1
|
Wolf MTF, Bonsib SM, Larsen CP, Hildebrandt F. Nephronophthisis: a pathological and genetic perspective. Pediatr Nephrol 2024; 39:1977-2000. [PMID: 37930417 DOI: 10.1007/s00467-023-06174-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 11/07/2023]
Abstract
Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease and is one of the most frequent genetic causes for kidney failure (KF) in children and adolescents. Over 20 genes cause NPHP and over 90 genes contribute to renal ciliopathies often involving multiple organs. About 15-20% of NPHP patients have additional extrarenal symptoms affecting other organs than the kidneys. The involvement of additional organ systems in syndromic forms of NPHP is explained by shared expression of most NPHP gene products in centrosomes and primary cilia, a sensory organelle present in most mammalian cells. This finding resulted in the classification of NPHP as a ciliopathy. If extrarenal symptoms are present in addition to NPHP, these disorders are defined as NPHP-related ciliopathies (NPHP-RC) and can involve the retina (e.g., with Senior-Løken syndrome), CNS (central nervous system) (e.g., with Joubert syndrome), liver (e.g., Boichis and Arima syndromes), or bone (e.g., Mainzer-Saldino and Sensenbrenner syndromes). This review focuses on the pathological findings and the recent genetic advances in NPHP and NPHP-RC. Different mechanisms and signaling pathways are involved in NPHP ranging from planar cell polarity, sonic hedgehog signaling (Shh), DNA damage response pathway, Hippo, mTOR, and cAMP signaling. A number of therapeutic interventions appear to be promising, ranging from vasopressin receptor 2 antagonists such as tolvaptan, cyclin-dependent kinase inhibitors such as roscovitine, Hh agonists such as purmorphamine, and mTOR inhibitors such as rapamycin.
Collapse
Affiliation(s)
- Matthias T F Wolf
- Division of Pediatric Nephrology, University of Texas, Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
- Division of Pediatric Nephrology, C.S. Mott Children's Hospital, University of Michigan, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109, USA.
| | | | | | | |
Collapse
|
2
|
Grlić S, Gregurović V, Martinić M, Davidović M, Kos I, Galić S, Fištrek Prlić M, Vuković Brinar I, Vrljičak K, Lamot L. Single-Center Experience of Pediatric Cystic Kidney Disease and Literature Review. CHILDREN (BASEL, SWITZERLAND) 2024; 11:392. [PMID: 38671609 PMCID: PMC11048964 DOI: 10.3390/children11040392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
INTRODUCTION Pediatric cystic kidney disease (CyKD) includes conditions characterized by renal cysts. Despite extensive research in this field, there are no reliable genetics or other biomarkers to estimate the phenotypic consequences. Therefore, CyKD in children heavily relies on clinical and diagnostic testing to predict the long-term outcomes. AIM A retrospective study aimed to provide a concise overview of this condition and analyze real-life data from a single-center pediatric CyKD cohort followed during a 12-year period. METHODS AND MATERIALS Medical records were reviewed for extensive clinical, laboratory, and radiological data, treatment approaches, and long-term outcomes. RESULTS During the study period, 112 patients received a diagnosis of pediatric CyKD. Male patients were more involved than female (1:0.93). Fifty-six patients had a multicystic dysplastic kidney; twenty-one of them had an autosomal dominant disorder; fifteen had an isolated renal cyst; ten had been diagnosed with autosomal recessive polycystic kidney disease; three had the tuberous sclerosis complex; two patients each had Bardet-Biedl, Joubert syndrome, and nephronophthisis; and one had been diagnosed with the trisomy 13 condition. Genetic testing was performed in 17.9% of the patients, revealing disease-causing mutations in three-quarters (75.0%) of the tested patients. The most commonly presenting symptoms were abdominal distension (21.4%), abdominal pain (15.2%), and oligohydramnios (12.5%). Recurrent urinary tract infections (UTI) were documented in one-quarter of the patients, while 20.5% of them developed hypertension during the long-term follow-up. Antibiotic prophylaxis and antihypertensive treatment were the most employed therapeutic modalities. Seventeen patients progressed to chronic kidney disease (CKD), with thirteen of them eventually reaching end-stage renal disease (ESRD). The time from the initial detection of cysts on an ultrasound (US) to the onset of CKD across the entire cohort was 59.0 (7.0-31124.0) months, whereas the duration from the detection of cysts on an US to the onset of ESRD across the whole cohort was 127.0 (33.0-141.0) months. The median follow-up duration in the cohort was 3.0 (1.0-7.0) years. The patients who progressed to ESRD had clinical symptoms at the time of initial clinical presentation. CONCLUSION This study is the first large cohort of patients reported from Croatia. The most common CyKD was the multicystic dysplastic kidney disease. The most common clinical presentation was abdominal distention, abdominal pain, and oliguria. The most common long-term complications were recurrent UTIs, hypertension, CKD, and ESRD.
Collapse
Affiliation(s)
- Sara Grlić
- Department of Pediatrics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.G.); (I.V.B.); (L.L.)
| | - Viktorija Gregurović
- Department of Pediatrics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.G.); (I.V.B.); (L.L.)
| | - Mislav Martinić
- Department of Pediatrics, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (M.M.); (M.D.); (I.K.); (S.G.); (K.V.)
| | - Maša Davidović
- Department of Pediatrics, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (M.M.); (M.D.); (I.K.); (S.G.); (K.V.)
| | - Ivanka Kos
- Department of Pediatrics, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (M.M.); (M.D.); (I.K.); (S.G.); (K.V.)
| | - Slobodan Galić
- Department of Pediatrics, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (M.M.); (M.D.); (I.K.); (S.G.); (K.V.)
| | - Margareta Fištrek Prlić
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, 10000 Zagreb, Croatia;
| | - Ivana Vuković Brinar
- Department of Pediatrics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.G.); (I.V.B.); (L.L.)
- Department of Internal Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Kristina Vrljičak
- Department of Pediatrics, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (M.M.); (M.D.); (I.K.); (S.G.); (K.V.)
| | - Lovro Lamot
- Department of Pediatrics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.G.); (I.V.B.); (L.L.)
- Department of Pediatrics, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (M.M.); (M.D.); (I.K.); (S.G.); (K.V.)
| |
Collapse
|
3
|
Munir A, Afsar S, Rehman AU. A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023. BMC Ophthalmol 2024; 24:55. [PMID: 38317096 PMCID: PMC10840256 DOI: 10.1186/s12886-024-03319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Inherited retinal degenerations (IRDs) are a group of rare genetic conditions affecting retina of the eye that range in prevalence from 1 in 2000 to 1 in 4000 people globally. This review is based on a retrospective analysis of research articles reporting IRDs associated genetic findings in Pakistani families between 1999 and April 2023. METHODS Articles were retrieved through survey of online sources, notably, PubMed, Google Scholar, and Web of Science. Following a stringent selection criterion, a total of 126 research articles and conference abstracts were considered. All reported variants were cross-checked and validated for their correct genomic nomenclature using different online resources/databases, and their pathogenicity scores were explained as per ACMG guidelines. RESULTS A total of 277 unique sequence variants in 87 distinct genes, previously known to cause IRDs, were uncovered. In around 70% cases, parents of the index patient were consanguineously married, and approximately 88.81% of the detected variants were found in a homozygous state. Overall, more than 95% of the IRDs cases were recessively inherited. Missense variants were predominant (41.88%), followed by Indels/frameshift (26.35%), nonsense (19.13%), splice site (12.27%) and synonymous change (0.36%). Non-syndromic IRDs were significantly higher than syndromic IRDs (77.32% vs. 22.68%). Retinitis pigmentosa (RP) was the most frequently observed IRD followed by Leber's congenital amaurosis (LCA). Altogether, mutations in PDE6A gene was the leading cause of IRDs in Pakistani families followed by mutations in TULP1 gene. CONCLUSION In summary, Pakistani families are notable in expressing recessively inherited monogenic disorders including IRDs likely due to the highest prevalence of consanguinity in the country that leads to expression of rare pathogenic variants in homozygous state.
Collapse
Affiliation(s)
- Asad Munir
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Salma Afsar
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan.
| |
Collapse
|
4
|
Moran AL, Louzao-Martinez L, Norris DP, Peters DJM, Blacque OE. Transport and barrier mechanisms that regulate ciliary compartmentalization and ciliopathies. Nat Rev Nephrol 2024; 20:83-100. [PMID: 37872350 DOI: 10.1038/s41581-023-00773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
Primary cilia act as cell surface antennae, coordinating cellular responses to sensory inputs and signalling molecules that regulate developmental and homeostatic pathways. Cilia are therefore critical to physiological processes, and defects in ciliary components are associated with a large group of inherited pleiotropic disorders - known collectively as ciliopathies - that have a broad spectrum of phenotypes and affect many or most tissues, including the kidney. A central feature of the cilium is its compartmentalized structure, which imparts its unique molecular composition and signalling environment despite its membrane and cytosol being contiguous with those of the cell. Such compartmentalization is achieved via active transport pathways that bring protein cargoes to and from the cilium, as well as gating pathways at the ciliary base that establish diffusion barriers to protein exchange into and out of the organelle. Many ciliopathy-linked proteins, including those involved in kidney development and homeostasis, are components of the compartmentalizing machinery. New insights into the major compartmentalizing pathways at the cilium, namely, ciliary gating, intraflagellar transport, lipidated protein flagellar transport and ciliary extracellular vesicle release pathways, have improved our understanding of the mechanisms that underpin ciliary disease and associated renal disorders.
Collapse
Affiliation(s)
- Ailis L Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Laura Louzao-Martinez
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
| |
Collapse
|
5
|
Kazemein Jasemi NS, Mehrabipour M, Magdalena Estirado E, Brunsveld L, Dvorsky R, Ahmadian MR. Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily. Cells 2024; 13:195. [PMID: 38275820 PMCID: PMC10814857 DOI: 10.3390/cells13020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
SRC homology 3 (SH3) domains are critical interaction modules that orchestrate the assembly of protein complexes involved in diverse biological processes. They facilitate transient protein-protein interactions by selectively interacting with proline-rich motifs (PRMs). A database search revealed 298 SH3 domains in 221 human proteins. Multiple sequence alignment of human SH3 domains is useful for phylogenetic analysis and determination of their selectivity towards PRM-containing peptides (PRPs). However, a more precise functional classification of SH3 domains is achieved by constructing a phylogenetic tree only from PRM-binding residues and using existing SH3 domain-PRP structures and biochemical data to determine the specificity within each of the 10 families for particular PRPs. In addition, the C-terminal proline-rich domain of the RAS activator SOS1 covers 13 of the 14 recognized proline-rich consensus sequence motifs, encompassing differential PRP pattern selectivity among all SH3 families. To evaluate the binding capabilities and affinities, we conducted fluorescence dot blot and polarization experiments using 25 representative SH3 domains and various PRPs derived from SOS1. Our analysis has identified 45 interacting pairs, with binding affinities ranging from 0.2 to 125 micromolar, out of 300 tested and potential new SH3 domain-SOS1 interactions. Furthermore, it establishes a framework to bridge the gap between SH3 and PRP interactions and provides predictive insights into the potential interactions of SH3 domains with PRMs based on sequence specifications. This novel framework has the potential to enhance the understanding of protein networks mediated by SH3 domain-PRM interactions and be utilized as a general approach for other domain-peptide interactions.
Collapse
Affiliation(s)
- Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands; (E.M.E.); (L.B.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands; (E.M.E.); (L.B.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| |
Collapse
|
6
|
Kalot R, Sentell Z, Kitzler TM, Torban E. Primary cilia and actin regulatory pathways in renal ciliopathies. FRONTIERS IN NEPHROLOGY 2024; 3:1331847. [PMID: 38292052 PMCID: PMC10824913 DOI: 10.3389/fneph.2023.1331847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
Ciliopathies are a group of rare genetic disorders caused by defects to the structure or function of the primary cilium. They often affect multiple organs, leading to brain malformations, congenital heart defects, and anomalies of the retina or skeletal system. Kidney abnormalities are among the most frequent ciliopathic phenotypes manifesting as smaller, dysplastic, and cystic kidneys that are often accompanied by renal fibrosis. Many renal ciliopathies cause chronic kidney disease and often progress to end-stage renal disease, necessitating replacing therapies. There are more than 35 known ciliopathies; each is a rare hereditary condition, yet collectively they account for a significant proportion of chronic kidney disease worldwide. The primary cilium is a tiny microtubule-based organelle at the apex of almost all vertebrate cells. It serves as a "cellular antenna" surveying environment outside the cell and transducing this information inside the cell to trigger multiple signaling responses crucial for tissue morphogenesis and homeostasis. Hundreds of proteins and unique cellular mechanisms are involved in cilia formation. Recent evidence suggests that actin remodeling and regulation at the base of the primary cilium strongly impacts ciliogenesis. In this review, we provide an overview of the structure and function of the primary cilium, focusing on the role of actin cytoskeleton and its regulators in ciliogenesis. We then describe the key clinical, genetic, and molecular aspects of renal ciliopathies. We highlight what is known about actin regulation in the pathogenesis of these diseases with the aim to consider these recent molecular findings as potential therapeutic targets for renal ciliopathies.
Collapse
Affiliation(s)
- Rita Kalot
- Department of Medicine and Department of Physiology, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Zachary Sentell
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas M. Kitzler
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Health Center, Montreal, QC, Canada
| | - Elena Torban
- Department of Medicine and Department of Physiology, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, Canada
| |
Collapse
|
7
|
Reddy S, Simmers R, Shah A, Couser N. NPHP1-Related ciliopathies: A new case and major review of the ophthalmic manifestations of 147 reported cases. Clin Case Rep 2023; 11:e7818. [PMID: 37663822 PMCID: PMC10468586 DOI: 10.1002/ccr3.7818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023] Open
Abstract
Our case report and review contribute to the understanding of ocular manifestations in NPHP1 ciliopathies by reinforcing the relationship between pathogenic genetic variants and a wide array of ophthalmic abnormalities.
Collapse
Affiliation(s)
- Shivania Reddy
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Russell Simmers
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Arth Shah
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Natario Couser
- Department of Human and Molecular GeneticsVirginia Commonwealth University School of MedicineRichmondVirginiaUSA
- Department of OphthalmologyVirginia Commonwealth University School of MedicineRichmondVirginiaUSA
- Department of PediatricsVirginia Commonwealth University School of Medicine, Children's Hospital of Richmond at VCURichmondVirginiaUSA
| |
Collapse
|
8
|
Mehrabipour M, Jasemi NSK, Dvorsky R, Ahmadian MR. A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling. Cells 2023; 12:2054. [PMID: 37626864 PMCID: PMC10453029 DOI: 10.3390/cells12162054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
SRC homology 3 (SH3) domains are fundamental modules that enable the assembly of protein complexes through physical interactions with a pool of proline-rich/noncanonical motifs from partner proteins. They are widely studied modular building blocks across all five kingdoms of life and viruses, mediating various biological processes. The SH3 domains are also implicated in the development of human diseases, such as cancer, leukemia, osteoporosis, Alzheimer's disease, and various infections. A database search of the human proteome reveals the existence of 298 SH3 domains in 221 SH3 domain-containing proteins (SH3DCPs), ranging from 13 to 720 kilodaltons. A phylogenetic analysis of human SH3DCPs based on their multi-domain architecture seems to be the most practical way to classify them functionally, with regard to various physiological pathways. This review further summarizes the achievements made in the classification of SH3 domain functions, their binding specificity, and their significance for various diseases when exploiting SH3 protein modular interactions as drug targets.
Collapse
Affiliation(s)
- Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, 040 01 Košice, Slovakia
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| |
Collapse
|
9
|
Leggatt GP, Seaby EG, Veighey K, Gast C, Gilbert RD, Ennis S. A Role for Genetic Modifiers in Tubulointerstitial Kidney Diseases. Genes (Basel) 2023; 14:1582. [PMID: 37628633 PMCID: PMC10454709 DOI: 10.3390/genes14081582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
With the increased availability of genomic sequencing technologies, the molecular bases for kidney diseases such as nephronophthisis and mitochondrially inherited and autosomal-dominant tubulointerstitial kidney diseases (ADTKD) has become increasingly apparent. These tubulointerstitial kidney diseases (TKD) are monogenic diseases of the tubulointerstitium and result in interstitial fibrosis and tubular atrophy (IF/TA). However, monogenic inheritance alone does not adequately explain the highly variable onset of kidney failure and extra-renal manifestations. Phenotypes vary considerably between individuals harbouring the same pathogenic variant in the same putative monogenic gene, even within families sharing common environmental factors. While the extreme end of the disease spectrum may have dramatic syndromic manifestations typically diagnosed in childhood, many patients present a more subtle phenotype with little to differentiate them from many other common forms of non-proteinuric chronic kidney disease (CKD). This review summarises the expanding repertoire of genes underpinning TKD and their known phenotypic manifestations. Furthermore, we collate the growing evidence for a role of modifier genes and discuss the extent to which these data bridge the historical gap between apparently rare monogenic TKD and polygenic non-proteinuric CKD (excluding polycystic kidney disease).
Collapse
Affiliation(s)
- Gary P. Leggatt
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Eleanor G. Seaby
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| | - Kristin Veighey
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Christine Gast
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
| | - Rodney D. Gilbert
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Sarah Ennis
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| |
Collapse
|
10
|
Wang J, Li S, Jiang Y, Wang Y, Ouyang J, Yi Z, Sun W, Jia X, Xiao X, Wang P, Zhang Q. Pathogenic Variants in CEP290 or IQCB1 Cause Earlier-Onset Retinopathy in Senior-Loken Syndrome Compared to Those in INVS, NPHP3, or NPHP4. Am J Ophthalmol 2023; 252:188-204. [PMID: 36990420 DOI: 10.1016/j.ajo.2023.03.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE Senior-Loken syndrome (SLSN) is an autosomal recessive disorder characterized by retinopathy and nephronophthisis. This study aimed to evaluate whether different phenotypes are associated with different variants or subsets of 10 SLSN-associated genes based on an in-house data set and a literature review. DESIGN Retrospective case series. METHODS Patients with biallelic variants in SLSN-associated genes, including NPHP1, INVS, NPHP3, NPHP4, IQCB1, CEP290, SDCCAG8, WDR19, CEP164, and TRAF3IP1, were recruited. Ocular phenotypes and nephrology medical records were collected for comprehensive analysis. RESULTS Variants in 5 genes were identified in 74 patients from 70 unrelated families, including CEP290 (61.4%), IQCB1 (28.6%), NPHP1 (4.2%), NPHP4 (2.9%), and WDR19 (2.9%). The median age at the onset of retinopathy was approximately 1 month (since birth). Nystagmus was the most common initial sign in patients with CEP290 (28 of 44, 63.6%) or IQCB1 (19 of 22, 86.4%) variants. Cone and rod responses were extinguished in 53 of 55 patients (96.4%). Characteristic fundus changes were observed in CEP290- and IQCB1-associated patients. During follow-up, 70 of the 74 patients were referred to nephrology, among whom nephronophthisis was not detected in 62 patients (88.6%) at a median age of 6 years but presented in 8 patients (11.4%) aged approximately 9 years. CONCLUSIONS Patients with pathogenic variants in CEP290 or IQCB1 presented early with retinopathy, whereas other patients with INVS, NPHP3, or NPHP4 variants first developed nephropathy. Therefore, awareness of the genetic and clinical features may facilitate the clinical management of SLSN, especially early intervention of kidney problems for patients with eyes affected first.
Collapse
Affiliation(s)
- Junwen Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Shiqiang Li
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yi Jiang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yingwei Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiamin Ouyang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhen Yi
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Wenmin Sun
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xiaoyun Jia
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xueshan Xiao
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Panfeng Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Qingjiong Zhang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China.
| |
Collapse
|
11
|
Leggatt G, Cheng G, Narain S, Briseño-Roa L, Annereau JP, Gast C, Gilbert RD, Ennis S. A genotype-to-phenotype approach suggests under-reporting of single nucleotide variants in nephrocystin-1 (NPHP1) related disease (UK 100,000 Genomes Project). Sci Rep 2023; 13:9369. [PMID: 37296294 PMCID: PMC10256716 DOI: 10.1038/s41598-023-32169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/23/2023] [Indexed: 06/12/2023] Open
Abstract
Autosomal recessive whole gene deletions of nephrocystin-1 (NPHP1) result in abnormal structure and function of the primary cilia. These deletions can result in a tubulointerstitial kidney disease known as nephronophthisis and retinal (Senior-Løken syndrome) and neurological (Joubert syndrome) diseases. Nephronophthisis is a common cause of end-stage kidney disease (ESKD) in children and up to 1% of adult onset ESKD. Single nucleotide variants (SNVs) and small insertions and deletions (Indels) have been less well characterised. We used a gene pathogenicity scoring system (GenePy) and a genotype-to-phenotype approach on individuals recruited to the UK Genomics England (GEL) 100,000 Genomes Project (100kGP) (n = 78,050). This approach identified all participants with NPHP1-related diseases reported by NHS Genomics Medical Centres and an additional eight participants. Extreme NPHP1 gene scores, often underpinned by clear recessive inheritance, were observed in patients from diverse recruitment categories, including cancer, suggesting the possibility of a more widespread disease than previously appreciated. In total, ten participants had homozygous CNV deletions with eight homozygous or compound heterozygous with SNVs. Our data also reveals strong in-silico evidence that approximately 44% of NPHP1 related disease may be due to SNVs with AlphaFold structural modelling evidence for a significant impact on protein structure. This study suggests historical under-reporting of SNVS in NPHP1 related diseases compared with CNVs.
Collapse
Affiliation(s)
- Gary Leggatt
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK.
- Wessex Kidney Centre, Portsmouth Hospitals University NHS Trust, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK.
- University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK.
| | - Guo Cheng
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
| | - Sumit Narain
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
| | - Luis Briseño-Roa
- Medetia, Imagine Institute for Genetic Diseases, 24 Boulevard du Montparnasse, 75015, Paris, France
| | - Jean-Philippe Annereau
- Medetia, Imagine Institute for Genetic Diseases, 24 Boulevard du Montparnasse, 75015, Paris, France
| | - Christine Gast
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
- Wessex Kidney Centre, Portsmouth Hospitals University NHS Trust, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK
| | - Rodney D Gilbert
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
- Southampton Children's Hospital, Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
| | - Sarah Ennis
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
| |
Collapse
|
12
|
Labat-de-Hoz L, Rubio-Ramos A, Correas I, Alonso MA. The MAL Family of Proteins: Normal Function, Expression in Cancer, and Potential Use as Cancer Biomarkers. Cancers (Basel) 2023; 15:2801. [PMID: 37345137 DOI: 10.3390/cancers15102801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/06/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
The MAL family of integral membrane proteins consists of MAL, MAL2, MALL, PLLP, CMTM8, MYADM, and MYADML2. The best characterized members are elements of the machinery that controls specialized pathways of membrane traffic and cell signaling. This review aims to help answer the following questions about the MAL-family genes: (i) is their expression regulated in cancer and, if so, how? (ii) What role do they play in cancer? (iii) Might they have biomedical applications? Analysis of large-scale gene expression datasets indicated altered levels of MAL-family transcripts in specific cancer types. A comprehensive literature search provides evidence of MAL-family gene dysregulation and protein function repurposing in cancer. For MAL, and probably for other genes of the family, dysregulation is primarily a consequence of gene methylation, although copy number alterations also contribute to varying degrees. The scrutiny of the two sources of information, datasets and published studies, reveals potential prognostic applications of MAL-family members as cancer biomarkers-for instance, MAL2 in breast cancer, MAL2 and MALL in pancreatic cancer, and MAL and MYADM in lung cancer-and other biomedical uses. The availability of validated antibodies to some MAL-family proteins sanctions their use as cancer biomarkers in routine clinical practice.
Collapse
Affiliation(s)
- Leticia Labat-de-Hoz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Armando Rubio-Ramos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Isabel Correas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Miguel A Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
13
|
Higgins K, Moore BA, Berberovic Z, Adissu HA, Eskandarian M, Flenniken AM, Shao A, Imai DM, Clary D, Lanoue L, Newbigging S, Nutter LMJ, Adams DJ, Bosch F, Braun RE, Brown SDM, Dickinson ME, Dobbie M, Flicek P, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Chin HJG, Mammano F, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, Lloyd KCK, McKerlie C, Moshiri A. Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes. Sci Rep 2022; 12:20791. [PMID: 36456625 PMCID: PMC9715561 DOI: 10.1038/s41598-022-19710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/02/2022] [Indexed: 12/05/2022] Open
Abstract
We searched a database of single-gene knockout (KO) mice produced by the International Mouse Phenotyping Consortium (IMPC) to identify candidate ciliopathy genes. We first screened for phenotypes in mouse lines with both ocular and renal or reproductive trait abnormalities. The STRING protein interaction tool was used to identify interactions between known cilia gene products and those encoded by the genes in individual knockout mouse strains in order to generate a list of "candidate ciliopathy genes." From this list, 32 genes encoded proteins predicted to interact with known ciliopathy proteins. Of these, 25 had no previously described roles in ciliary pathobiology. Histological and morphological evidence of phenotypes found in ciliopathies in knockout mouse lines are presented as examples (genes Abi2, Wdr62, Ap4e1, Dync1li1, and Prkab1). Phenotyping data and descriptions generated on IMPC mouse line are useful for mechanistic studies, target discovery, rare disease diagnosis, and preclinical therapeutic development trials. Here we demonstrate the effective use of the IMPC phenotype data to uncover genes with no previous role in ciliary biology, which may be clinically relevant for identification of novel disease genes implicated in ciliopathies.
Collapse
Affiliation(s)
- Kendall Higgins
- The University of Miami Leonard M. Miller School of Medicine, Miami, FL, 33136, USA
| | - Bret A Moore
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, Gainesville, FL, 32608, USA
| | - Zorana Berberovic
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | | | - Mohammad Eskandarian
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Andy Shao
- University of Reno, Nevada, School of Medicine, Reno, NV, 89557, USA
| | - Denise M Imai
- Comparative Pathology Laboratory, U.C. Davis, Davis, 95616, USA
| | - Dave Clary
- Mouse Biology Program, U.C. Davis, Davis, CA, 95618, USA
| | - Louise Lanoue
- Mouse Biology Program, U.C. Davis, Davis, CA, 95618, USA
| | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fatima Bosch
- Centre of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | | | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Mary E Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael Dobbie
- Phenomics Australia, The Australian National University, 131 Garran Rd, Acton, Canberra, ACT, 2601, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | - Sanjeev Galande
- Indian Institutes of Science Education and Research, Dr. Homi Bhabha Rd, Ward No. 8, NCL Colony, Pashan, Pune, Maharashtra, 411008, India
| | - Anne Grobler
- Faculty of Health Sciences, PCDDP North-West University, North-West University Potchefstroom Campus 11 Hoffman Street, Potchefstroom, 2531, South Africa
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67400, Illkirch, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, Université of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Hsian-Jean Genie Chin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), 3F., No. 106, Sec. 2, Heping E. Rd., Da'an Dist., Taipei City, 106214, Taiwan (R.O.C.)
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via Ramarini, 00015, Monterotondo Scalo, Italy
| | - Chuan Qin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), Beijing, China
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Science, 5 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | | | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, IMG BIOCEV Building SO.02 Prumyslova 595, 252 50, Vestec, Czech Republic
| | - J-K Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul, 08826, South Korea
| | - Ying Xu
- CAM-SU Genomic Resource Center, Soochow University, Organization Planning of No. 1 Shizi Street, Suzhou, 215123, China
| | - K C Kent Lloyd
- Mouse Biology Program, U.C. Davis, Davis, CA, 95618, USA
- Department of Surgery, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA
| | - Colin McKerlie
- The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
- Department of Laboratory Medicine and Pathobiology, Hospital for Sick Children (SickKids), The Centre for Phenogenomics, Faculty of Medicine, University of Toronto, 25 Orde Street, Toronto, ON, M5T 3H7, USA.
| | - Ala Moshiri
- Department of Ophthalmology and Vision Science, School of Medicine, U.C. Davis Eye Center, 4860 Y. Street, Suite 2400, Sacramento, CA, 95817, USA.
| |
Collapse
|
14
|
Kayser N, Zaiser F, Veenstra AC, Wang H, Göcmen B, Eckert P, Franz H, Köttgen A, Walz G, Yakulov TA. Clock genes rescue nphp mutations in zebrafish. Hum Mol Genet 2022; 31:4143-4158. [PMID: 35861640 PMCID: PMC9759334 DOI: 10.1093/hmg/ddac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 01/21/2023] Open
Abstract
The zebrafish pronephros model, using morpholino oligonucleotides (MO) to deplete target genes, has been extensively used to characterize human ciliopathy phenotypes. Recently, discrepancies between MO and genetically defined mutants have questioned this approach. We analyzed zebrafish with mutations in the nphp1-4-8 module to determine the validity of MO-based results. While MO-mediated depletion resulted in glomerular cyst and cloaca malformation, these ciliopathy-typical manifestations were observed at a much lower frequency in zebrafish embryos with defined nphp mutations. All nphp1-4-8 mutant zebrafish were viable and displayed decreased manifestations in the next (F2) generation, lacking maternal RNA contribution. While genetic compensation was further supported by the observation that nphp4-deficient mutants became partially refractory to MO-based nphp4 depletion, zebrafish embryos, lacking one nphp gene, became more sensitive to MO-based depletion of additional nphp genes. Transcriptome analysis of nphp8 mutant embryos revealed an upregulation of the circadian clock genes cry1a and cry5. MO-mediated depletion of cry1a and cry5 caused ciliopathy phenotypes in wild-type embryos, while cry1a and cry5 depletion in maternal zygotic nphp8 mutant embryos increased the frequency of glomerular cysts compared to controls. Importantly, cry1a and cry5 rescued the nephropathy-related phenotypes in nphp1, nphp4 or nphp8-depleted zebrafish embryos. Our results reveal that nphp mutant zebrafish resemble the MO-based phenotypes, albeit at a much lower frequency. Rapid adaption through upregulation of circadian clock genes seems to ameliorate the loss of nphp genes, contributing to phenotypic differences.
Collapse
Affiliation(s)
| | | | | | | | - Burulca Göcmen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79106, Germany
| | - Priska Eckert
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Henriette Franz
- Department of Biomedicine, University of Basel, Pestalozzistr. 20, Basel CH-4056, Switzerland
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79106, Germany
| | - Gerd Walz
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Albertstrasse 19, Freiburg 79104, Germany
| | - Toma A Yakulov
- To whom correspondence should be addressed. Tel: +49 76127063036;
| |
Collapse
|
15
|
Zhong Z, Yan X, Fang Z, Dong Y, Tan J, Xie J, Hu L, Zhang S, Qin W. Case Report: Adolescent-Onset Isolated Nephronophthisis Caused by a Novel Homozygous Inversin Mutation. Front Genet 2022; 13:847397. [PMID: 35664325 PMCID: PMC9157817 DOI: 10.3389/fgene.2022.847397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/07/2022] [Indexed: 02/05/2023] Open
Abstract
Objective: Nephronophthisis (NPHP) is a rare autosomal recessive inherited kidney disease that can cause cystic enlargement of the kidneys, and lead to end-stage renal disease (ESRD) before the age of 30 years. Herein we describe a case of adolescent-onset NPHP with a novel homozygous mutation in the inversin gene (INVS). Methods: The patient was a 15-year-old Chinese boy who presented with ESRD. Genetic testing was performed via whole exome sequencing and validated via Sanger sequencing. A novel homozygous INVS mutation was identified (c. 1909C > T; p. Gln637Ter). Results: The results of laboratory examinations included urinary protein 1.05 g/24 h, urine erythrocyte count 5/high-power field, serum creatinine 1,026.2 μmol/L, and estimated glomerular filtration rate 5.8 ml/min/1.73 mm2. Extrarenal features included hypertension and moderate anemia, and his parents were consanguineous (first cousins). A homozygous 1-bp substitution resulting in a nonsense mutation (c. 1909C > T; p. Gln637Ter) in exon 15 of INVS was detected via whole exome sequencing, and validated via Sanger sequencing. According to the classification system of the American College of Medical Genetics and Genomics, the mutated gene in INVS is strongly pathogenic (PVS1+PM2+PP3+PP5). His parents and a younger brother were heterozygous carriers. Based on the above results he was diagnosed with juvenile type 2 NPHP. He underwent hemodialysis, and received a kidney transplant after 2 months. He is currently recovering well, with a serum creatinine level of 117 μmol/L and an estimated glomerular filtration rate of 79.6 ml/min/1.73 mm2. Conclusion: Here we have described an extremely rare case of adolescent-onset type 2 NPHP caused by a homozygous INVS mutation. The patient had progressed to ESRD by the age of 15 years. The current report will deepen our understanding of the clinical and genetic basis of this disease.
Collapse
Affiliation(s)
- Zhengxia Zhong
- Division of Nephrology, Department of Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiaoyong Yan
- Division of Nephrology, Department of Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhengying Fang
- Department of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yijun Dong
- Division of Nephrology, Department of Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiaxing Tan
- Division of Nephrology, Department of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jingyuan Xie
- Department of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Linhong Hu
- Division of Nephrology, Department of Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shibin Zhang
- Laboratory Animal Centers, Zunyi Medical University, Zunyi, China
| | - Wei Qin
- Division of Nephrology, Department of Medicine, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
16
|
Van De Weghe JC, Gomez A, Doherty D. The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. Annu Rev Genomics Hum Genet 2022; 23:301-329. [PMID: 35655331 DOI: 10.1146/annurev-genom-121321-093528] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Joubert syndrome (JS), Meckel syndrome (MKS), and nephronophthisis (NPH) ciliopathy spectrum could be the poster child for advances and challenges in Mendelian human genetics over the past half century. Progress in understanding these conditions illustrates many core concepts of human genetics. The JS phenotype alone is caused by pathogenic variants in more than 40 genes; remarkably, all of the associated proteins function in and around the primary cilium. Primary cilia are near-ubiquitous, microtubule-based organelles that play crucial roles in development and homeostasis. Protruding from the cell, these cellular antennae sense diverse signals and mediate Hedgehog and other critical signaling pathways. Ciliary dysfunction causes many human conditions termed ciliopathies, which range from multiple congenital malformations to adult-onset single-organ failure. Research on the genetics of the JS-MKS-NPH spectrum has spurred extensive functional work exploring the broadly important role of primary cilia in health and disease. This functional work promises to illuminate the mechanisms underlying JS-MKS-NPH in humans, identify therapeutic targets across genetic causes, and generate future precision treatments. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA;
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
| |
Collapse
|
17
|
Rubio-Ramos A, Bernabé-Rubio M, Labat-de-Hoz L, Casares-Arias J, Kremer L, Correas I, Alonso MA. MALL, a membrane-tetra-spanning proteolipid overexpressed in cancer, is present in membraneless nuclear biomolecular condensates. Cell Mol Life Sci 2022; 79:236. [PMID: 35399121 PMCID: PMC8995265 DOI: 10.1007/s00018-022-04270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 12/04/2022]
Abstract
Proteolipids are proteins with unusual lipid-like properties. It has long been established that PLP and plasmolipin, which are two unrelated membrane-tetra-spanning myelin proteolipids, can be converted in vitro into a water-soluble form with a distinct conformation, raising the question of whether these, or other similar proteolipids, can adopt two different conformations in the cell to adapt their structure to distinct environments. Here, we show that MALL, another proteolipid with a membrane-tetra-spanning structure, distributes in membranes outside the nucleus and, within the nucleus, in membrane-less, liquid-like PML body biomolecular condensates. Detection of MALL in one or other environment was strictly dependent on the method of cell fixation used, suggesting that MALL adopts different conformations depending on its physical environment —lipidic or aqueous— in the cell. The acquisition of the condensate-compatible conformation requires PML expression. Excess MALL perturbed the distribution of the inner nuclear membrane proteins emerin and LAP2β, and that of the DNA-binding protein BAF, leading to the formation of aberrant nuclei. This effect, which is consistent with studies identifying overexpressed MALL as an unfavorable prognostic factor in cancer, could contribute to cell malignancy. Our study establishes a link between proteolipids, membranes and biomolecular condensates, with potential biomedical implications.
Collapse
Affiliation(s)
- Armando Rubio-Ramos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Miguel Bernabé-Rubio
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Leticia Labat-de-Hoz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Javier Casares-Arias
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Leonor Kremer
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Isabel Correas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Miguel A Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| |
Collapse
|
18
|
Gana S, Serpieri V, Valente EM. Genotype-phenotype correlates in Joubert syndrome: A review. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:72-88. [PMID: 35238134 PMCID: PMC9314610 DOI: 10.1002/ajmg.c.31963] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 01/20/2023]
Abstract
Joubert syndrome (JS) is a genetically heterogeneous primary ciliopathy characterized by a pathognomonic cerebellar and brainstem malformation, the “molar tooth sign,” and variable organ involvement. Over 40 causative genes have been identified to date, explaining up to 94% of cases. To date, gene‐phenotype correlates have been delineated only for a handful of genes, directly translating into improved counseling and clinical care. For instance, JS individuals harboring pathogenic variants in TMEM67 have a significantly higher risk of liver fibrosis, while pathogenic variants in NPHP1, RPGRIP1L, and TMEM237 are frequently associated to JS with renal involvement, requiring a closer monitoring of liver parameters, or renal functioning. On the other hand, individuals with causal variants in the CEP290 or AHI1 need a closer surveillance for retinal dystrophy and, in case of CEP290, also for chronic kidney disease. These examples highlight how an accurate description of the range of clinical symptoms associated with defects in each causative gene, including the rare ones, would better address prognosis and help guiding a personalized management. This review proposes to address this issue by assessing the available literature, to confirm known, as well as to propose rare gene‐phenotype correlates in JS.
Collapse
Affiliation(s)
- Simone Gana
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Enza Maria Valente
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| |
Collapse
|
19
|
Gupta S, Ozimek-Kulik JE, Phillips JK. Nephronophthisis-Pathobiology and Molecular Pathogenesis of a Rare Kidney Genetic Disease. Genes (Basel) 2021; 12:genes12111762. [PMID: 34828368 PMCID: PMC8623546 DOI: 10.3390/genes12111762] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The exponential rise in our understanding of the aetiology and pathophysiology of genetic cystic kidney diseases can be attributed to the identification of cystogenic genes over the last three decades. The foundation of this was laid by positional cloning strategies which gradually shifted towards next-generation sequencing (NGS) based screenings. This shift has enabled the discovery of novel cystogenic genes at an accelerated pace unlike ever before and, most notably, the past decade has seen the largest increase in identification of the genes which cause nephronophthisis (NPHP). NPHP is a monogenic autosomal recessive cystic kidney disease caused by mutations in a diverse clade of over 26 identified genes and is the most common genetic cause of renal failure in children. NPHP gene types present with some common pathophysiological features alongside a diverse range of extra-renal phenotypes associated with specific syndromic presentations. This review provides a timely update on our knowledge of this disease, including epidemiology, pathophysiology, anatomical and molecular features. We delve into the diversity of the NPHP causing genes and discuss known molecular mechanisms and biochemical pathways that may have possible points of intersection with polycystic kidney disease (the most studied renal cystic pathology). We delineate the pathologies arising from extra-renal complications and co-morbidities and their impact on quality of life. Finally, we discuss the current diagnostic and therapeutic modalities available for disease management, outlining possible avenues of research to improve the prognosis for NPHP patients.
Collapse
Affiliation(s)
- Shabarni Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- Correspondence:
| | - Justyna E. Ozimek-Kulik
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia
- Department of Paediatric Nephrology, Sydney Children’s Hospital Network, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Jacqueline Kathleen Phillips
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
| |
Collapse
|
20
|
Li D, Hu M, Chen H, Wu X, Wei X, Lin H, Gao X, Wang H, Li M, Ong ACM, Yue Z, Sun L. An Nphp1 knockout mouse model targeting exon 2-20 demonstrates characteristic phenotypes of human Nephronophthisis. Hum Mol Genet 2021; 31:232-243. [PMID: 34415307 DOI: 10.1093/hmg/ddab239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/30/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Nephronophthisis (NPH) is the most prevalent monogenetic disorder leading to end-stage renal failure (ESRD) in childhood. Mutations in Nphp1, encoding a cilia-localized protein, account for the majority of NPH cases. Despite its identification many years ago, Nphp1 deletions targeting exon 4 or exon 20 have not reproduced the histological features of human NPH in murine models. In this study, we deleted exon 2-20 of Nphp1 by CRISPR/Cas9 gene editing to create a near-total knockout (KO) mouse model (Nphp1del2-20/del2-20). Nphp1del2-20/del2-20 mice faithfully reproduced the renal and extrarenal phenotypes associated with human NPH, including renal cyst development, tubular basement membrane thickening, retinal degeneration and abnormal spermatogenesis. Importantly, Nphp1 re-expression using an adenoviral-associated-virus-9 (AAV9) vector could partially rescue both renal and retinal phenotypes in Nphp1del2-20/del2-20 mice. Our results reported the first relevant Nphp1 mouse model with renal phenotypes for human disease. It will be a valuable model for future studies of Nphp1 function and to develop novel treatments for this common childhood disease.
Collapse
Affiliation(s)
- Dantong Li
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Miaoyue Hu
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Huamu Chen
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaohong Wu
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoya Wei
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hongrong Lin
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xuefei Gao
- Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haiyan Wang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Min Li
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Albert C M Ong
- Kidney Genetics Group, Academic Nephrology Unit, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK
| | - Zhihui Yue
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Liangzhong Sun
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| |
Collapse
|
21
|
Akira M, Suzuki H, Ikeda A, Iwasaki M, Honda D, Takahara H, Rinno H, Tomita S, Suzuki Y. Atypical histological abnormalities in an adult patient with nephronophthisis harboring NPHP1 deletion: a case report. BMC Nephrol 2021; 22:261. [PMID: 34246230 PMCID: PMC8272369 DOI: 10.1186/s12882-021-02466-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Nephronophthisis (NPHP) is a chronic tubular interstitial disorder that exhibits an autosomal recessive genetic form and causes progressive renal failure in children. Patients with NPHP rarely show urinary abnormalities, edema, or hypertension. Thus, NPHP is often detected only when renal failure becomes advanced. NPHP can be divided into three types based on the age of end-stage renal failure, i.e., infant type (approximately 5 years old), juvenile type (approximately 13-14 years old), and adolescent type (approximately 19 years old). Here, we report a case of NPHP diagnosed by genetic analysis at 26 years of age with atypical histological abnormalities. CASE PRESENTATION A 26-year-old woman showed no growth disorders or urinary abnormalities in annual school physical examinations. However, at a check-up at 26 years old, she exhibited renal dysfunction (eGFR 26 mL/min/1.73 m2). Urine tests indicated low specific gravity of urine, but not proteinuria or microscopic hematuria. Urinary β2-microglobulin was high (805 μg/L), and renal biopsy was performed for definitive diagnosis. Histological findings showed no significant findings in glomeruli. However, moderate fibrosis was observed in the interstitial area, and moderate atrophy was observed in the tubules. There were no significant findings in immunofluorescence analysis, and no electron dense deposits were detected by electron microscopy. Although cyst-like expansion of the tubules was unclear, tubular atrophy was dominantly found in the distal tubule by cytokeratin 7 staining. Genetic analysis of the NPHP1 gene showed complete deletion of this gene, leading to a definitive diagnosis of NPHP. CONCLUSIONS NPHP is not merely a pediatric disease and is relatively high incidence in patients with adult onset end-stage of renal disease. In this case, typical histological abnormalities, such as cyst-like expansion of the tubular lesion, were not observed, and diagnosis was achieved by genetic analysis of the NPHP1 gene, which is responsible for the onset of NPHP. In patients with renal failure with tubular interstitial disease dominantly in the distal tubules, it is necessary to discriminate NPHP, even in adult cases.
Collapse
Affiliation(s)
- Maiko Akira
- Department of Nephrology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-shi, Chiba, 279-0021, Japan
| | - Hitoshi Suzuki
- Department of Nephrology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-shi, Chiba, 279-0021, Japan.
| | - Arisa Ikeda
- Department of Nephrology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-shi, Chiba, 279-0021, Japan
| | - Masako Iwasaki
- Department of Nephrology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-shi, Chiba, 279-0021, Japan
| | - Daisuke Honda
- Department of Nephrology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-shi, Chiba, 279-0021, Japan
| | - Hisatsugu Takahara
- Department of Nephrology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-shi, Chiba, 279-0021, Japan
| | - Hisaki Rinno
- Department of Nephrology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-shi, Chiba, 279-0021, Japan
| | - Shigeki Tomita
- Department of Pathology, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Yusuke Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| |
Collapse
|
22
|
Birtel J, Spital G, Book M, Habbig S, Bäumner S, Riehmer V, Beck BB, Rosenkranz D, Bolz HJ, Dahmer-Heath M, Herrmann P, König J, Charbel Issa P. NPHP1 gene-associated nephronophthisis is associated with an occult retinopathy. Kidney Int 2021; 100:1092-1100. [PMID: 34153329 DOI: 10.1016/j.kint.2021.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Biallelic deletions in the NPHP1 gene are the most frequent molecular defect of nephronophthisis, a kidney ciliopathy and leading cause of hereditary end-stage kidney disease. Nephrocystin 1, the gene product of NPHP1, is also expressed in photoreceptors where it plays an important role in intra-flagellar transport between the inner and outer segments. However, the human retinal phenotype has never been investigated in detail. Here, we characterized retinal features of 16 patients with homozygous deletions of the entire NPHP1 gene. Retinal assessment included multimodal imaging (optical coherence tomography, fundus autofluorescence) and visual function testing (visual acuity, full-field electroretinography, color vision, visual field). Fifteen patients had a mild retinal phenotype that predominantly affected cones, but with relative sparing of the fovea. Despite a predominant cone dysfunction, night vision problems were an early symptom in some cases. The consistent retinal phenotype on optical coherence tomography images included reduced reflectivity and often a granular appearance of the ellipsoid zone, fading or loss of the interdigitation zone, and mild outer retinal thinning. However, there were usually no obvious structural changes visible upon clinical examination and fundus autofluorescence imaging (occult retinopathy). More advanced retinal degeneration might occur with ageing. An identified additional CEP290 variant in one patient with a more severe retinal degeneration may indicate a potential role for genetic modifiers, although this requires further investigation. Thus, diagnostic awareness about this distinct retinal phenotype has implications for the differential diagnosis of nephronophthisis and for individual prognosis of visual function.
Collapse
Affiliation(s)
- Johannes Birtel
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Georg Spital
- Eye Center at St. Franziskus-Hospital Münster, Münster, Germany
| | - Marius Book
- Eye Center at St. Franziskus-Hospital Münster, Münster, Germany
| | - Sandra Habbig
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sören Bäumner
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Vera Riehmer
- Institute of Human Genetics, University of Cologne, University Hospital of Cologne, Cologne, Germany
| | - Bodo B Beck
- Institute of Human Genetics, University of Cologne, University Hospital of Cologne, Cologne, Germany; Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases Cologne, University of Cologne, University Hospital of Cologne, Cologne, Germany
| | | | - Hanno J Bolz
- Institute of Human Genetics, University of Cologne, University Hospital of Cologne, Cologne, Germany; Senckenberg Centre for Human Genetics, Frankfurt, Germany
| | - Mareike Dahmer-Heath
- Department of General Pediatrics, University Children's Hospital, Münster, Germany
| | | | - Jens König
- Department of General Pediatrics, University Children's Hospital, Münster, Germany
| | - Peter Charbel Issa
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| |
Collapse
|
23
|
Stokman MF, Saunier S, Benmerah A. Renal Ciliopathies: Sorting Out Therapeutic Approaches for Nephronophthisis. Front Cell Dev Biol 2021; 9:653138. [PMID: 34055783 PMCID: PMC8155538 DOI: 10.3389/fcell.2021.653138] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in in vitro and/or in vivo models. Despite identification of numerous candidate drugs in rodent models, there has been a lack of clinical trials and there is currently no therapy that halts disease progression in NPH patients. This review covers the most important findings of therapeutic approaches in NPH model systems to date, including hypothesis-driven therapies and untargeted drug screens, approached from the pathophysiology of NPH. Importantly, most animal models used in these studies represent the cystic infantile form of NPH, which is less prevalent than the juvenile form. It appears therefore important to develop new models relevant for juvenile/adult NPH. Alternative non-orthologous animal models and developments in patient-based in vitro model systems are discussed, as well as future directions in personalized therapy for NPH.
Collapse
Affiliation(s)
- Marijn F Stokman
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Sophie Saunier
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Alexandre Benmerah
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| |
Collapse
|
24
|
Datta P, Cribbs JT, Seo S. Differential requirement of NPHP1 for compartmentalized protein localization during photoreceptor outer segment development and maintenance. PLoS One 2021; 16:e0246358. [PMID: 33961633 PMCID: PMC8104407 DOI: 10.1371/journal.pone.0246358] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
Nephrocystin (NPHP1) is a ciliary transition zone protein and its ablation causes nephronophthisis (NPHP) with partially penetrant retinal dystrophy. However, the precise requirements of NPHP1 in photoreceptors are not well understood. Here, we characterize retinal degeneration in a mouse model of NPHP1 and show that NPHP1 is required to prevent infiltration of inner segment plasma membrane proteins into the outer segment during the photoreceptor maturation. We demonstrate that Nphp1 gene-trap mutant mice, which were previously described as null, are likely hypomorphs due to the production of a small quantity of functional mRNAs derived from nonsense-associated altered splicing and skipping of two exons including the one harboring the gene-trap. In homozygous mutant animals, inner segment plasma membrane proteins such as syntaxin-3 (STX3), synaptosomal-associated protein 25 (SNAP25), and interphotoreceptor matrix proteoglycan 2 (IMPG2) accumulate in the outer segment when outer segments are actively elongating. This phenotype, however, is spontaneously ameliorated after the outer segment elongation is completed. Consistent with this, some photoreceptor cell loss (~30%) occurs during the photoreceptor maturation period but it stops afterward. We further show that Nphp1 genetically interacts with Cep290, another NPHP gene, and that a reduction of Cep290 gene dose results in retinal degeneration that continues until adulthood in Nphp1 mutant mice. These findings demonstrate that NPHP1 is required for the confinement of inner segment plasma membrane proteins during the outer segment development, but its requirement diminishes as photoreceptors mature. Our study also suggests that additional mutations in other NPHP genes may influence the penetrance of retinopathy in human NPHP1 patients.
Collapse
Affiliation(s)
- Poppy Datta
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, United States of America
- Institute for Vision Research, The University of Iowa, Iowa City, IA, United States of America
| | - J. Thomas Cribbs
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, United States of America
- Institute for Vision Research, The University of Iowa, Iowa City, IA, United States of America
| | - Seongjin Seo
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, United States of America
- Institute for Vision Research, The University of Iowa, Iowa City, IA, United States of America
- * E-mail:
| |
Collapse
|
25
|
Abdelwahed M, Maaloul I, Benoit V, Hilbert P, Hachicha M, Kamoun H, Keskes-Ammar L, Belguith N. Copy-number variation of the NPHP1 gene in patients with juvenile Nephronophthisis. Acta Clin Belg 2021; 76:16-24. [PMID: 31402777 DOI: 10.1080/17843286.2019.1655231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective: Juvenile nephronophthisis (NPHP) is an autosomal recessive cystic disease of the kidney. It represents the most frequent genetic cause of chronic renal failure in children. Methods: we investigated clinical and molecular features in two children with Juvenile nephronophthisis using firstly Multiplex ligation-dependent probe amplification (MLPA) and secondly multiplex PCR. Results: we report a homozygous NPHP1 deletion in two children. Conclusion: NPHP1 deletion analysis using diagnostic methods (e.g. MLPA, Multiplex PCR) should always be considered in patients with nephronophthisis, especially from consanguineous families. Our results provide insights into genotype-phenotype correlations in juvenile nephronophthisis that can be utilized in genetic counseling.
Collapse
Affiliation(s)
- Mayssa Abdelwahed
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Ines Maaloul
- Pediatric Department of Hedi Chaker Hospital, Sfax, Tunisia
| | - Valerie Benoit
- Center of Human Genetics, Institute of Pathology and Genetics, Biopark Charleroi Brussels, Gosselies, Belgium
| | - Pascale Hilbert
- Center of Human Genetics, Institute of Pathology and Genetics, Biopark Charleroi Brussels, Gosselies, Belgium
| | | | - Hassen Kamoun
- Medical Genetics Department of Hedi Chaker Hospital, Sfax, Tunisia
| | - Leila Keskes-Ammar
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
- Medical Genetics Department of Hedi Chaker Hospital, Sfax, Tunisia
| |
Collapse
|
26
|
Santoni M, Piva F, Cimadamore A, Giulietti M, Battelli N, Montironi R, Cosmai L, Porta C. Exploring the Spectrum of Kidney Ciliopathies. Diagnostics (Basel) 2020; 10:E1099. [PMID: 33339422 PMCID: PMC7766105 DOI: 10.3390/diagnostics10121099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022] Open
Abstract
Ciliopathies are a group of multi-organ diseases caused by the disruption of the primary cilium. This event leads to a variety of kidney disorders, including nephronophthisis, renal cystic dysplasia, and renal cell carcinoma (RCC). Primary cilium contributes to the regulation of the cell cycle and protein homeostasis, that is, the balance between protein synthesis and degradation by acting on the ubiquitin-proteasome system, autophagy, and mTOR signaling. Many proteins are involved in renal ciliopathies. In particular, fibrocystin (PKHD1) is involved in autosomal recessive polycystic kidney disease (ARPKD), while polycystin-1 (PKD1) and polycystin-2 (PKD2) are implicated in autosomal dominant polycystic kidney disease (ADPKD). Moreover, primary cilia are associated with essential signaling pathways, such as Hedgehog, Wnt, and Platelet-Derived Growth Factor (PDGF). In this review, we focused on the ciliopathies associated with kidney diseases, exploring genes and signaling pathways associated with primary cilium and the potential role of cilia as therapeutic targets in renal disorders.
Collapse
Affiliation(s)
- Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (F.P.); (M.G.)
| | - Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy;
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (F.P.); (M.G.)
| | | | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy;
| | - Laura Cosmai
- Division of Nephrology and Dialysis, ASST Fatebenefratelli-Sacco, Fatebenefratelli Hospital, 20121 Milan, Italy;
| | - Camillo Porta
- Chair of Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari ‘A. Moro’, 70121 Bari, Italy;
- Division of Medical Oncology, A.O.U. ConsorzialePoliclinico di Bari, 70124 Bari, Italy
| |
Collapse
|
27
|
Borowicz P, Chan H, Hauge A, Spurkland A. Adaptor proteins: Flexible and dynamic modulators of immune cell signalling. Scand J Immunol 2020; 92:e12951. [DOI: 10.1111/sji.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Paweł Borowicz
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Hanna Chan
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anette Hauge
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anne Spurkland
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| |
Collapse
|
28
|
The Role of Wnt Signalling in Chronic Kidney Disease (CKD). Genes (Basel) 2020; 11:genes11050496. [PMID: 32365994 PMCID: PMC7290783 DOI: 10.3390/genes11050496] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
Chronic kidney disease (CKD) encompasses a group of diverse diseases that are associated with accumulating kidney damage and a decline in glomerular filtration rate (GFR). These conditions can be of an acquired or genetic nature and, in many cases, interactions between genetics and the environment also play a role in disease manifestation and severity. In this review, we focus on genetically inherited chronic kidney diseases and dissect the links between canonical and non-canonical Wnt signalling, and this umbrella of conditions that result in kidney damage. Most of the current evidence on the role of Wnt signalling in CKD is gathered from studies in polycystic kidney disease (PKD) and nephronophthisis (NPHP) and reveals the involvement of β-catenin. Nevertheless, recent findings have also linked planar cell polarity (PCP) signalling to CKD, with further studies being required to fully understand the links and molecular mechanisms.
Collapse
|
29
|
Chen F, Dai L, Zhang J, Li F, Cheng J, Zhao J, Zhang B. A case report of NPHP1 deletion in Chinese twins with nephronophthisis. BMC MEDICAL GENETICS 2020; 21:84. [PMID: 32306954 PMCID: PMC7168837 DOI: 10.1186/s12881-020-01025-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/13/2020] [Indexed: 12/02/2022]
Abstract
Background Nephronophthisis (NPHP) is a rare autosomal recessive inherited disorder with high heterogeneity. The majority of NPHP patients progress to end-stage renal disease (ESRD) within the first three decades of life. As an inherited disorder with highly genetic heterogeneity and clinical presentations, NPHP still poses a challenging task for nephrologists without special training to make a well-judged decision on its precise diagnosis, let alone its mechanism and optimal therapy. Case presentation A Chinese family with NPHP was recruited in current study. The clinical characteristics (including findings from renal biopsy) of NPHP patients were collected from medical records and the potential responsible genes were explored by the whole exome sequencing (WES). A homozygous deletion of NPHP1 (1–20 exons) was found in both affected patients, which was further confirmed by quantitative PCR. Conclusions Homozygous full gene deletion of the NPHP1 gene was identified in a Chinese family with NPHP, which was the molecular pathogenic basis of this disorder. Furthermore, identification of the pathogenic genes for those affected patients can help to have a full knowledge on NPHP’s molecular mechanism and precise treatment.
Collapse
Affiliation(s)
- Feng Chen
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Limeng Dai
- Department of Medical Genetics, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Jun Zhang
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Furong Li
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Jinbo Cheng
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Jinghong Zhao
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Bo Zhang
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China.
| |
Collapse
|
30
|
Al Alawi I, Al Salmi I, Al Rahbi F, Al Riyami M, Al Kalbani N, Al Ghaithi B, Al Mawali A, Sayer JA. Molecular Genetic Diagnosis of Omani Patients With Inherited Cystic Kidney Disease. Kidney Int Rep 2019; 4:1751-1759. [PMID: 31844813 PMCID: PMC6895654 DOI: 10.1016/j.ekir.2019.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 02/05/2023] Open
Affiliation(s)
- Intisar Al Alawi
- Institute of Genetic Medicine, International Centre for Life, University of Newcastle, Newcastle upon Tyne, Tyne and Wear, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Issa Al Salmi
- Renal Medicine Department, Ministry of Health, Royal Hospital, Muscat, Oman
| | - Fatma Al Rahbi
- Renal Medicine Department, Ministry of Health, Royal Hospital, Muscat, Oman
| | - Mohamed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Ministry of Health, Royal Hospital, Muscat, Oman
| | - Naifain Al Kalbani
- Pediatric Nephrology Unit, Department of Child Health, Ministry of Health, Royal Hospital, Muscat, Oman
| | - Badria Al Ghaithi
- Pediatric Nephrology Unit, Department of Child Health, Ministry of Health, Royal Hospital, Muscat, Oman
| | - Adhra Al Mawali
- Center of Studies and Research, Ministry of Health, Muscat, Oman
| | - John A. Sayer
- Institute of Genetic Medicine, International Centre for Life, University of Newcastle, Newcastle upon Tyne, Tyne and Wear, UK
- Renal Services, Newcastle Upon Tyne Hospitals National Health Service Trust, Newcastle upon Tyne, Tyne and Wear, UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, Tyne and Wear, UK
- Correspondence: John A. Sayer, Professor of Renal Medicine, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, Tyne and Wear, NE1 3BZ, UK.
| |
Collapse
|
31
|
Mannella V, Quilici G, Nigro EA, Lampis M, Minici C, Degano M, Boletta A, Musco G. The N-Terminal Domain of NPHP1 Folds into a Monomeric Left-Handed Antiparallel Three-Stranded Coiled Coil with Anti-apoptotic Function. ACS Chem Biol 2019; 14:1845-1854. [PMID: 31345020 DOI: 10.1021/acschembio.9b00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mutations in the NPHP1 gene, coding for human nephrocystin-1 (NPHP1), cause the autosomal recessive disease nephronophthisis, the most common cause of end-stage renal disease in children and adolescents. The function and structure of NPHP1 are still poorly characterized. NPHP1 presents a modular structure well in keeping with its role as an adaptor protein: it harbors an SH3 domain flanked by two glutamic acid-rich regions and a conserved C-terminal nephrocystin homology domain (NHD). Similar to other NPHP protein family members, its N-terminus contains a putative coiled-coil domain (NPHP1CC) that is supposed to play an important role in NPHP1 self-association and/or protein-protein interactions. Structural studies proving its structure and its oligomerization state are still lacking. Here we demonstrate that NPHP1CC is monomeric in solution and unexpectedly folds into an autonomous domain forming a three-stranded antiparallel coiled coil suitable for protein-protein interactions. Notably, we found that the NPHP1CC shares remarkable structural similarities with the three-stranded coiled coil of the BAG domain protein family, which is known to mediate the anti-apoptotic function of these proteins, suggesting a possible similar role for NPHP1CC. In agreement with this hypothesis, we show that in the context of the full-length protein the NPHP1CC is fundamental to regulate resistance to apoptotic stimuli.
Collapse
Affiliation(s)
- Valeria Mannella
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Giacomo Quilici
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Elisa Agnese Nigro
- Molecular Basis of PKD Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Matteo Lampis
- Molecular Basis of PKD Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Claudia Minici
- Biocrystallography Unit, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Massimo Degano
- Biocrystallography Unit, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Alessandra Boletta
- Molecular Basis of PKD Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| |
Collapse
|
32
|
Baehr W, Hanke-Gogokhia C, Sharif A, Reed M, Dahl T, Frederick JM, Ying G. Insights into photoreceptor ciliogenesis revealed by animal models. Prog Retin Eye Res 2018; 71:26-56. [PMID: 30590118 DOI: 10.1016/j.preteyeres.2018.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022]
Abstract
Photoreceptors are polarized neurons, with very specific subcellular compartmentalization and unique requirements for protein expression and trafficking. Each photoreceptor contains an outer segment, the site of photon capture that initiates vision, an inner segment that houses the biosynthetic machinery and a synaptic terminal for signal transmission to downstream neurons. Outer segments and inner segments are connected by a connecting cilium (CC), the equivalent of a transition zone (TZ) of primary cilia. The connecting cilium is part of the basal body/axoneme backbone that stabilizes the outer segment. This report will update the reader on late developments in photoreceptor ciliogenesis and transition zone formation, specifically in mouse photoreceptors, focusing on early events in photoreceptor ciliogenesis. The connecting cilium, an elongated and narrow structure through which all outer segment proteins and membrane components must traffic, functions as a gate that controls access to the outer segment. Here we will review genes and their protein products essential for basal body maturation and for CC/TZ genesis, sorted by phenotype. Emphasis is given to naturally occurring mouse mutants and gene knockouts that interfere with CC/TZ formation and ciliogenesis.
Collapse
Affiliation(s)
- Wolfgang Baehr
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA.
| | - Christin Hanke-Gogokhia
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Ali Sharif
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Michelle Reed
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Tiffanie Dahl
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Jeanne M Frederick
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Guoxin Ying
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| |
Collapse
|
33
|
Verbitsky M, Westland R, Perez A, Kiryluk K, Liu Q, Krithivasan P, Mitrotti A, Fasel DA, Batourina E, Sampson MG, Bodria M, Werth M, Kao C, Martino J, Capone VP, Vivante A, Shril S, Kil BH, Marasà M, Zhang JY, Na YJ, Lim TY, Ahram D, Weng PL, Heinzen EL, Carrea A, Piaggio G, Gesualdo L, Manca V, Masnata G, Gigante M, Cusi D, Izzi C, Scolari F, van Wijk JAE, Saraga M, Santoro D, Conti G, Zamboli P, White H, Drozdz D, Zachwieja K, Miklaszewska M, Tkaczyk M, Tomczyk D, Krakowska A, Sikora P, Jarmoliński T, Borszewska-Kornacka MK, Pawluch R, Szczepanska M, Adamczyk P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Dobson MG, Darlow JM, Puri P, Barton DE, Furth SL, Warady BA, Gucev Z, Lozanovski VJ, Tasic V, Pisani I, Allegri L, Rodas LM, Campistol JM, Jeanpierre C, Alam S, Casale P, Wong CS, Lin F, Miranda DM, Oliveira EA, Simões-E-Silva AC, Barasch JM, Levy B, Wu N, Hildebrandt F, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Zhang F, Hakonarson H, Papaioannou VE, Mendelsohn CL, Gharavi AG, Sanna-Cherchi S. The copy number variation landscape of congenital anomalies of the kidney and urinary tract. Nat Genet 2018; 51:117-127. [PMID: 30578417 PMCID: PMC6668343 DOI: 10.1038/s41588-018-0281-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/18/2018] [Indexed: 12/18/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of pediatric kidney failure. We performed a genome-wide analysis of copy number variants (CNVs) in 2,824 cases and 21,498 controls. Affected individuals carried a significant burden of rare exonic (i.e. affecting coding regions) CNVs and were enriched for known genomic disorders (GD). Kidney anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD-CNVs and novel deletions; obstructive uropathy (OU) had a lower CNV burden and an intermediate prevalence of GD-CNVs; vesicoureteral reflux (VUR) had the fewest GD-CNVs but was enriched for novel exonic CNVs, particularly duplications. Six loci (1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12, and 22q11.2) accounted for 65% of patients with GD-CNVs. Deletions at 17q12, 4p16.1-p16.3, and 22q11.2 were specific for KA; the 16p11.2 locus showed extensive pleiotropy. Using a multidisciplinary approach, we identified TBX6 as a driver for the CAKUT subphenotypes in the 16p11.2 microdeletion syndrome.
Collapse
Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.,Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Alejandra Perez
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Qingxue Liu
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - David A Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Ekaterina Batourina
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Max Werth
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Charlly Kao
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Valentina P Capone
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Jun Y Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Young-Ji Na
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dina Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Patricia L Weng
- Department of Pediatric Nephrology, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, CA, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alba Carrea
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Valeria Manca
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Giuseppe Masnata
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Daniele Cusi
- National Research Council of Italy, Inst. Biomedical Technologies Milano Bio4dreams Scientific Unit, Milano, Italy
| | - Claudia Izzi
- Dipartimento Ostetrico-Ginecologico e Seconda Divisione di Nefrologia ASST, Spedali Civili e Presidio di Montichiari, Brescia, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia, Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia, Italy
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia.,School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria "G. Martino", Messina, Italy
| | - Pasquale Zamboli
- Division of Nephrology, University of Campania "Luigi Vanvitell", Naples, Italy
| | - Hope White
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology, Jagiellonian University Medical College, Krakow, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Anna Krakowska
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, Lublin, Poland
| | | | - Maria K Borszewska-Kornacka
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Robert Pawluch
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Mark G Dobson
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - John M Darlow
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Hospital Tallaght, Dublin, Ireland
| | - David E Barton
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,University College Dublin UCD School of Medicine, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Susan L Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Division of Nephrology, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Bradley A Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Division of Nephrology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Zoran Gucev
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Vladimir J Lozanovski
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia.,University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Velibor Tasic
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Isabella Pisani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Lida M Rodas
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Josep M Campistol
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pasquale Casale
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.,Mount Sinai Medical Center, Kravis Children's Hospital, New York, NY, USA
| | - Craig S Wong
- Division of Pediatric Nephrology, University of New Mexico Children's Hospital, Albuquerque, NM, USA
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Débora M Miranda
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Eduardo A Oliveira
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Cristina Simões-E-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Jonathan M Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Medical Research Center of Orthopedics, all at Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA.
| | - Cathy L Mendelsohn
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Ali G Gharavi
- 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.
| |
Collapse
|
34
|
Compound heterozygous splice site variants in the SCLT1 gene highlight an additional candidate locus for Senior-Løken syndrome. Sci Rep 2018; 8:16733. [PMID: 30425282 PMCID: PMC6233217 DOI: 10.1038/s41598-018-35152-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/29/2018] [Indexed: 12/19/2022] Open
Abstract
Senior Løken syndrome (SLS) is a heterogeneous disorder characterized by severe retinal degenerations and juvenile-onset nephronophthisis. Genetic variants in ten different genes have been reported as the causes of SLS. Clinical evaluation of a patient with SLS and her unaffected parents revealed that the patient had infantile-onset retinal dystrophy and juvenile-onset nephronophthisis. Other systemic abnormalities included hepatic dysfunction, megacystis, mild learning disability, autism, obesity, and hyperinsulinemia. Whole-exome sequencing identified compound heterozygous SCLT1 variants (c.1218 + 3insT and c.1631A > G) in the patient. The unaffected parents were heterozygous for each variant. Transcript analysis using reverse transcription PCR demonstrated that the c.1218 + 3insT variant leads to exon 14 skipping (p.V383_M406del), while the other variant (c.1631A > G) primarily leads to exon 17 skipping (p.D480EfsX11) as well as minor amounts of two transcripts (6 bps deletion in the last of exon 17 [p.V543_K544del] and exons 17 and 18 skipping [p.D480E, S481_K610del]). Immunohistochemical analysis demonstrated that the Sclt1 protein was localized to the distal appendage of the photoreceptor basal body, indicating a ciliary protein. In conclusion, we identified compound heterozygous splice site variants of SCLT1 in a patient with a new form of ciliopathies that exhibits clinical features of SLS.
Collapse
|
35
|
Viau A, Bienaimé F, Lukas K, Todkar AP, Knoll M, Yakulov TA, Hofherr A, Kretz O, Helmstädter M, Reichardt W, Braeg S, Aschman T, Merkle A, Pfeifer D, Dumit VI, Gubler MC, Nitschke R, Huber TB, Terzi F, Dengjel J, Grahammer F, Köttgen M, Busch H, Boerries M, Walz G, Triantafyllopoulou A, Kuehn EW. Cilia-localized LKB1 regulates chemokine signaling, macrophage recruitment, and tissue homeostasis in the kidney. EMBO J 2018; 37:embj.201798615. [PMID: 29925518 PMCID: PMC6068446 DOI: 10.15252/embj.201798615] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/13/2018] [Accepted: 05/22/2018] [Indexed: 12/24/2022] Open
Abstract
Polycystic kidney disease (PKD) and other renal ciliopathies are characterized by cysts, inflammation, and fibrosis. Cilia function as signaling centers, but a molecular link to inflammation in the kidney has not been established. Here, we show that cilia in renal epithelia activate chemokine signaling to recruit inflammatory cells. We identify a complex of the ciliary kinase LKB1 and several ciliopathy‐related proteins including NPHP1 and PKD1. At homeostasis, this ciliary module suppresses expression of the chemokine CCL2 in tubular epithelial cells. Deletion of LKB1 or PKD1 in mouse renal tubules elevates CCL2 expression in a cell‐autonomous manner and results in peritubular accumulation of CCR2+ mononuclear phagocytes, promoting a ciliopathy phenotype. Our findings establish an epithelial organelle, the cilium, as a gatekeeper of tissue immune cell numbers. This represents an unexpected disease mechanism for renal ciliopathies and establishes a new model for how epithelial cells regulate immune cells to affect tissue homeostasis.
Collapse
Affiliation(s)
- Amandine Viau
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,INSERM U1151, Institut Necker Enfants Malades, Department of Growth and Signaling, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Frank Bienaimé
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,INSERM U1151, Institut Necker Enfants Malades, Department of Growth and Signaling, Université Paris Descartes-Sorbonne Paris Cité, Paris, France.,Service d'Explorations Fonctionnelles, Hôpital Necker-Enfants Malades, Paris, France
| | - Kamile Lukas
- Renal Department, University Medical Center, Freiburg, Germany
| | | | - Manuel Knoll
- Department of Rheumatology and Clinical Immunology, University Medical Center, Freiburg, Germany
| | - Toma A Yakulov
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexis Hofherr
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Kretz
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Neuroanatomy, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Helmstädter
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wilfried Reichardt
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Medical Physics, Department of Radiology, and Comprehensive Cancer Center, University Medical Center, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone Braeg
- Renal Department, University Medical Center, Freiburg, Germany
| | - Tom Aschman
- Department of Rheumatology and Clinical Immunology, University Medical Center, Freiburg, Germany
| | - Annette Merkle
- Medical Physics, Department of Radiology, and Comprehensive Cancer Center, University Medical Center, Freiburg, Germany
| | - Dietmar Pfeifer
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, Freiburg, Germany
| | - Verónica I Dumit
- Center for Biological Systems Analysis (ZBSA), Core Facility Proteomics, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Marie-Claire Gubler
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France.,Imagine Institute, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Roland Nitschke
- Center for Biological Systems Analysis (ZBSA), Life Imaging Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Tobias B Huber
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Fabiola Terzi
- INSERM U1151, Institut Necker Enfants Malades, Department of Growth and Signaling, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Jörn Dengjel
- Center for Biological Systems Analysis (ZBSA), Core Facility Proteomics, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Florian Grahammer
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Köttgen
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hauke Busch
- German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research (IMMZ), Albert-Ludwigs-University, Freiburg, Germany
| | - Gerd Walz
- Renal Department, University Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Antigoni Triantafyllopoulou
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, University Medical Center, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, Charité - University Medical Centre Berlin, Berlin, Germany
| | - E Wolfgang Kuehn
- Renal Department, University Medical Center, Freiburg, Germany .,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| |
Collapse
|
36
|
|
37
|
König J, Kranz B, König S, Schlingmann KP, Titieni A, Tönshoff B, Habbig S, Pape L, Häffner K, Hansen M, Büscher A, Bald M, Billing H, Schild R, Walden U, Hampel T, Staude H, Riedl M, Gretz N, Lablans M, Bergmann C, Hildebrandt F, Omran H, Konrad M. Phenotypic Spectrum of Children with Nephronophthisis and Related Ciliopathies. Clin J Am Soc Nephrol 2017; 12:1974-1983. [PMID: 29146700 PMCID: PMC5718263 DOI: 10.2215/cjn.01280217] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/18/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Genetic heterogeneity and phenotypic variability are major challenges in familial nephronophthisis and related ciliopathies. To date, mutations in 20 different genes (NPHP1 to -20) have been identified causing either isolated kidney disease or complex multiorgan disorders. In this study, we provide a comprehensive and detailed characterization of 152 children with a special focus on extrarenal organ involvement and the long-term development of ESRD. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We established an online-based registry (www.nephreg.de) to assess the clinical course of patients with nephronophthisis and related ciliopathies on a yearly base. Cross-sectional and longitudinal data were collected. Mean observation time was 7.5±6.1 years. RESULTS In total, 51% of the children presented with isolated nephronophthisis, whereas the other 49% exhibited related ciliopathies. Monogenetic defects were identified in 97 of 152 patients, 89 affecting NPHP genes. Eight patients carried mutations in other genes related to cystic kidney diseases. A homozygous NPHP1 deletion was, by far, the most frequent genetic defect (n=60). We observed a high prevalence of extrarenal manifestations (23% [14 of 60] for the NPHP1 group and 66% [61 of 92] for children without NPHP1). A homozygous NPHP1 deletion not only led to juvenile nephronophthisis but also was able to present as a predominantly neurologic phenotype. However, irrespective of the initial clinical presentation, the kidney function of all patients carrying NPHP1 mutations declined rapidly between the ages of 8 and 16 years, with ESRD at a mean age of 11.4±2.4 years. In contrast within the non-NPHP1 group, there was no uniform pattern regarding the development of ESRD comprising patients with early onset and others preserving normal kidney function until adulthood. CONCLUSIONS Mutations in NPHP genes cause a wide range of ciliopathies with multiorgan involvement and different clinical outcomes.
Collapse
Affiliation(s)
- Jens König
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Abstract
The police brought a 65-year-old female patient to the EADU after being found 'roaming the streets' in an apparent state of confusion. This was her third admission under the same circumstances during the last 3 years. Neurological examination revealed (1) cognitive impairment, (2) oculomotor apraxia, (3) abnormal cancellation of vestibular ocular reflex, (4) mild ataxia and (5) mild hypotonia. Renal function was abnormal and liver function was normal. No retinal disturbance was found. The head CT on admission was normal for stroke and the lumbar puncture was negative for encephalitis. Her brain MRI showed 'molar tooth sign', suggestive of Joubert syndrome, which was confirmed by genetic testing showing anomalous NPHP1 gene.
Collapse
Affiliation(s)
- Carlo Canepa
- Department of Stroke and Neurology, James Paget University Hospital, Norwich, UK
| | - Ben Burton
- Stroke Services, James Paget University Hospitals NHS Foundation Trust, Great Yarmouth, Great Yarmouth, UK
| | - Abdul Muhith
- Stroke Services, James Paget University Hospitals NHS Foundation Trust, Great Yarmouth, Great Yarmouth, UK
| |
Collapse
|
39
|
Jávorszky E, Morinière V, Kerti A, Balogh E, Pikó H, Saunier S, Karcagi V, Antignac C, Tory K. QMPSF is sensitive and specific in the detection of NPHP1 heterozygous deletions. ACTA ACUST UNITED AC 2017; 55:809-816. [DOI: 10.1515/cclm-2016-0819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Background:
Nephronophthisis, an autosomal recessive nephropathy, is responsible for 10% of childhood chronic renal failure. The deletion of its major gene, NPHP1, with a minor allele frequency of 0.24% in the general population, is the most common mutation leading to a monogenic form of childhood chronic renal failure. It is challenging to detect it in the heterozygous state. We aimed to evaluate the sensitivity and the specificity of the quantitative multiplex PCR of short fluorescent fragments (QMPSF) in its detection.
Methods:
After setting up the protocol of QMPSF, we validated it on 39 individuals diagnosed by multiplex ligation-dependent probe amplification (MLPA) with normal NPHP1 copy number (n=17), with heterozygous deletion (n=13, seven parents and six patients), or with homozygous deletion (n=9). To assess the rate of the deletions that arise from independent events, deleted alleles were haplotyped.
Results:
The results of QMPSF and MLPA correlated perfectly in the identification of 76 heterozygously deleted and 56 homozygously deleted exons. The inter-experimental variability of the dosage quotient obtained by QMPSF was low: control, 1.05 (median; range, 0.86−1.33, n = 102 exons); heterozygous deletion, 0.51 (0.42−0.67, n = 76 exons); homozygous deletion, 0 (0−0, n = 56 exons). All patients harboring a heterozygous deletion were found to carry a hemizygous mutation. At least 15 out of 18 deletions appeared on different haplotypes and one deletion appeared de novo.
Conclusions:
The cost- and time-effective QMPSF has a 100% sensitivity and specificity in the detection of NPHP1 deletion. The potential de novo appearance of NPHP1 deletions makes its segregation analysis highly recommended in clinical practice.
Collapse
|
40
|
Kishimoto K, Nomura J, Ellegood J, Fukumoto K, Lerch JP, Moreno-De-Luca D, Bourgeron T, Tamada K, Takumi T. Behavioral and neuroanatomical analyses in a genetic mouse model of 2q13 duplication. Genes Cells 2017; 22:436-451. [PMID: 28370817 DOI: 10.1111/gtc.12487] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/24/2017] [Indexed: 12/12/2022]
Abstract
Duplications of human chromosome 2q13 have been reported in patients with neurodevelopmental disorder including autism spectrum disorder. Nephronophthisis-1 (NPHP1) was identified as a causative gene in the minimal deletion on chromosome 2q13 for familial juvenile type 1 nephronophthisis and Joubert syndrome, an autosomal recessive neurodevelopmental disorder characterized by a cerebellar and brain stem malformation, hypotonia, developmental delay, ataxia, and sometimes associated with cognitive impairment. NPHP1 encodes a ciliary protein, nephrocystin-1, which is expressed in the brain, yet its function in the brain remains largely unknown. In this study, we generated bacterial artificial chromosome-based transgenic mice, called 2q13 dup, that recapitulate human chromosome 2q13 duplication and contain one extra copy of the Nphp1 transgene. To analyze any behavioral alterations in 2q13 dup mice, we conducted a battery of behavioral tests. Although 2q13 dup mice show no significant differences in social behavior, they show deficits in spontaneous alternation behavior and fear memory. We also carried out magnetic resonance imaging to confirm whether copy number gain in this locus affects the neuroanatomy. There was a trend toward a decrease in the cerebellar paraflocculus of 2q13 dup mice. This is the first report of a genetic mouse model for human 2q13 duplication.
Collapse
Affiliation(s)
- Keiko Kishimoto
- RIKEN Brain Science Institute (BSI), Wako, Saitama, 351-0198, Japan.,Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, 734-8553, Japan
| | - Jun Nomura
- RIKEN Brain Science Institute (BSI), Wako, Saitama, 351-0198, Japan
| | - Jacob Ellegood
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Keita Fukumoto
- RIKEN Brain Science Institute (BSI), Wako, Saitama, 351-0198, Japan.,Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, 734-8553, Japan
| | - Jason P Lerch
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Daniel Moreno-De-Luca
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Human Behavior, Brown University, Providence, RI, 02908, USA
| | | | - Kota Tamada
- RIKEN Brain Science Institute (BSI), Wako, Saitama, 351-0198, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute (BSI), Wako, Saitama, 351-0198, Japan.,Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, 734-8553, Japan
| |
Collapse
|
41
|
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.
Collapse
|
42
|
Garcia-Gonzalo FR, Reiter JF. Open Sesame: How Transition Fibers and the Transition Zone Control Ciliary Composition. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028134. [PMID: 27770015 DOI: 10.1101/cshperspect.a028134] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cilia are plasma membrane protrusions that act as cellular propellers or antennae. To perform these functions, cilia must maintain a composition distinct from those of the contiguous cytosol and plasma membrane. The specialized composition of the cilium depends on the ciliary gate, the region at the ciliary base separating the cilium from the rest of the cell. The ciliary gate's main structural features are electron dense struts connecting microtubules to the adjacent membrane. These structures include the transition fibers, which connect the distal basal body to the base of the ciliary membrane, and the Y-links, which connect the proximal axoneme and ciliary membrane within the transition zone. Both transition fibers and Y-links form early during ciliogenesis and play key roles in ciliary assembly and trafficking. Accordingly, many human ciliopathies are caused by mutations that perturb ciliary gate function.
Collapse
Affiliation(s)
- Francesc R Garcia-Gonzalo
- Departamento de Bioquímica, Facultad de Medicina, and Instituto de Investigaciones Biomédicas Alberto Sols UAM-CSIC, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94158
| |
Collapse
|
43
|
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: 80] [Impact Index Per Article: 11.4] [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.
Collapse
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
| |
Collapse
|
44
|
Grammatikopoulos T, Sambrotta M, Strautnieks S, Foskett P, Knisely AS, Wagner B, Deheragoda M, Starling C, Mieli-Vergani G, Smith J, Bull L, Thompson RJ. Mutations in DCDC2 (doublecortin domain containing protein 2) in neonatal sclerosing cholangitis. J Hepatol 2016; 65:1179-1187. [PMID: 27469900 PMCID: PMC5116266 DOI: 10.1016/j.jhep.2016.07.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Neonatal sclerosing cholangitis (NSC) is a severe neonatal-onset cholangiopathy commonly leading to liver transplantation (LT) for end-stage liver disease in childhood. Liver biopsy findings histopathologically resemble those in biliary atresia (BA); however, in NSC extrahepatic bile ducts are patent, whilst in BA their lumina are obliterated. NSC is commonly seen in consanguineous kindreds, suggesting autosomal recessive inheritance. METHODS From 29 NSC patients (24 families) identified, DNA was available in 24 (21 families). Thirteen (7 male) patients (12 families) of consanguineous parentage were selected for whole exome sequencing. Sequence variants were filtered for homozygosity, pathogenicity, minor allele frequency, quality score, and encoded protein expression pattern. RESULTS Four of 13 patients were homozygous and two were compound heterozygous for mutations in the doublecortin domain containing 2 gene (DCDC2), which encodes DCDC2 protein and is expressed in cholangiocyte cilia. Another 11 patients were sequenced: one (with one sibling pair) was compound heterozygous for DCDC2 mutations. All mutations were protein-truncating. In available liver tissue from patients with DCDC2 mutations, immunostaining for human DCDC2 and the ciliary protein acetylated alpha-tubulin (ACALT) showed no expression (n=6) and transmission electron microscopy found that cholangiocytes lacked primary cilia (n=5). DCDC2 and ACALT were expressed in NSC patients without DCDC2 mutations (n=22). Of the patients carrying DCDC2 mutations, one died awaiting LT; five came to LT, of whom one died 2years later. The other 4 are well. CONCLUSION Among 24 NSC patients with available DNA, 7 had mutations in DCDC2 (6 of 19 families). NSC patients in substantial proportion harbour mutations in DCDC2. Their disease represents a novel liver-based ciliopathy. LAY SUMMARY Neonatal sclerosing cholangitis (NSC) is a rare genetic form of liver disease presenting in infancy. Through next generation sequencing we identified mutations in the gene encoding for doublecortin domain containing 2 (DCDC2) protein in a group of NSC children. DCDC2 is a signalling and structural protein found in primary cilia of cholangiocytes. Cholangiocytes are the cells forming the biliary system which is the draining system of the liver.
Collapse
Affiliation(s)
- Tassos Grammatikopoulos
- Paediatric Liver, GI & Nutrition Centre, King's College Hospital, London, UK; Institute of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, King's College London, London, UK.
| | - Melissa Sambrotta
- Institute of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, King's College London, London, UK
| | | | - Pierre Foskett
- Institute of Liver Studies, King's College Hospital, London, UK
| | - A S Knisely
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Bart Wagner
- Histopathology Department, Royal Hallamshire Hospital, Sheffield, UK
| | | | - Chris Starling
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Giorgina Mieli-Vergani
- Paediatric Liver, GI & Nutrition Centre, King's College Hospital, London, UK; Institute of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, King's College London, London, UK
| | - Joshua Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Laura Bull
- Liver Center Laboratory, Department of Medicine and Institute for Human Genetics, University of California San Francisco, CA, USA
| | - Richard J Thompson
- Paediatric Liver, GI & Nutrition Centre, King's College Hospital, London, UK; Institute of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, King's College London, London, UK
| |
Collapse
|
45
|
Kang HG, Lee HK, Ahn YH, Joung JG, Nam J, Kim NKD, Ko JM, Cho MH, Shin JI, Kim J, Park HW, Park YS, Ha IS, Chung WY, Lee DY, Kim SY, Park WY, Cheong HI. Targeted exome sequencing resolves allelic and the genetic heterogeneity in the genetic diagnosis of nephronophthisis-related ciliopathy. Exp Mol Med 2016; 48:e251. [PMID: 27491411 PMCID: PMC5007639 DOI: 10.1038/emm.2016.63] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 02/29/2016] [Accepted: 03/11/2016] [Indexed: 01/02/2023] Open
Abstract
Nephronophthisis-related ciliopathy (NPHP-RC) is a common genetic cause of end-stage renal failure during childhood and adolescence and exhibits an autosomal recessive pattern of inheritance. Genetic diagnosis is quite limited owing to genetic heterogeneity in NPHP-RC. We designed a novel approach involving the step-wise screening of Sanger sequencing and targeted exome sequencing for the genetic diagnosis of 55 patients with NPHP-RC. First, five NPHP-RC genes were analyzed by Sanger sequencing in phenotypically classified patients. Known pathogenic mutations were identified in 12 patients (21.8%); homozygous deletions of NPHP1 in 4 juvenile nephronophthisis patients, IQCB1/NPHP5 mutations in 3 Senior–Løken syndrome patients, a CEP290/NPHP6 mutation in 1 Joubert syndrome patient, and TMEM67/MKS3 mutations in 4 Joubert syndrome patients with liver involvement. In the remaining undiagnosed patients, we applied targeted exome sequencing of 34 ciliopathy-related genes to detect known pathogenic mutations in 7 (16.3%) of 43 patients. Another 18 likely damaging heterozygous variants were identified in 13 NPHP-RC genes in 18 patients. In this study, we report a variety of pathogenic and candidate mutations identified in 55 patients with NPHP-RC in Korea using a step-wise application of two genetic tests. These results support the clinical utility of targeted exome sequencing to resolve the issue of allelic and genetic heterogeneity in NPHP-RC.
Collapse
Affiliation(s)
- Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Hyun Kyung Lee
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Yo Han Ahn
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jaeyong Nam
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Min Hyun Cho
- Department of Pediatrics, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hye Won Park
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Young Seo Park
- Department of Pediatrics, Asian Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Il-Soo Ha
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Woo Yeong Chung
- Department of Pediatrics, College of Medicine, Inje University, Busan Paik Hospital, Busan, Republic of Korea
| | - Dae-Yeol Lee
- Department of Pediatrics, College of Medicine, Chonbuk National University, Jeonju, Republic of Korea
| | - Su Young Kim
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan, Republic of Korea
| | - Woong Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| |
Collapse
|
46
|
Lindstrand A, Frangakis S, Carvalho C, Richardson E, McFadden K, Willer J, Pehlivan D, Liu P, Pediaditakis I, Sabo A, Lewis R, Banin E, Lupski J, Davis E, Katsanis N. Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome. Am J Hum Genet 2016; 99:318-36. [PMID: 27486776 DOI: 10.1016/j.ajhg.2015.04.023] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/13/2016] [Indexed: 12/15/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a defining ciliopathy, notable for extensive allelic and genetic heterogeneity, almost all of which has been identified through sequencing. Recent data have suggested that copy-number variants (CNVs) also contribute to BBS. We used a custom oligonucleotide array comparative genomic hybridization (aCGH) covering 20 genes that encode intraflagellar transport (IFT) components and 74 ciliopathy loci to screen 92 unrelated individuals with BBS, irrespective of their known mutational burden. We identified 17 individuals with exon-disruptive CNVs (18.5%), including 13 different deletions in eight BBS genes (BBS1, BBS2, ARL6/BBS3, BBS4, BBS5, BBS7, BBS9, and NPHP1) and a deletion and a duplication in other ciliopathy-associated genes (ALMS1 and NPHP4, respectively). By contrast, we found a single heterozygous exon-disruptive event in a BBS-associated gene (BBS9) in 229 control subjects. Superimposing these data with resequencing revealed CNVs to (1) be sufficient to cause disease, (2) Mendelize heterozygous deleterious alleles, and (3) contribute oligogenic alleles by combining point mutations and exonic CNVs in multiple genes. Finally, we report a deletion and a splice site mutation in IFT74, inherited under a recessive paradigm, defining a candidate BBS locus. Our data suggest that CNVs contribute pathogenic alleles to a substantial fraction of BBS-affected individuals and highlight how either deletions or point mutations in discrete splice isoforms can induce hypomorphic mutations in genes otherwise intolerant to deleterious variation. Our data also suggest that CNV analyses and resequencing studies unbiased for previous mutational burden is necessary to delineate the complexity of disease architecture.
Collapse
|
47
|
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: 51] [Impact Index Per Article: 6.4] [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.
Collapse
|
48
|
Ronquillo CC, Hanke-Gogokhia C, Revelo MP, Frederick JM, Jiang L, Baehr W. Ciliopathy-associated IQCB1/NPHP5 protein is required for mouse photoreceptor outer segment formation. FASEB J 2016; 30:3400-3412. [PMID: 27328943 DOI: 10.1096/fj.201600511r] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022]
Abstract
Null mutations in the human IQCB1/NPHP5 (nephrocystin-5) gene that encodes NPHP5 are the most frequent cause of Senior-Løken syndrome, a ciliopathy that is characterized by Leber congenital amaurosis and nephronophthisis. We generated germline Nphp5-knockout mice by placing a β-Geo gene trap in intron 4, thereby truncating NPHP5 at Leu87 and removing all known functional domains. At eye opening, Nphp5-/- mice exhibited absence of scotopic and photopic electroretinogram responses, a phenotype that resembles Leber congenital amaurosis. Outer segment transmembrane protein accumulation in Nphp5-/- endoplasmic reticulum was evident as early as postnatal day (P)6. EGFP-CETN2, a centrosome and transition zone marker, identified basal bodies in Nphp5-/- photoreceptors, but without fully developed transition zones. Ultrastructure of P6 and 10 Nphp5-/- photoreceptors revealed aberrant transition zones of reduced diameter. Nphp5-/- photoreceptor degeneration was complete at 1 mo of age but was delayed significantly in Nphp5-/-;Nrl-/- (cone only) retina. Nphp5-/- mouse embryonic fibroblast developed normal cilia, and Nphp5-/- kidney histology at 1 yr of age showed no significant pathology. Results establish that nephrocystin-5 is essential for photoreceptor outer segment formation but is dispensable for kidney and mouse embryonic fibroblast ciliary formation.-Ronquillo, C. C., Hanke-Gogokhia, C., Revelo, M. P., Frederick, J. M., Jiang, L., Baehr, W. Ciliopathy-associated IQCB1/NPHP5 protein is required for mouse photoreceptor outer segment formation.
Collapse
Affiliation(s)
- Cecinio C Ronquillo
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah, USA
| | - Christin Hanke-Gogokhia
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah, USA; Department of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Monica P Revelo
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Jeanne M Frederick
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah, USA
| | - Li Jiang
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah, USA;
| | - Wolfgang Baehr
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah, USA; Department of Neurobiology and Anatomy, University of Utah Health Science Center, Salt Lake City, Utah, USA; and Department of Biology, University of Utah, Salt Lake City, Utah, USA
| |
Collapse
|
49
|
Triggs-Raine B, Dyck T, Boycott KM, Innes AM, Ober C, Parboosingh JS, Botkin A, Greenberg CR, Spriggs EL. Development of a diagnostic DNA chip to screen for 30 autosomal recessive disorders in the Hutterite population. Mol Genet Genomic Med 2016; 4:312-21. [PMID: 27247959 PMCID: PMC4867565 DOI: 10.1002/mgg3.206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/16/2015] [Accepted: 12/18/2015] [Indexed: 12/03/2022] Open
Abstract
Background The Hutterites are a religious isolate living in colonies across the North American prairies. This population originated from approximately 90 founders, resulting in a number of genetic diseases that are overrepresented, underrepresented, or unique. The founder effect in this population increases the likelihood that Hutterite couples carry the same recessive mutations. We have designed a diagnostic chip on a fee‐for‐service basis with Asper Biotech to provide Hutterites with the option of comprehensive carrier screening. Methods A total of 32 disease‐causing mutations in 30 genes were selected and primers were designed for array primer extension‐based testing. Selected mutations were limited to those leading to autosomal recessive disorders, maintaining its primary use as a test for determining carrier status. Results The DNA chip was developed and validated using 59 DNA controls for all but one of the mutations, for which a synthetic control was used. All mutations were readily detected except for a duplication causing restrictive dermopathy where heterozygotes and homozygotes could only be distinguished by sequencing. Blinded testing of 12 additional samples from healthy Hutterites was performed by Asper Biotech using chip testing. All known mutations from previous molecular testing were detected on the chip. As well, additional mutations identified by the chip in these 12 samples were subsequently verified by a second method. Conclusions Our analysis indicates that the chip is a sensitive and specific means of carrier testing in the Hutterite population and can serve as a model for other founder populations.
Collapse
Affiliation(s)
- Barbara Triggs-Raine
- Departments of Biochemistry & Medical GeneticsUniversity of ManitobaWinnipegCanada; Pediatrics & Child HealthUniversity of Manitoba745 Bannatyne Ave.WinnipegMB R3E 0J9Canada; The Manitoba Institute of Child Health513-715 McDermot Ave.WinnipegMB R3E 3P4Canada
| | - Tamara Dyck
- Clinical Biochemistry and Genetics Diagnostic Services Manitoba at Health Sciences Centre Winnipeg MB R3A 1R9 Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa ON K1H 8L1 Canada
| | - A Micheil Innes
- Department of Medical Genetics Alberta Children's Hospital and Alberta Children's Hospital Research Institute for Child and Maternal Health Cumming School of Medicine University of Calgary Calgary Alberta Canada
| | - Carole Ober
- Departments of Human Genetics and Obstetrics and Gynecology The University of Chicago Chicago Illinois
| | - Jillian S Parboosingh
- Department of Medical Genetics Alberta Children's Hospital and Alberta Children's Hospital Research Institute for Child and Maternal Health Cumming School of Medicine University of Calgary Calgary Alberta Canada
| | - Alexis Botkin
- Pediatrics & Child Health University of Manitoba 745 Bannatyne Ave. Winnipeg MB R3E 0J9 Canada
| | - Cheryl R Greenberg
- Departments of Biochemistry & Medical GeneticsUniversity of ManitobaWinnipegCanada; Pediatrics & Child HealthUniversity of Manitoba745 Bannatyne Ave.WinnipegMB R3E 0J9Canada; The Manitoba Institute of Child Health513-715 McDermot Ave.WinnipegMB R3E 3P4Canada
| | - Elizabeth L Spriggs
- Departments of Biochemistry & Medical GeneticsUniversity of ManitobaWinnipegCanada; Pediatrics & Child HealthUniversity of Manitoba745 Bannatyne Ave.WinnipegMB R3E 0J9Canada; Clinical Biochemistry and GeneticsDiagnostic Services Manitoba at Health Sciences CentreWinnipegMB R3A 1R9Canada
| |
Collapse
|
50
|
Chan SC, Rayat J, Sauvé Y, MacDonald IM. Brothers with ocular motor apraxia, juvenile nephronophthisis, and mild cerebellar defects. Can J Ophthalmol 2016; 51:e85-8. [DOI: 10.1016/j.jcjo.2016.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 01/20/2016] [Accepted: 01/24/2016] [Indexed: 11/30/2022]
|