, and identified 5 novel candidate genes (RBM48, FAM186B, PIAS1, INCENP, and RCOR1) for renal ciliopathies. Thus, whole exome sequencing allows the detection of the causative mutation in 2/3 of affected individuals, thereby presenting the etiologic diagnosis and allows identification of novel candidate genes.
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Affiliation(s)
- Daniela A Braun
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Markus Schueler
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan Halbritter
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan D Porath
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Lawson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rannar Airik
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan J Allen
- Department of Pediatrics, University of Michigan, Michigan, USA
| | - Deborah Stein
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adila Al Kindy
- Department of Genetics, Sultan Qaboos University Hospital, Sultanate of Oman
| | - Bodo B Beck
- Institute for Human Genetics, University of Cologne, Germany
| | - Nurcan Cengiz
- Baskent University, School of Medicine, Adana Medical Training and Research Center, Department of Pediatric Nephrology, Adana, Turkey
| | - Khemchand N Moorani
- Department of Pediatric Nephrology, National Institute of Child Health, Karachi 75510, Pakistan
| | - Fatih Ozaltin
- Faculty of Medicine, Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey.,Nephrogenetics Laboratory, Faculty of Medicine, Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey.,Center for Biobanking and Genomics, Hacettepe University, Ankara, Turkey
| | - Seema Hashmi
- Department of Pediatric Nephrology, Sindh Institute of Urology and Transplantation, SIUT, Karachi, Pakistan
| | - John A Sayer
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Detlef Bockenhauer
- University College London, Institute of Child Health and Pediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Edgar A Otto
- Department of Pediatrics, University of Michigan, Michigan, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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38
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Srivastava S, Molinari E, Raman S, Sayer JA. Many Genes-One Disease? Genetics of Nephronophthisis (NPHP) and NPHP-Associated Disorders. Front Pediatr 2017; 5:287. [PMID: 29379777 PMCID: PMC5770800 DOI: 10.3389/fped.2017.00287] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022] Open
Abstract
Nephronophthisis (NPHP) is a renal ciliopathy and an autosomal recessive cause of cystic kidney disease, renal fibrosis, and end-stage renal failure, affecting children and young adults. Molecular genetic studies have identified more than 20 genes underlying this disorder, whose protein products are all related to cilia, centrosome, or mitotic spindle function. In around 15% of cases, there are additional features of a ciliopathy syndrome, including retinal defects, liver fibrosis, skeletal abnormalities, and brain developmental disorders. Alongside, gene identification has arisen molecular mechanistic insights into the disease pathogenesis. The genetic causes of NPHP are discussed in terms of how they help us to define treatable disease pathways including the cyclic adenosine monophosphate pathway, the mTOR pathway, Hedgehog signaling pathways, and DNA damage response pathways. While the underlying pathology of the many types of NPHP remains similar, the defined disease mechanisms are diverse, and a personalized medicine approach for therapy in NPHP patients is likely to be required.
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Affiliation(s)
- Shalabh Srivastava
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.,Renal Unit, City Hospitals Sunderland and South Tyneside NHS Foundation Trust, Sunderland, United Kingdom
| | - Elisa Molinari
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shreya Raman
- Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.,Renal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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39
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Vichot AA, Zsengellér ZK, Shmukler BE, Adams ND, Dahl NK, Alper SL. Loss of kAE1 expression in collecting ducts of end-stage kidneys from a family with SLC4A1 G609R-associated distal renal tubular acidosis. Clin Kidney J 2016. [PMID: 28638614 PMCID: PMC5469557 DOI: 10.1093/ckj/sfw074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Distal renal tubular acidosis caused by missense mutations in kidney isoform of anion exchanger 1 (kAE1/SLC4A1), the basolateral membrane Cl−/HCO3− exchanger of renal alpha-intercalated cells, has been extensively investigated in heterologous expression systems but rarely in human kidneys. The preferential apical localization of distal renal tubular acidosis (dRTA)-associated kAE1 mutants R901X, G609R and M909T in cultured epithelial monolayers has not been examined in human kidney. Here, we present kidney tissues from dRTA-affected siblings heterozygous for kAE1 G609R, characterized by predominant absence rather than mistargeting of kAE1 in intercalated cells. Thus, studies of heterologous recombinant expression of mutant proteins should be, whenever possible, interpreted in comparison to affected patient tissues.
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Affiliation(s)
- Alfred A Vichot
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Zsuzsanna K Zsengellér
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Boris E Shmukler
- Division of Nephrology and Vascular Biology Research Center, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Nancy D Adams
- Division of Nephrology, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Neera K Dahl
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Seth L Alper
- Division of Nephrology and Vascular Biology Research Center, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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40
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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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41
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Vivante A, Hwang DY, Kohl S, Chen J, Shril S, Schulz J, van der Ven A, Daouk G, Soliman NA, Kumar AS, Senguttuvan P, Kehinde EO, Tasic V, Hildebrandt F. Exome Sequencing Discerns Syndromes in Patients from Consanguineous Families with Congenital Anomalies of the Kidneys and Urinary Tract. J Am Soc Nephrol 2016; 28:69-75. [PMID: 27151922 DOI: 10.1681/asn.2015080962] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/16/2016] [Indexed: 12/22/2022] Open
Abstract
Congenital anomalies of the kidneys and urinary tract (CAKUT) are the leading cause of CKD in children, featuring a broad variety of malformations. A monogenic cause can be detected in around 12% of patients. However, the morphologic clinical phenotype of CAKUT frequently does not indicate specific genes to be examined. To determine the likelihood of detecting causative recessive mutations by whole-exome sequencing (WES), we analyzed individuals with CAKUT from 33 different consanguineous families. Using homozygosity mapping and WES, we identified the causative mutations in nine of the 33 families studied (27%). We detected recessive mutations in nine known disease-causing genes: ZBTB24, WFS1, HPSE2, ATRX, ASPH, AGXT, AQP2, CTNS, and PKHD1 Notably, when mutated, these genes cause multiorgan syndromes that may include CAKUT as a feature (syndromic CAKUT) or cause renal diseases that may manifest as phenocopies of CAKUT. None of the above monogenic disease-causing genes were suspected on clinical grounds before this study. Follow-up clinical characterization of those patients allowed us to revise and detect relevant new clinical features in a more appropriate pathogenetic context. Thus, applying WES to the diagnostic approach in CAKUT provides opportunities for an accurate and early etiology-based diagnosis and improved clinical management.
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Affiliation(s)
- Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Stefan Kohl
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pediatrics, Cologne Children's Hospital, Cologne, Germany
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julian Schulz
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amelie van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ghaleb Daouk
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Aravind Selvin Kumar
- Pediatric Nephrology Department, Institute of Child Health and Hospital for Children, Chennai, Tamil Nadu, India
| | - Prabha Senguttuvan
- Pediatric Nephrology Department, Institute of Child Health and Hospital for Children, Chennai, Tamil Nadu, India
| | - Elijah O Kehinde
- Division of Urology, Department of Surgery, Kuwait University, Safat, Kuwait
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia; and
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; .,Howard Hughes Medical Institute, Chevy Chase, Maryland
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Bracken C, Beauverger P, Duclos O, Russo RJ, Rogers KA, Husson H, Natoli TA, Ledbetter SR, Janiak P, Ibraghimov-Beskrovnaya O, Bukanov NO. CaMKII as a pathological mediator of ER stress, oxidative stress, and mitochondrial dysfunction in a murine model of nephronophthisis. Am J Physiol Renal Physiol 2016; 310:F1414-22. [PMID: 27076647 DOI: 10.1152/ajprenal.00426.2015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 04/11/2016] [Indexed: 11/22/2022] Open
Abstract
Polycystic kidney diseases (PKDs) are genetic diseases characterized by renal cyst formation with increased cell proliferation, apoptosis, and transition to a secretory phenotype at the expense of terminal differentiation. Despite recent progress in understanding PKD pathogenesis and the emergence of potential therapies, the key molecular mechanisms promoting cystogenesis are not well understood. Here, we demonstrate that mechanisms including endoplasmic reticulum stress, oxidative damage, and compromised mitochondrial function all contribute to nephronophthisis-associated PKD. Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) is emerging as a critical mediator of these cellular processes. Therefore, we reasoned that pharmacological targeting of CaMKII may translate into effective inhibition of PKD in jck mice. Our data demonstrate that CaMKII is activated within cystic kidney epithelia in jck mice. Blockade of CaMKII with a selective inhibitor results in effective inhibition of PKD in jck mice. Mechanistic experiments in vitro and in vivo demonstrated that CaMKII inhibition relieves endoplasmic reticulum stress and oxidative damage and improves mitochondrial integrity and membrane potential. Taken together, our data support CaMKII inhibition as a new and effective therapeutic avenue for the treatment of cystic diseases.
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Affiliation(s)
- Christina Bracken
- Rare Diseases, Sanofi-Genzyme R&D Center, Framingham, Massachusetts; and
| | | | | | - Ryan J Russo
- Rare Diseases, Sanofi-Genzyme R&D Center, Framingham, Massachusetts; and
| | - Kelly A Rogers
- Rare Diseases, Sanofi-Genzyme R&D Center, Framingham, Massachusetts; and
| | - Hervé Husson
- Rare Diseases, Sanofi-Genzyme R&D Center, Framingham, Massachusetts; and
| | - Thomas A Natoli
- Rare Diseases, Sanofi-Genzyme R&D Center, Framingham, Massachusetts; and
| | - Steven R Ledbetter
- Rare Diseases, Sanofi-Genzyme R&D Center, Framingham, Massachusetts; and
| | - Philip Janiak
- Cardiovascular Research, Sanofi, Chilly-Mazarin, France
| | | | - Nikolay O Bukanov
- Rare Diseases, Sanofi-Genzyme R&D Center, Framingham, Massachusetts; and
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Yamamura T, Morisada N, Nozu K, Minamikawa S, Ishimori S, Toyoshima D, Ninchoji T, Yasui M, Taniguchi-Ikeda M, Morioka I, Nakanishi K, Nishio H, Iijima K. Rare renal ciliopathies in non-consanguineous families that were identified by targeted resequencing. Clin Exp Nephrol 2016; 21:136-142. [PMID: 26968886 DOI: 10.1007/s10157-016-1256-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/29/2016] [Indexed: 01/23/2023]
Abstract
BACKGROUND Nephronophthisis-related ciliopathies (NPHP-RC) are a frequent cause of renal failure for children and adolescents. Although diagnosing these diseases clinically is difficult, a comprehensive genetic screening approach of targeted resequencing can uncover the genetic background in this complicated family of diseases. METHODS We studied three Japanese female patients with renal insufficiency from non-consanguineous parents. A renal biopsy for clinical reasons was not performed. Therefore, we did not know the diagnosis of these patients from a clinical aspect. We performed comprehensive genetic analysis using the TruSight One Sequencing Panel next generation sequencing technique. RESULTS We identified three different rare NPHP-RC variants in the following genes: SDCCAG8, MKKS, and WDR35. Patient 1 with SDCCAG8 homozygous deletions showed no ciliopathy-specific extrarenal manifestations, such as retinitis pigmentosa or polydactyly prior to genetic analysis. Patient 2 with a MKKS splice site homozygous mutation and a subsequent 39-amino acid deletion in the substrate-binding apical domain, had clinical symptoms of Bardet-Biedl syndrome. She and her deceased elder brother had severe renal insufficiency soon after birth. Patient 3 with a compound heterozygous WDR35 mutation had ocular coloboma and intellectual disability. CONCLUSIONS Our results suggest that a comprehensive genetic screening system using target resequencing is useful and non-invasive for the diagnosis of patients with an unknown cause of pediatric end-stage renal disease.
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Affiliation(s)
- Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Naoya Morisada
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan. .,Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Shogo Minamikawa
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Kakogawa West City Hospital, 384-1, Hiratsu, Yoneda-cho, Kakogawa, 675-8611, Japan
| | - Daisaku Toyoshima
- Department of Child Neurology, Hyogo Prefectural Kobe Children's Hospital, 1-1-1, Takakuradai, Suma-ku, Kobe, 654-0081, Japan
| | - Takeshi Ninchoji
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Masato Yasui
- Department of Pediatrics, Fukuyama Capital Hospital, 5-23-1, Zao-cho, Fukuyama, 721-0971, Japan
| | - Mariko Taniguchi-Ikeda
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Ichiro Morioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Koichi Nakanishi
- Department of Pediatrics, Wakayama Medical College, 811-1, Kimiidera, Wakayama, 641-8509, Japan
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
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de Goede C, Yue WW, Yan G, Ariyaratnam S, Chandler KE, Downes L, Khan N, Mohan M, Lowe M, Banka S. Role of reverse phenotyping in interpretation of next generation sequencing data and a review of INPP5E related disorders. Eur J Paediatr Neurol 2016; 20:286-295. [PMID: 26748598 DOI: 10.1016/j.ejpn.2015.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 11/05/2015] [Accepted: 11/23/2015] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Next Generation Sequencing (NGS) is a useful tool in diagnosis of rare disorders but the interpretation of data can be challenging in clinical settings. We present results of extended studies on a family of multiple members with global developmental delay and learning disability, where another research group postulated the underlying cause to be a homozygous RABL6 missense variant. METHODS AND RESULTS Using data from the Exome Variant Server, we show that missense RABL6 variants are unlikely to cause early onset rare developmental disorder. Protein structural analysis, cellular functional studies and reverse phenotyping proved that the condition in this family is due to a homozygous INPP5E mutation. An in-depth review of mutational and phenotypic spectrum associated with INPP5E demonstrated that mutations in this gene lead to a range of cilliopathy-phenotypes. DISCUSSION We use this study as an example to demonstrate the importance of careful clinical evaluation of multiple family members, reverse phenotyping, considering the unknown phenotypic variability of rare diseases, utilizing publically available genomic databases and conducting appropriate bioinformatics and functional studies while interpreting results from NGS in uncertain cases. We emphasize that interpretation of NGS data is an iterative process and its dynamic nature should be explained to patients and families. Our study shows that developmental delay, intellectual disability, hypotonia and ocular motor apraxia are common in INPP5E-related disorders and considerable intra-familial phenotypic variability is possible. We have compiled the INPP5E mutational spectrum and provided novel insights into their molecular mechanisms.
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Affiliation(s)
- Christian de Goede
- Department of Paediatric Neurology, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK; Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Wyatt W Yue
- Structural Genomics Consortium, Old Road Campus Research Building, University of Oxford, Oxford, UK
| | - Guanhua Yan
- Faculty of Life Sciences, University of Manchester, UK
| | - Shyamala Ariyaratnam
- Department of Community and Neurodevelopmental Paediatrics, Royal Blackburn Hospital, East Lancashire Hospital NHS Trust, Blackburn, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Laura Downes
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Nasaim Khan
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Meyyammai Mohan
- Department of Ophthalmology, Royal Blackburn Hospital, East Lancashire Hospital NHS Trust, Blackburn, UK
| | - Martin Lowe
- Faculty of Life Sciences, University of Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK.
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45
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Gee HY, Sadowski CE, Aggarwal PK, Porath JD, Yakulov TA, Schueler M, Lovric S, Ashraf S, Braun DA, Halbritter J, Fang H, Airik R, Vega-Warner V, Cho KJ, Chan TA, Morris LGT, ffrench-Constant C, Allen N, McNeill H, Büscher R, Kyrieleis H, Wallot M, Gaspert A, Kistler T, Milford DV, Saleem MA, Keng WT, Alexander SI, Valentini RP, Licht C, Teh JC, Bogdanovic R, Koziell A, Bierzynska A, Soliman NA, Otto EA, Lifton RP, Holzman LB, Sibinga NES, Walz G, Tufro A, Hildebrandt F. FAT1 mutations cause a glomerulotubular nephropathy. Nat Commun 2016; 7:10822. [PMID: 26905694 PMCID: PMC4770090 DOI: 10.1038/ncomms10822] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 01/25/2016] [Indexed: 01/12/2023] Open
Abstract
Steroid-resistant nephrotic syndrome (SRNS) causes 15% of chronic kidney disease (CKD). Here we show that recessive mutations in FAT1 cause a distinct renal disease entity in four families with a combination of SRNS, tubular ectasia, haematuria and facultative neurological involvement. Loss of FAT1 results in decreased cell adhesion and migration in fibroblasts and podocytes and the decreased migration is partially reversed by a RAC1/CDC42 activator. Podocyte-specific deletion of Fat1 in mice induces abnormal glomerular filtration barrier development, leading to podocyte foot process effacement. Knockdown of Fat1 in renal tubular cells reduces migration, decreases active RAC1 and CDC42, and induces defects in lumen formation. Knockdown of fat1 in zebrafish causes pronephric cysts, which is partially rescued by RAC1/CDC42 activators, confirming a role of the two small GTPases in the pathogenesis. These findings provide new insights into the pathogenesis of SRNS and tubulopathy, linking FAT1 and RAC1/CDC42 to podocyte and tubular cell function.
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Affiliation(s)
- Heon Yung Gee
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Carolin E Sadowski
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pardeep K Aggarwal
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jonathan D Porath
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Toma A Yakulov
- University Freiburg Medical Center, Freiburg 79106, Germany
| | - Markus Schueler
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Svjetlana Lovric
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shazia Ashraf
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Daniela A Braun
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jan Halbritter
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Humphrey Fang
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rannar Airik
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Virginia Vega-Warner
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kyeong Jee Cho
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Luc G T Morris
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Charles ffrench-Constant
- MRC Centre for Regenerative Medicine, Multiple Sclerosis Society Centre for Translational Research, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Nicholas Allen
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Helen McNeill
- Department of Molecular Genetics, Samuel Lunenfeld-Tanenbaum Research Institute, University of Toronto, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Rainer Büscher
- Department of Pediatrics II, University Hospital of Essen, Essen 45147, Germany
| | | | - Michael Wallot
- Department of Pediatrics, Bethanien Hospital, Moers 47441, Germany
| | - Ariana Gaspert
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Thomas Kistler
- Division of Nephrology, Kantonsspital Winterthur, Winterthur 8401, Switzerland
| | - David V Milford
- Department of Paediatric Nephrology, Birmingham Children's Hospital, Birmingham B4 6NH, UK
| | - Moin A Saleem
- Children's and Academic Renal Unit, University of Bristol, Bristol BS1 5NB, UK
| | - Wee Teik Keng
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur 50586, Malaysia
| | - Stephen I Alexander
- Centre for Kidney Research, Children's Hospital at Westmead, Westmead 2145, Australia
| | - Rudolph P Valentini
- Department of Pediatrics, Division of Pediatric Nephrology, Children's Hospital of Michigan/Wayne State University, Detroit, Michigan 48201, USA
| | - Christoph Licht
- Division of Nephrology, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada M5G 1X8
| | - Jun C Teh
- Division of Nephrology, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada M5G 1X8
| | - Radovan Bogdanovic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade 11000, Serbia
| | - Ania Koziell
- Department of Experimental Immunobiology, Division of Transplantation Immunology &Mucosal Biology, King's College London, Faculty of Life Sciences &Medicine, 5th floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | | | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology &Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo 11562, Egypt.,Egyptian Group for Orphan Renal Diseases, Cairo 11562, Egypt
| | - Edgar A Otto
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Nicholas E S Sibinga
- Wilf Family Cardiovascular Research Institute and Department of Medicine/Cardiology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Gerd Walz
- University Freiburg Medical Center, Freiburg 79106, Germany
| | - Alda Tufro
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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Vivante A, Hildebrandt F. Exploring the genetic basis of early-onset chronic kidney disease. Nat Rev Nephrol 2016; 12:133-46. [PMID: 26750453 DOI: 10.1038/nrneph.2015.205] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The primary causes of chronic kidney disease (CKD) in children differ from those of CKD in adults. In the USA the most common diagnostic groups of renal disease that manifest before the age of 25 years are congenital anomalies of the kidneys and urinary tract, steroid-resistant nephrotic syndrome, chronic glomerulonephritis and renal cystic ciliopathies, which together encompass >70% of early-onset CKD diagnoses. Findings from the past decade suggest that early-onset CKD is caused by mutations in any one of over 200 different monogenic genes. Developments in high-throughput sequencing in the past few years has rendered identification of causative mutations in this high number of genes feasible. Use of genetic analyses in patients with early onset-CKD will provide patients and their families with a molecular genetic diagnosis, generate new insights into disease mechanisms, facilitate aetiology-based classifications of patient cohorts for clinical studies, and might have consequences for personalized approaches to the prevention and treatment of CKD. In this Review, we discuss the implications of next-generation sequencing in clinical genetic diagnostics and the discovery of novel genes in early-onset CKD. We also delineate the resulting opportunities for deciphering disease mechanisms and the therapeutic implications of these findings.
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Affiliation(s)
- Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
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47
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Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
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Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
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Schueler M, Halbritter J, Phelps IG, Braun DA, Otto EA, Porath JD, Gee HY, Shendure J, O'Roak BJ, Lawson JA, Nabhan MM, Soliman NA, Doherty D, Hildebrandt F. Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies. J Med Genet 2015; 53:208-14. [PMID: 26673778 DOI: 10.1136/jmedgenet-2015-103304] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/13/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The term nephronophthisis-related ciliopathies (NPHP-RC) describes a group of rare autosomal-recessive cystic kidney diseases, characterised by broad genetic and clinical heterogeneity. NPHP-RC is frequently associated with extrarenal manifestations and accounts for the majority of genetically caused chronic kidney disease (CKD) during childhood and adolescence. Generation of a molecular diagnosis has been impaired by this broad genetic heterogeneity. However, recently developed high-throughput exon sequencing techniques represent powerful and efficient tools to screen large cohorts for dozens of causative genes. METHODS Therefore, we performed massively multiplexed targeted sequencing using the modified molecular inversion probe strategy (MIPs) in an international cohort of 384 patients diagnosed with NPHP-RC. RESULTS As a result, we established the molecular diagnoses in 81/384 unrelated individuals (21.1%). We detected 127 likely disease-causing mutations in 18 of 34 evaluated NPHP-RC genes, 22 of which were novel. We further compared a subgroup of current findings to the results of a previous study in which we used an array-based microfluidic PCR technology in the same cohort. While 78 likely disease-causing mutations were previously detected by the array-based microfluidic PCR, the MIPs approach identified 94 likely pathogenic mutations. Compared with the previous approach, MIPs redetected 66 out of 78 variants and 28 previously unidentified variants, for a total of 94 variants. CONCLUSIONS In summary, we demonstrate that the modified MIPs technology is a useful approach to screen large cohorts for a multitude of established NPHP genes in order to identify the underlying molecular cause. Combined application of two independent library preparation and sequencing techniques, however, may still be indicated for Mendelian diseases with extensive genetic heterogeneity in order to further increase diagnostic sensitivity.
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Affiliation(s)
- Markus Schueler
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan Halbritter
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Divison of Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany
| | - Ian G Phelps
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Daniela A Braun
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edgar A Otto
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan D Porath
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jay Shendure
- University of Washington, Genome Sciences, Seattle, Washington, USA
| | - Brian J O'Roak
- Oregon Health and Science University, Molecular and Medical Genetics, Portland, Oregon, USA
| | - Jennifer A Lawson
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marwa M Nabhan
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Friedhelm Hildebrandt
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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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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Perrault I, Halbritter J, Porath JD, Gérard X, Braun DA, Gee HY, Fathy HM, Saunier S, Cormier-Daire V, Thomas S, Attié-Bitach T, Boddaert N, Taschner M, Schueler M, Lorentzen E, Lifton RP, Lawson JA, Garfa-Traore M, Otto EA, Bastin P, Caillaud C, Kaplan J, Rozet JM, Hildebrandt F. IFT81, encoding an IFT-B core protein, as a very rare cause of a ciliopathy phenotype. J Med Genet 2015; 52:657-65. [PMID: 26275418 PMCID: PMC4621372 DOI: 10.1136/jmedgenet-2014-102838] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 06/15/2015] [Indexed: 11/06/2022]
Abstract
Background Bidirectional intraflagellar transport (IFT) consists of two major protein complexes, IFT-A and IFT-B. In contrast to the IFT-B complex, all components of IFT-A have recently been linked to human ciliopathies when defective. We therefore hypothesised that mutations in additional IFT-B encoding genes can be found in patients with multisystemic ciliopathies. Methods We screened 1628 individuals with reno-ocular ciliopathies by targeted next-generation sequencing of ciliary candidate genes, including all IFT-B encoding genes. Results Consequently, we identified a homozygous mutation in IFT81 affecting an obligatory donor splice site in an individual with nephronophthisis and polydactyly. Further, we detected a loss-of-stop mutation with extension of the deduced protein by 10 amino acids in an individual with neuronal ceroid lipofuscinosis-1. This proband presented with retinal dystrophy and brain lesions including cerebellar atrophy, a phenotype to which the IFT81 variant might contribute. Cultured fibroblasts of this latter affected individual showed a significant decrease in ciliated cell abundance compared with controls and increased expression of the transcription factor GLI2 suggesting deranged sonic hedgehog signalling. Conclusions This work describes identification of mutations of IFT81 in individuals with symptoms consistent with the clinical spectrum of ciliopathies. It might represent the rare case of a core IFT-B complex protein found associated with human disease. Our data further suggest that defects in the IFT-B core are an exceedingly rare finding, probably due to its indispensable role for ciliary assembly in development.
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Affiliation(s)
- Isabelle Perrault
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Jan Halbritter
- Division of Endocrinology and Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan D Porath
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Daniela A Braun
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Sophie Saunier
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Molecular bases of hereditary kidney diseases, Nephronophthisis and Hypodysplasia, Paris, France
| | - Valérie Cormier-Daire
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Molecular and Physiopathological bases of osteochondrodysplasia, Paris, France
| | - Sophie Thomas
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Embryology and genetics of human malformation, Paris, France
| | - Tania Attié-Bitach
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Embryology and genetics of human malformation, Paris, France
| | - Nathalie Boddaert
- Department of Pediatric Radiology, Hôpital Necker-Enfants Malades, APHP, Descartes University, Paris, France
| | - Michael Taschner
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Markus Schueler
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Richard P Lifton
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, USA
| | - Jennifer A Lawson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meriem Garfa-Traore
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Cell imaging platform, Paris, France
| | - Edgar A Otto
- Departments of Pediatrics, University of Michigan, Ann Arbor, USA
| | - Philippe Bastin
- Trypanosome Cell Biology Unit, Institut Pasteur and CNRS, URA 2581, Paris, France
| | | | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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