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Arai Y, Ito H, Shimizu T, Shimoda Y, Song D, Matsuo-Takasaki M, Hayata T, Hayashi Y. Patient-derived and gene-edited pluripotent stem cells lacking NPHP1 recapitulate juvenile nephronophthisis in abnormalities of primary cilia and renal cyst formation. Front Cell Dev Biol 2024; 12:1370723. [PMID: 38989059 PMCID: PMC11233770 DOI: 10.3389/fcell.2024.1370723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/21/2024] [Indexed: 07/12/2024] Open
Abstract
Juvenile nephronophthisis is an inherited renal ciliopathy with cystic kidney disease, renal fibrosis, and end-stage renal failure in children and young adults. Mutations in the NPHP1 gene encoding nephrocystin-1 protein have been identified as the most frequently responsible gene and cause the formation of cysts in the renal medulla. The molecular pathogenesis of juvenile nephronophthisis remains elusive, and no effective medicines to prevent end-stage renal failure exist even today. No human cellular models have been available yet. Here, we report a first disease model of juvenile nephronophthisis using patient-derived and gene-edited human induced pluripotent stem cells (hiPSCs) and kidney organoids derived from these hiPSCs. We established NPHP1-overexpressing hiPSCs from patient-derived hiPSCs and NPHP1-deficient hiPSCs from healthy donor hiPSCs. Comparing these series of hiPSCs, we found abnormalities in primary cilia associated with NPHP1 deficiency in hiPSCs. Kidney organoids generated from the hiPSCs lacking NPHP1 formed renal cysts frequently in suspension culture with constant rotation. This cyst formation in patient-derived kidney organoids was rescued by overexpression of NPHP1. Transcriptome analysis on these kidney organoids revealed that loss of NPHP1 caused lower expression of genes related to primary cilia in epithelial cells and higher expression of genes related to the cell cycle. These findings suggested the relationship between abnormality in primary cilia induced by NPHP1 loss and abnormal proliferative characteristics in the formation of renal cysts. These findings demonstrated that hiPSC-based systematic disease modeling of juvenile nephronophthisis contributed to elucidating the molecular pathogenesis and developing new therapies.
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Affiliation(s)
- Yutaka Arai
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Hidenori Ito
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Tomoya Shimizu
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yuzuno Shimoda
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Dan Song
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Mami Matsuo-Takasaki
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Tadayoshi Hayata
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yohei Hayashi
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, Japan
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2
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Faviez C, Chen X, Garcelon N, Zaidan M, Billot K, Petzold F, Faour H, Douillet M, Rozet JM, Cormier-Daire V, Attié-Bitach T, Lyonnet S, Saunier S, Burgun A. Objectivizing issues in the diagnosis of complex rare diseases: lessons learned from testing existing diagnosis support systems on ciliopathies. BMC Med Inform Decis Mak 2024; 24:134. [PMID: 38789985 PMCID: PMC11127295 DOI: 10.1186/s12911-024-02538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND There are approximately 8,000 different rare diseases that affect roughly 400 million people worldwide. Many of them suffer from delayed diagnosis. Ciliopathies are rare monogenic disorders characterized by a significant phenotypic and genetic heterogeneity that raises an important challenge for clinical diagnosis. Diagnosis support systems (DSS) applied to electronic health record (EHR) data may help identify undiagnosed patients, which is of paramount importance to improve patients' care. Our objective was to evaluate three online-accessible rare disease DSSs using phenotypes derived from EHRs for the diagnosis of ciliopathies. METHODS Two datasets of ciliopathy cases, either proven or suspected, and two datasets of controls were used to evaluate the DSSs. Patient phenotypes were automatically extracted from their EHRs and converted to Human Phenotype Ontology terms. We tested the ability of the DSSs to diagnose cases in contrast to controls based on Orphanet ontology. RESULTS A total of 79 cases and 38 controls were selected. Performances of the DSSs on ciliopathy real world data (best DSS with area under the ROC curve = 0.72) were not as good as published performances on the test set used in the DSS development phase. None of these systems obtained results which could be described as "expert-level". Patients with multisystemic symptoms were generally easier to diagnose than patients with isolated symptoms. Diseases easily confused with ciliopathy generally affected multiple organs and had overlapping phenotypes. Four challenges need to be considered to improve the performances: to make the DSSs interoperable with EHR systems, to validate the performances in real-life settings, to deal with data quality, and to leverage methods and resources for rare and complex diseases. CONCLUSION Our study provides insights into the complexities of diagnosing highly heterogenous rare diseases and offers lessons derived from evaluation existing DSSs in real-world settings. These insights are not only beneficial for ciliopathy diagnosis but also hold relevance for the enhancement of DSS for various complex rare disorders, by guiding the development of more clinically relevant rare disease DSSs, that could support early diagnosis and finally make more patients eligible for treatment.
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Affiliation(s)
- Carole Faviez
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France.
- HeKA, Inria Paris, Paris, F-75012, France.
- Universite Paris Cite, Paris, France.
| | - Xiaoyi Chen
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France
- HeKA, Inria Paris, Paris, F-75012, France
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Nicolas Garcelon
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France
- HeKA, Inria Paris, Paris, F-75012, France
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Mohamad Zaidan
- Service de Néphrologie, Dialyse et Transplantation, Hôpital Universitaire Bicêtre, Assistance Publique-Hôpitaux de Paris (AP-HP), Kremlin Bicêtre, F-94270, France
| | - Katy Billot
- Laboratory of Renal Hereditary Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
| | - Friederike Petzold
- Laboratory of Renal Hereditary Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Hassan Faour
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Maxime Douillet
- Data Science Platform, Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, F-75015, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
| | - Valérie Cormier-Daire
- Reference Centre for Constitutional Bone Diseases, laboratory of Osteochondrodysplasia, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
| | - Tania Attié-Bitach
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
| | - Stanislas Lyonnet
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris Cité, Paris, F-75015, France
| | - Sophie Saunier
- Laboratory of Renal Hereditary Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, F-75015, France
| | - Anita Burgun
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, F-75006, France
- HeKA, Inria Paris, Paris, F-75012, France
- Department of Medical Informatics, Hôpital Necker-Enfants Malades, AP-HP, Paris, F-75015, France
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Faviez C, Vincent M, Garcelon N, Boyer O, Knebelmann B, Heidet L, Saunier S, Chen X, Burgun A. Performance and clinical utility of a new supervised machine-learning pipeline in detecting rare ciliopathy patients based on deep phenotyping from electronic health records and semantic similarity. Orphanet J Rare Dis 2024; 19:55. [PMID: 38336713 PMCID: PMC10858490 DOI: 10.1186/s13023-024-03063-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Rare diseases affect approximately 400 million people worldwide. Many of them suffer from delayed diagnosis. Among them, NPHP1-related renal ciliopathies need to be diagnosed as early as possible as potential treatments have been recently investigated with promising results. Our objective was to develop a supervised machine learning pipeline for the detection of NPHP1 ciliopathy patients from a large number of nephrology patients using electronic health records (EHRs). METHODS AND RESULTS We designed a pipeline combining a phenotyping module re-using unstructured EHR data, a semantic similarity module to address the phenotype dependence, a feature selection step to deal with high dimensionality, an undersampling step to address the class imbalance, and a classification step with multiple train-test split for the small number of rare cases. The pipeline was applied to thirty NPHP1 patients and 7231 controls and achieved good performances (sensitivity 86% with specificity 90%). A qualitative review of the EHRs of 40 misclassified controls showed that 25% had phenotypes belonging to the ciliopathy spectrum, which demonstrates the ability of our system to detect patients with similar conditions. CONCLUSIONS Our pipeline reached very encouraging performance scores for pre-diagnosing ciliopathy patients. The identified patients could then undergo genetic testing. The same data-driven approach can be adapted to other rare diseases facing underdiagnosis challenges.
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Affiliation(s)
- Carole Faviez
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM UMR 1138, 75006, Paris, France.
- Inria, 75012, Paris, France.
| | - Marc Vincent
- Université Paris Cité, Imagine Institute, Data Science Platform, INSERM UMR 1163, 75015, Paris, France
| | - Nicolas Garcelon
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM UMR 1138, 75006, Paris, France
- Inria, 75012, Paris, France
- Université Paris Cité, Imagine Institute, Data Science Platform, INSERM UMR 1163, 75015, Paris, France
| | - Olivia Boyer
- Department of Pediatric Nephrology, APHP-Centre, Reference Center for Inherited Renal Diseases (MARHEA), Imagine Institute, Hôpital Necker-Enfants Malades, Université Paris Cité, 75015, Paris, France
- Laboratory of Renal Hereditary Diseases, INSERM UMR 1163, Imagine Institute, Université Paris Cité, 75015, Paris, France
| | - Bertrand Knebelmann
- Nephrology and Transplantation Department, MARHEA, Hôpital Necker-Enfants Malades, AP-HP, Université Paris Cité, 75015, Paris, France
| | - Laurence Heidet
- Department of Pediatric Nephrology, APHP-Centre, Reference Center for Inherited Renal Diseases (MARHEA), Imagine Institute, Hôpital Necker-Enfants Malades, Université Paris Cité, 75015, Paris, France
| | - Sophie Saunier
- Laboratory of Renal Hereditary Diseases, INSERM UMR 1163, Imagine Institute, Université Paris Cité, 75015, Paris, France
| | - Xiaoyi Chen
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM UMR 1138, 75006, Paris, France
- Inria, 75012, Paris, France
- Université Paris Cité, Imagine Institute, Data Science Platform, INSERM UMR 1163, 75015, Paris, France
| | - Anita Burgun
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM UMR 1138, 75006, Paris, France
- Inria, 75012, Paris, France
- Département d'informatique Médicale, Hôpital Necker-Enfants Malades, AP-HP, 75015, Paris, France
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Baker S, Nguyen TK, Wingert RA. Tails of nephron ciliated cell development: insights on patterning a functional tissue barrier from the zebrafish. Tissue Barriers 2024:2309025. [PMID: 38282263 DOI: 10.1080/21688370.2024.2309025] [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: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024] Open
Abstract
Cilia are hair-like structures found on the surface of nearly all vertebrate cell types where they have central roles in regulating development and orchestrating physiological events. There is growing interest in understanding the mechanisms of ciliogenesis due to the profound consequences that follow from the absence of proper ciliary function, which include diseases that affect the renal, respiratory, reproductive, nervous, visual, and digestive systems, among others. Now, a recent report has discerned new roles for the transcription factor estrogen-related receptor gamma a (esrrγa) in ciliated cell ontogeny within the embryonic zebrafish kidney and other tissues. Further, the team of researchers discovered that genetic ablation of murine homolog ERRγ in adult kidney epithelial cells led to shortened cilia, which precedes cystogenesis. These intriguing findings expand our fundamental understanding of the pathological basis of cilia defects, which is relevant for identifying future therapeutic targets for ciliopathies.
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Affiliation(s)
- Sophia Baker
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
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5
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Wesselman HM, Arceri L, Nguyen TK, Lara CM, Wingert RA. Genetic mechanisms of multiciliated cell development: from fate choice to differentiation in zebrafish and other models. FEBS J 2023. [PMID: 37997009 DOI: 10.1111/febs.17012] [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: 05/13/2023] [Revised: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
Multiciliated cells (MCCS) form bundles of cilia and their activities are essential for the proper development and physiology of many organ systems. Not surprisingly, defects in MCCs have profound consequences and are associated with numerous disease states. Here, we discuss the current understanding of MCC formation, with a special focus on the genetic and molecular mechanisms of MCC fate choice and differentiation. Furthermore, we cast a spotlight on the use of zebrafish to study MCC ontogeny and several recent advances made in understanding MCCs using this vertebrate model to delineate mechanisms of MCC emergence in the developing kidney.
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Affiliation(s)
| | - Liana Arceri
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Caroline M Lara
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, IN, USA
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6
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Garfa Traoré M, Roccio F, Miceli C, Ferri G, Parisot M, Cagnard N, Lhomme M, Dupont N, Benmerah A, Saunier S, Delous M. Fluid shear stress triggers cholesterol biosynthesis and uptake in inner medullary collecting duct cells, independently of nephrocystin-1 and nephrocystin-4. Front Mol Biosci 2023; 10:1254691. [PMID: 37916190 PMCID: PMC10616263 DOI: 10.3389/fmolb.2023.1254691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/15/2023] [Indexed: 11/03/2023] Open
Abstract
Renal epithelial cells are subjected to fluid shear stress of urine flow. Several cellular structures act as mechanosensors-the primary cilium, microvilli and cell adhesion complexes-that directly relay signals to the cytoskeleton to regulate various processes including cell differentiation and renal cell functions. Nephronophthisis (NPH) is an autosomal recessive tubulointerstitial nephropathy leading to end-stage kidney failure before adulthood. NPHP1 and NPHP4 are the major genes which code for proteins that form a complex at the transition zone of the primary cilium, a crucial region required for the maintenance of the ciliary composition integrity. These two proteins also interact with signaling components and proteins associated with the actin cytoskeleton at cell junctions. Due to their specific subcellular localization, we wondered whether NPHP1 and NPHP4 could ensure mechanosensory functions. Using a microfluidic set up, we showed that murine inner medullary collecting ductal cells invalidated for Nphp1 or Nphp4 are more responsive to immediate shear exposure with a fast calcium influx, and upon a prolonged shear condition, an inability to properly regulate cilium length and actin cytoskeleton remodeling. Following a transcriptomic study highlighting shear stress-induced gene expression changes, we showed that prolonged shear triggers both cholesterol biosynthesis pathway and uptake, processes that do not seem to involve neither NPHP1 nor NPHP4. To conclude, our study allowed us to determine a moderate role of NPHP1 and NPHP4 in flow sensation, and to highlight a new signaling pathway induced by shear stress, the cholesterol biosynthesis and uptake pathways, which would allow cells to cope with mechanical stress by strengthening their plasma membrane through the supply of cholesterol.
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Affiliation(s)
- Meriem Garfa Traoré
- Laboratory of Hereditary Kidney Disease, INSERM UMR 1163, Imagine Institute, Université Paris Cité, Paris, France
- Cell Imaging Platform, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Université Paris Cité, Paris, France
| | - Federica Roccio
- Institut Necker Enfants-Malades (INEM), INSERM U1151/CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Caterina Miceli
- Institut Necker Enfants-Malades (INEM), INSERM U1151/CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Giulia Ferri
- Laboratory of Hereditary Kidney Disease, INSERM UMR 1163, Imagine Institute, Université Paris Cité, Paris, France
| | - Mélanie Parisot
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UMS3633, Université Paris Cité, Paris, France
| | - Nicolas Cagnard
- Bioinformatic Platform, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UMS3633, Université Paris Cité, Paris, France
| | - Marie Lhomme
- ICAN Omics, IHU ICAN Foundation for Innovation in Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Nicolas Dupont
- Institut Necker Enfants-Malades (INEM), INSERM U1151/CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Disease, INSERM UMR 1163, Imagine Institute, Université Paris Cité, Paris, France
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Disease, INSERM UMR 1163, Imagine Institute, Université Paris Cité, Paris, France
| | - Marion Delous
- Laboratory of Hereditary Kidney Disease, INSERM UMR 1163, Imagine Institute, Université Paris Cité, Paris, France
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7
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Saito M, Otsu W, Miyadera K, Nishimura Y. Recent advances in the understanding of cilia mechanisms and their applications as therapeutic targets. Front Mol Biosci 2023; 10:1232188. [PMID: 37780208 PMCID: PMC10538646 DOI: 10.3389/fmolb.2023.1232188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
The primary cilium is a single immotile microtubule-based organelle that protrudes into the extracellular space. Malformations and dysfunctions of the cilia have been associated with various forms of syndromic and non-syndromic diseases, termed ciliopathies. The primary cilium is therefore gaining attention due to its potential as a therapeutic target. In this review, we examine ciliary receptors, ciliogenesis, and ciliary trafficking as possible therapeutic targets. We first discuss the mechanisms of selective distribution, signal transduction, and physiological roles of ciliary receptors. Next, pathways that regulate ciliogenesis, specifically the Aurora A kinase, mammalian target of rapamycin, and ubiquitin-proteasome pathways are examined as therapeutic targets to regulate ciliogenesis. Then, in the photoreceptors, the mechanism of ciliary trafficking which takes place at the transition zone involving the ciliary membrane proteins is reviewed. Finally, some of the current therapeutic advancements highlighting the role of large animal models of photoreceptor ciliopathy are discussed.
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Affiliation(s)
- Masaki Saito
- Department of Molecular Physiology and Pathology, School of Pharma-Sciences, Teikyo University, Tokyo, Japan
| | - Wataru Otsu
- Department of Biomedical Research Laboratory, Gifu Pharmaceutical University, Gifu, Japan
| | - Keiko Miyadera
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
- Mie University Research Center for Cilia and Diseases, Tsu, Mie, Japan
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8
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Benmerah A, Briseño-Roa L, Annereau JP, Saunier S. Repurposing small molecules for Nephronophthisis and related renal ciliopathies. Kidney Int 2023:S0085-2538(23)00390-3. [PMID: 37244473 DOI: 10.1016/j.kint.2023.04.027] [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: 12/20/2022] [Revised: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 05/29/2023]
Abstract
Nephronophthisis is an autosomal recessive tubulo-interstitial nephropathy, belonging to the ciliopathy disorders, characterized by fibrosis and/or cysts. It is the most common genetic cause of renal failure in children and young adults. Clinically and genetically heterogeneous, it is caused by variants in ciliary genes resulting in either an isolated kidney disease or syndromic forms in association with other manifestations of ciliopathy disorders. No curative treatment is currently available. Over the past two decades, advances in understanding disease mechanisms have identified several dysregulated signaling pathways, some shared with other cystic kidney diseases. Notably, molecules previously developed to target these pathways have shown promising beneficial effects in orthologous mouse models. In addition to these knowledge-based repurposing approaches, unbiased "in cellulo" phenotypic screens of "repurposing" libraries identified small molecules able to rescue the ciliogenesis defects observed in nephronophthisis conditions. Those compounds appeared to act on relevant pathways and, when tested, showed beneficial nephronophthisis-associated kidney and/or extra-renal defects in mice. In this review, we have summarized those studies which highlight the drug repurposing strategies in the context of a rare disorders such as nephronophthisis-related ciliopathies, with broad genetic heterogeneity and systemic manifestations but with shared disease mechanisms.
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Affiliation(s)
- Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, Université Paris Cité, INSERM UMR 1163, 75015 Paris, France
| | | | | | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, Université Paris Cité, INSERM UMR 1163, 75015 Paris, France.
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9
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Petzold F, Billot K, Chen X, Henry C, Filhol E, Martin Y, Avramescu M, Douillet M, Morinière V, Krug P, Jeanpierre C, Tory K, Boyer O, Burgun A, Servais A, Salomon R, Benmerah A, Heidet L, Garcelon N, Antignac C, Zaidan M, Saunier S. The genetic landscape and clinical spectrum of nephronophthisis and related ciliopathies. Kidney Int 2023:S0085-2538(23)00377-0. [PMID: 37230223 DOI: 10.1016/j.kint.2023.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
Nephronophthisis (NPH) is an autosomal-recessive ciliopathy representing one of the most frequent causes of kidney failure in childhood characterized by a broad clinical and genetic heterogeneity. Applied to one of the worldwide largest cohorts of patients with NPH, genetic analysis encompassing targeted and whole exome sequencing identified disease-causing variants in 600 patients from 496 families with a detection rate of 71%. Of 788 pathogenic variants, 40 known ciliopathy genes were identified. However, the majority of patients (53%) bore biallelic pathogenic variants in NPHP1. NPH-causing gene alterations affected all ciliary modules defined by structural and/or functional subdomains. Seventy six percent of these patients had progressed to kidney failure, of which 18% had an infantile form (under five years) and harbored variants affecting the Inversin compartment or intraflagellar transport complex A. Forty eight percent of patients showed a juvenile (5-15 years) and 34% a late-onset disease (over 15 years), the latter mostly carrying variants belonging to the Transition Zone module. Furthermore, while more than 85% of patients with an infantile form presented with extra-kidney manifestations, it only concerned half of juvenile and late onset cases. Eye involvement represented a predominant feature, followed by cerebellar hypoplasia and other brain abnormalities, liver and skeletal defects. The phenotypic variability were in a large part associated with mutation types, genes and corresponding ciliary modules with hypomorphic variants in ciliary genes playing a role in early steps of ciliogenesis associated with juvenile-to-late onset NPH forms. Thus, our data confirm a considerable proportion of late-onset NPH suggesting an underdiagnosis in adult chronic kidney disease.
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Affiliation(s)
- Friederike Petzold
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Division of Nephrology, Department of Endocrinology, Nephrology, and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Katy Billot
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Xiaoyi Chen
- Université de Paris, Imagine Institute, Data Science Platform, INSERM UMR 1163, Paris, France; Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
| | - Charline Henry
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Emilie Filhol
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Yoann Martin
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Marina Avramescu
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Maxime Douillet
- Université de Paris, Imagine Institute, Data Science Platform, INSERM UMR 1163, Paris, France; Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
| | - Vincent Morinière
- APHP, Génétique moléculaire, Hôpital universitaire Necker-Enfants malades, Paris, France
| | - Pauline Krug
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Kalman Tory
- Ist Department of Pediatrics, Semmelweis University, 1083 Budapest, Hungary
| | - Olivia Boyer
- Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Nephrology and Transplantation Department, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, France
| | - Anita Burgun
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France; Hôpital Necker-Enfants Malades, Department of Medical Informatics, AP-HP, Paris, France; PaRis Artificial Intelligence Research InstitutE (PRAIRIE), France
| | - Aude Servais
- Nephrology and Transplantation Department, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, France
| | - Remi Salomon
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris, Paris, France
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Laurence Heidet
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Nephrology and Transplantation Department, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, France
| | - Nicolas Garcelon
- Université de Paris, Imagine Institute, Data Science Platform, INSERM UMR 1163, Paris, France; Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Mohamad Zaidan
- Assistance Publique des Hôpitaux de Paris (AP-HP), Université Paris-Saclay, Hôpital de Bicêtre, Service de Néphrologie et Transplantation, Le Kremlin-Bicêtre, France; Centre de Compétence Maladies Rares « Syndrome Néphrotique Idiopathique », Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France.
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Devlin L, Dhondurao Sudhindar P, Sayer JA. Renal ciliopathies: promising drug targets and prospects for clinical trials. Expert Opin Ther Targets 2023; 27:325-346. [PMID: 37243567 DOI: 10.1080/14728222.2023.2218616] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Renal ciliopathies represent a collection of genetic disorders characterized by deficiencies in the biogenesis, maintenance, or functioning of the ciliary complex. These disorders, which encompass autosomal dominant polycystic kidney disease (ADPKD), autosomal recessive polycystic kidney disease (ARPKD), and nephronophthisis (NPHP), typically result in cystic kidney disease, renal fibrosis, and a gradual deterioration of kidney function, culminating in kidney failure. AREAS COVERED Here we review the advances in basic science and clinical research into renal ciliopathies which have yielded promising small compounds and drug targets, within both preclinical studies and clinical trials. EXPERT OPINION Tolvaptan is currently the sole approved treatment option available for ADPKD patients, while no approved treatment alternatives exist for ARPKD or NPHP patients. Clinical trials are presently underway to evaluate additional medications in ADPKD and ARPKD patients. Based on preclinical models, other potential therapeutic targets for ADPKD, ARPKD, and NPHP look promising. These include molecules targeting fluid transport, cellular metabolism, ciliary signaling and cell-cycle regulation. There is a real and urgent clinical need for translational research to bring novel treatments to clinical use for all forms of renal ciliopathies to reduce kidney disease progression and prevent kidney failure.
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Affiliation(s)
- Laura Devlin
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Praveen Dhondurao Sudhindar
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
- Renal Services, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne, UK
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Reducing GEF-H1 Expression Inhibits Renal Cyst Formation, Inflammation, and Fibrosis via RhoA Signaling in Nephronophthisis. Int J Mol Sci 2023; 24:ijms24043504. [PMID: 36834937 PMCID: PMC9967383 DOI: 10.3390/ijms24043504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Nephronophthisis (NPHP) is the most prevalent monogenic disease leading to end-stage renal failure in childhood. RhoA activation is involved in NPHP pathogenesis. This study explored the role of the RhoA activator guanine nucleotide exchange factor (GEF)-H1 in NPHP pathogenesis. We analyzed the expression and distribution of GEF-H1 in NPHP1 knockout (NPHP1KO) mice using Western blotting and immunofluorescence, followed by GEF-H1 knockdown. Immunofluorescence and renal histology were used to examine the cysts, inflammation, and fibrosis. A RhoA GTPase activation assay and Western blotting were used to detect the expression of downstream GTP-RhoA and p-MLC2, respectively. In NPHP1 knockdown (NPHP1KD) human kidney proximal tubular cells (HK2 cells), we detected the expressions of E-cadherin and α-smooth muscle actin (α-SMA). In vivo, increased expression and redistribution of GEF-H1, and higher levels of GTP-RhoA and p-MLC2 in renal tissue of NPHP1KO mice were observed, together with renal cysts, fibrosis, and inflammation. These changes were alleviated by GEF-H1 knockdown. In vitro, the expression of GEF-H1 and activation of RhoA were also increased, with increased expression of α-SMA and decreased E-cadherin. GEF-H1 knockdown reversed these changes in NPHP1KD HK2 cells. Thus, the GEF-H1/RhoA/MLC2 axis is activated in NPHP1 defects and may play a pivotal role in NPHP pathogenesis.
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Advances in Understanding the Genetic Mechanisms of Zebrafish Renal Multiciliated Cell Development. J Dev Biol 2022; 11:jdb11010001. [PMID: 36648903 PMCID: PMC9844391 DOI: 10.3390/jdb11010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Cilia are microtubule-based organelles that project from the cell surface. In humans and other vertebrates, possession of a single cilium structure enables an assortment of cellular processes ranging from mechanosensation to fluid propulsion and locomotion. Interestingly, cells can possess a single cilium or many more, where so-called multiciliated cells (MCCs) possess apical membrane complexes with several dozen or even hundreds of motile cilia that beat in a coordinated fashion. Development of MCCs is, therefore, integral to control fluid flow and/or cellular movement in various physiological processes. As such, MCC dysfunction is associated with numerous pathological states. Understanding MCC ontogeny can be used to address congenital birth defects as well as acquired disease conditions. Today, researchers used both in vitro and in vivo experimental models to address our knowledge gaps about MCC specification and differentiation. In this review, we summarize recent discoveries from our lab and others that have illuminated new insights regarding the genetic pathways that direct MCC ontogeny in the embryonic kidney using the power of the zebrafish animal model.
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