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Sendino Garví E, van Slobbe GJJ, Zaal EA, de Baaij JHF, Hoenderop JG, Masereeuw R, Janssen MJ, van Genderen AM. KCNJ16-depleted kidney organoids recapitulate tubulopathy and lipid recovery upon statins treatment. Stem Cell Res Ther 2024; 15:268. [PMID: 39183338 PMCID: PMC11346019 DOI: 10.1186/s13287-024-03881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/11/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND The KCNJ16 gene has been associated with a novel kidney tubulopathy phenotype, viz. disturbed acid-base homeostasis, hypokalemia and altered renal salt transport. KCNJ16 encodes for Kir5.1, which together with Kir4.1 constitutes a potassium channel located at kidney tubular cell basolateral membranes. Preclinical studies provided mechanistic links between Kir5.1 and tubulopathy, however, the disease pathology remains poorly understood. Here, we aimed at generating and characterizing a novel advanced in vitro human kidney model that recapitulates the disease phenotype to investigate further the pathophysiological mechanisms underlying the tubulopathy and potential therapeutic interventions. METHODS We used CRISPR/Cas9 to generate KCNJ16 mutant (KCNJ16+/- and KCNJ16-/-) cell lines from healthy human induced pluripotent stem cells (iPSC) KCNJ16 control (KCNJ16WT). The iPSCs were differentiated following an optimized protocol into kidney organoids in an air-liquid interface. RESULTS KCNJ16-depleted kidney organoids showed transcriptomic and potential functional impairment of key voltage-dependent electrolyte and water-balance transporters. We observed cysts formation, lipid droplet accumulation and fibrosis upon Kir5.1 function loss. Furthermore, a large scale, glutamine tracer flux metabolomics analysis demonstrated that KCNJ16-/- organoids display TCA cycle and lipid metabolism impairments. Drug screening revealed that treatment with statins, particularly the combination of simvastatin and C75, prevented lipid droplet accumulation and collagen-I deposition in KCNJ16-/- kidney organoids. CONCLUSIONS Mature kidney organoids represent a relevant in vitro model for investigating the function of Kir5.1. We discovered novel molecular targets for this genetic tubulopathy and identified statins as a potential therapeutic strategy for KCNJ16 defects in the kidney.
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Affiliation(s)
- E Sendino Garví
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - G J J van Slobbe
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - E A Zaal
- Division of Cell Biology, Metabolism and Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - J H F de Baaij
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - J G Hoenderop
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - R Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - M J Janssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands.
| | - A M van Genderen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands.
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2
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Yang G, Mack H, Harraka P, Colville D, Savige J. Ocular manifestations of the genetic renal tubulopathies. Ophthalmic Genet 2023; 44:515-529. [PMID: 37702059 DOI: 10.1080/13816810.2023.2253901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND The genetic tubulopathies are rare and heterogenous disorders that are often difficult to identify. This study examined the tubulopathy-causing genes for ocular associations that suggested their genetic basis and, in some cases, the affected gene. METHODS Sixty-seven genes from the Genomics England renal tubulopathy panel were reviewed for ocular features, and for retinal expression in the Human Protein Atlas and an ocular phenotype in mouse models in the Mouse Genome Informatics database. The genes resulted in disease affecting the proximal tubules (n = 24); the thick ascending limb of the loop of Henle (n = 10); the distal convoluted tubule (n = 15); or the collecting duct (n = 18). RESULTS Twenty-five of the tubulopathy-associated genes (37%) had ocular features reported in human disease, 49 (73%) were expressed in the retina, although often at low levels, and 16 (24%) of the corresponding mouse models had an ocular phenotype. Ocular abnormalities were more common in genes affected in the proximal tubulopathies (17/24, 71%) than elsewhere (7/43, 16%). They included structural features (coloboma, microphthalmia); refractive errors (myopia, astigmatism); crystal deposition (in oxalosis, cystinosis) and sclerochoroidal calcification (in Bartter, Gitelman syndromes). Retinal atrophy was common in the mitochondrial-associated tubulopathies. Structural abnormalities and crystal deposition were present from childhood, but sclerochoroidal calcification typically occurred after middle age. CONCLUSIONS Ocular abnormalities are uncommon in the genetic tubulopathies but may be helpful in recognizing the underlying genetic disease. The retinal expression and mouse phenotype data suggest that further ocular associations may become apparent with additional reports. Early identification may be necessary to monitor and treat visual complications.
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Affiliation(s)
- GeFei Yang
- Department of Medicine (Melbourne Health and Northern Health), The University of Melbourne, Royal Melbourne Hospital, Parkville, Australia
| | - Heather Mack
- Department of Surgery (Ophthalmology), The University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Philip Harraka
- Department of Medicine (Melbourne Health and Northern Health), The University of Melbourne, Royal Melbourne Hospital, Parkville, Australia
| | - Deb Colville
- Department of Surgery (Ophthalmology), The University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Judy Savige
- Department of Medicine (Melbourne Health and Northern Health), The University of Melbourne, Royal Melbourne Hospital, Parkville, Australia
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Sambri I, Ferniani M, Campostrini G, Testa M, Meraviglia V, de Araujo MEG, Dokládal L, Vilardo C, Monfregola J, Zampelli N, Vecchio Blanco FD, Torella A, Ruosi C, Fecarotta S, Parenti G, Staiano L, Bellin M, Huber LA, De Virgilio C, Trepiccione F, Nigro V, Ballabio A. RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome. Nat Commun 2023; 14:2775. [PMID: 37188688 DOI: 10.1038/s41467-023-38428-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Heterozygous mutations in the gene encoding RagD GTPase were shown to cause a novel autosomal dominant condition characterized by kidney tubulopathy and cardiomyopathy. We previously demonstrated that RagD, and its paralogue RagC, mediate a non-canonical mTORC1 signaling pathway that inhibits the activity of TFEB and TFE3, transcription factors of the MiT/TFE family and master regulators of lysosomal biogenesis and autophagy. Here we show that RagD mutations causing kidney tubulopathy and cardiomyopathy are "auto- activating", even in the absence of Folliculin, the GAP responsible for RagC/D activation, and cause constitutive phosphorylation of TFEB and TFE3 by mTORC1, without affecting the phosphorylation of "canonical" mTORC1 substrates, such as S6K. By using HeLa and HK-2 cell lines, human induced pluripotent stem cell-derived cardiomyocytes and patient-derived primary fibroblasts, we show that RRAGD auto-activating mutations lead to inhibition of TFEB and TFE3 nuclear translocation and transcriptional activity, which impairs the response to lysosomal and mitochondrial injury. These data suggest that inhibition of MiT/TFE factors plays a key role in kidney tubulopathy and cardiomyopathy syndrome.
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Affiliation(s)
- Irene Sambri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Marco Ferniani
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | | | - Marialuisa Testa
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | | | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Ladislav Dokládal
- Department of Biology, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Claudia Vilardo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | - Jlenia Monfregola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | - Nicolina Zampelli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Carolina Ruosi
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Simona Fecarotta
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Giancarlo Parenti
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Institute for Genetic and Biomedical Research, National Research Council (CNR), Milan, Italy
| | - Milena Bellin
- Leiden University Medical Center, 2333ZC, Leiden, the Netherlands
- Department of Biology, University of Padua, 35131, Padua, Italy
- Veneto Institute of Molecular Medicine, 35129, Padua, Italy
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Francesco Trepiccione
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
- Biogem Research Institute Ariano Irpino, Ariano Irpino, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy.
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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Sinha R, Pradhan S, Banerjee S, Jahan A, Akhtar S, Pahari A, Raut S, Parakh P, Basu S, Srivastava P, Nayak S, Thenral SG, Ramprasad V, Ashton E, Bockenhauer D, Mandal K. Whole-exome sequencing and variant spectrum in children with suspected inherited renal tubular disorder: the East India Tubulopathy Gene Study. Pediatr Nephrol 2022; 37:1811-1836. [PMID: 35006361 DOI: 10.1007/s00467-021-05388-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Inherited tubulopathies are a heterogeneous group of genetic disorders making whole-exome sequencing (WES) the preferred diagnostic methodology. METHODS This was a multicenter descriptive study wherein children (< 18 years) with clinically suspected tubular disorders were recruited for molecular testing through WES. Multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing were done when required. Variants were classified as per American College of Medical Genetics 2015 guidelines and pathogenic (P)/likely pathogenic (LP) variants were considered causative. RESULTS There were 77 index cases (male =73%). Median age at diagnosis was 48 months (IQR 18.5 to 108 months). At recruitment, the number of children in each clinical group was as follows: distal renal tubular acidosis (dRTA) = 25; Bartter syndrome = 18; isolated hypophosphatemic rickets (HP) = 6; proximal tubular dysfunction (pTD) = 12; nephrogenic diabetes insipidus (NDI) = 6; kidney stone/nephrocalcinosis (NC) = 6; others = 4. We detected 55 (24 novel) P/LP variants, providing genetic diagnoses in 54 children (70%). The diagnostic yield of WES was highest for NDI (100%), followed by HP (83%; all X-linked HP), Bartter syndrome (78%), pTD (75%), dRTA (64%), and NC (33%). Molecular testing had a definite impact on clinical management in 24 (31%) children. This included revising clinical diagnosis among 14 children (26% of those with a confirmed genetic diagnosis and 18% of the overall cohort), detection of previously unrecognized co-morbidities among 8 children (sensorineural deafness n = 5, hemolytic anemia n = 2, and dental changes n = 1) and facilitating specific medical treatment for 7 children (primary hyperoxaluria n = 1, cystinosis n = 4, tyrosinemia n = 2). CONCLUSION WES is a powerful tool in the diagnosis and management of children with inherited tubulopathies in the Indian population. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Rajiv Sinha
- Institute of Child Health, Kolkata, India
- Apollo Hospital, Kolkata, India
| | | | - Sushmita Banerjee
- Institute of Child Health, Kolkata, India
- Calcutta Medical and Research Institute, Kolkata, India
| | - Afsana Jahan
- Renowell Clinic and Pratiksha Hospital, Gauhati, India
| | | | | | | | | | | | - Priyanka Srivastava
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | | | | | - Emma Ashton
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Detlef Bockenhauer
- UCL Department of Renal Medicine and Renal Unit, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India.
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Zhang J, Zhang C, Gao E, Zhou Q. Next-Generation Sequencing-Based Genetic Diagnostic Strategies of Inherited Kidney Diseases. KIDNEY DISEASES (BASEL, SWITZERLAND) 2021; 7:425-437. [PMID: 34901190 DOI: 10.1159/000519095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/10/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND At least 10% of adults and most of the children who receive renal replacement therapy have inherited kidney diseases. These disorders substantially decrease their life quality and have a large effect on the health-care system. Multisystem complications, with typical challenges for rare disorders, including variable phenotypes and fragmented clinical and biological data, make genetic diagnosis of inherited kidney disorders difficult. In current clinical practice, genetic diagnosis is important for clinical management, estimating disease development, and applying personal treatment for patients. SUMMARY Inherited kidney diseases comprise hundreds of different disorders. Here, we have summarized various monogenic kidney disorders. These disorders are caused by mutations in genes coding for a wide range of proteins including receptors, channels/transporters, enzymes, transcription factors, and structural components that might also have a role in extrarenal organs (bone, eyes, brain, skin, ear, etc.). With the development of next-generation sequencing technologies, genetic testing and analysis become more accessible, promoting our understanding of the pathophysiologic mechanisms of inherited kidney diseases. However, challenges exist in interpreting the significance of genetic variants and translating them to guide clinical managements. Alport syndrome is chosen as an example to introduce the practical application of genetic testing and diagnosis on inherited kidney diseases, considering its clinical features, genetic backgrounds, and genetic testing for making a genetic diagnosis. KEY MESSAGES Recent advances in genomics have highlighted the complexity of Mendelian disorders, which is due to allelic heterogeneity (distinct mutations in the same gene produce distinct phenotypes), locus heterogeneity (mutations in distinct genes result in similar phenotypes), reduced penetrance, variable expressivity, modifier genes, and/or environmental factors. Implementation of precision medicine in clinical nephrology can improve the clinical diagnostic rate and treatment efficiency of kidney diseases, which requires a good understanding of genetics for nephrologists.
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Affiliation(s)
- Jiahui Zhang
- Life Sciences Institute, The Key Laboratory of Biosystems Homeostasis & Protection of Ministry of Education, Zhejiang University, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Changming Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.,Zhejiang University School of Medicine, Hangzhou, China
| | - Erzhi Gao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qing Zhou
- Life Sciences Institute, The Key Laboratory of Biosystems Homeostasis & Protection of Ministry of Education, Zhejiang University, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
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Schutgens F, Rookmaaker M, Verhaar M. A Perspective on a Urine-Derived Kidney Tubuloid Biobank from Patients with Hereditary Tubulopathies. Tissue Eng Part C Methods 2021; 27:177-182. [PMID: 33544041 DOI: 10.1089/ten.tec.2020.0366] [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: 11/12/2022] Open
Abstract
Inherited kidney tubulopathies comprise a group of rare diseases with a significant societal impact, as lifelong treatment is often required and no therapies are available to prevent progression of renal damage. Diagnosis of inherited tubulopathies has improved with the advances of next generation sequencing. However, difficulties remain, such as a lack of genotype-phenotype correlation and unknown pathogenicity of newly identified variants. In addition, treatment remains mainly symptomatic. Both diagnosis and treatment can be improved by addition of in vitro functional studies to clinical care. Urine-derived kidney organoids ("tubuloids") are a promising platform for these studies. International collections of patient-derived tubuloids in a living biobank offer additional advantages for drug development and pathophysiological studies. In this review, we discuss how diagnosis and treatment of tubulopathies can be improved by in vitro studies using a tubuloid biobank. We also address practical challenges in the development of such biobank. Impact statement This review provides readers insight into aspects related to diagnosis and treatment of hereditary kidney tubulopathies that can be improved. In addition, it explains why in vitro functional analyses using a kidney organoid model (tubuloids) may be useful as a method to improve these aspects. Finally, the additional advantages and practical hurdles of collecting tubuloid lines in a biobank are discussed.
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Affiliation(s)
- Frans Schutgens
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, The Netherlands.,Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maarten Rookmaaker
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Marianne Verhaar
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, The Netherlands
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