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Yeung KC, Fryml E, Lanktree MB. How Does ADPKD Severity Differ Between Family Members? Kidney Int Rep 2024; 9:1198-1209. [PMID: 38707833 PMCID: PMC11068977 DOI: 10.1016/j.ekir.2024.01.053] [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: 09/26/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/07/2024] Open
Abstract
Thousands of pathogenic variants in more than 100 genes can cause kidney cysts with substantial variability in phenotype and risk of subsequent kidney failure. Despite an established genotype-phenotype correlation in cystic kidney diseases, incomplete penetrance and variable disease expressivity are present as is the case in all monogenic diseases. In family members with autosomal dominant polycystic kidney disease (ADPKD), the same causal variant is responsible in all affected family members; however, there can still be striking discordance in phenotype severity. This narrative review explores contributors to within-family discordance in ADPKD severity. Cases of biallelic and digenic inheritance, where 2 rare pathogenic variants in cystogenic genes are coexistent in one family, account for a small proportion of within-family discordance. Genetic background, including cis and trans factors and the polygenic propensity for comorbid disease, also plays a role but has not yet been exhaustively quantified. Environmental exposures, including diet; smoking; alcohol, salt, and protein intake, and comorbid diseases, including obesity, diabetes, hypertension, kidney stones, dyslipidemia, and additional coexistent kidney diseases all contribute to ADPKD phenotypic variability among family members. Given that many of the factors contributing to phenotype variability are preventable, modifiable, or treatable, health care providers and patients need to be aware of these factors and address them in the treatment of ADPKD.
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Affiliation(s)
- Klement C. Yeung
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Elise Fryml
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew B. Lanktree
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Division of Nephrology, St. Joseph’s Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Health Research Methodology, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
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2
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Long HY, Qian ZP, Lan Q, Xu YJ, Da JJ, Yu FX, Zha Y. Human pluripotent stem cell-derived kidney organoids: Current progress and challenges. World J Stem Cells 2024; 16:114-125. [PMID: 38455108 PMCID: PMC10915962 DOI: 10.4252/wjsc.v16.i2.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 02/26/2024] Open
Abstract
Human pluripotent stem cell (hPSC)-derived kidney organoids share similarities with the fetal kidney. However, the current hPSC-derived kidney organoids have some limitations, including the inability to perform nephrogenesis and lack of a corticomedullary definition, uniform vascular system, and coordinated exit pathway for urinary filtrate. Therefore, further studies are required to produce hPSC-derived kidney organoids that accurately mimic human kidneys to facilitate research on kidney development, regeneration, disease modeling, and drug screening. In this review, we discussed recent advances in the generation of hPSC-derived kidney organoids, how these organoids contribute to the understanding of human kidney development and research in disease modeling. Additionally, the limitations, future research focus, and applications of hPSC-derived kidney organoids were highlighted.
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Affiliation(s)
- Hong-Yan Long
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Zu-Ping Qian
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Qin Lan
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Yong-Jie Xu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Jing-Jing Da
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Fu-Xun Yu
- Key Laboratory of Diagnosis and Treatment of Pulmonary Immune Diseases, National Health Commission, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Yan Zha
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China.
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3
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Orr S, Olinger E, Iosifidou S, Barroso-Gil M, Neatu R, Wood K, Wilson I, Sayer JA. Molecular genetic diagnosis of kidney ciliopathies: Lessons from interpreting genomic sequencing data and the requirement for accurate phenotypic data. Ann Hum Genet 2024; 88:76-85. [PMID: 37042117 DOI: 10.1111/ahg.12508] [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: 01/30/2023] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023]
Abstract
INTRODUCTION Massively parallel sequencing (MPS) techniques have made a major impact on the identification of the genetic basis of inherited kidney diseases such as the ciliopathy autosomal dominant polycystic kidney disease (ADPKD). Great care must be taken when analysing MPS data in isolation from accurate phenotypic information, as this can cause misdiagnosis. METHODS Here, we describe a family trio, recruited to the Genomics England 100,000 Genomes Project, labelled as having cystic kidney disease, who were genetically unsolved following routine data analysis pipelines. We performed a bespoke reanalysis of Whole Genome Sequencing (WGS) data and coupled this with revised phenotypic data and targeted PCR and Sanger sequencing to provide a precise molecular genetic diagnosis. RESULTS We detected a heterozygous PKD1 frameshift variant within the WGS data which segregated with the redefined ADPKD phenotypes. An additional heterozygous exon deletion in ALG8 was also found in affected and unaffected individuals, but its precise clinical significance remains unclear. CONCLUSION This case illustrates that reanalysis of WGS data in unsolved cases of cystic kidney disease is valuable. Clinical phenotypes must be reassessed as these may have been incorrectly recorded and evolve over time. Undertaking additional studies including genotype-phenotype correlation in wider family members provides useful diagnostic information.
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Affiliation(s)
- Sarah Orr
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sotia Iosifidou
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ruxandra Neatu
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katrina Wood
- Histopathology Department, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ian Wilson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John Andrew Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Renal Services Centre, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
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4
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Lanktree MB, Kline T, Pei Y. Assessing the Risk of Progression to Kidney Failure in Patients With Autosomal Dominant Polycystic Kidney Disease. ADVANCES IN KIDNEY DISEASE AND HEALTH 2023; 30:407-416. [PMID: 38097331 DOI: 10.1053/j.akdh.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 12/18/2023]
Abstract
While autosomal dominant polycystic kidney disease (ADPKD) is a dichotomous diagnosis, substantial variability in disease severity exists. Identification of inherited risk through family history, genetic testing, and environmental risk factors through clinical assessment are important components of risk assessment for optimal management of patients with ADPKD. Genetic testing is especially helpful in cases with diagnostic uncertainty, particularly in cases with no apparent family history, in young cases (age less than 25 years) where a definitive diagnosis is sought, or in atypical presentations with early, severe, or discordant findings. Currently, risk assessment in ADPKD may be performed with the use of age-adjusted estimated glomerular filtration rate thresholds, evidence of rapid estimated glomerular filtration rate decline on serial measurements, age- and height-adjusted total kidney volume by Mayo Clinic Imaging Classification, or evidence of early hypertension and urological complications combined with PKD1 or PKD2 mutation class; however, caveats exist with each of these approaches. Fine-tuning of risk stratification with advanced imaging features and biomarkers is the subject of research but is not yet ready for general clinical practice. While conservative treatment strategies will be advised for all patients, those with the greatest rate of disease progression will have the most benefit from aggressive disease-modifying therapy. In this narrative review, we will summarize the evidence behind the clinical assessment and risk stratification of patients with ADPKD.
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Affiliation(s)
- Matthew B Lanktree
- Division of Nephrology, Department of Medicine, St Joseph's Healthcare Hamilton, McMaster University, Hamilton, Ontario, Canada; Population Health Research Institute, Hamilton, Ontario, Canada
| | - Timothy Kline
- Mayo Clinic, Department of Radiology and Division of Nephrology and Hypertension, Rochester, MN
| | - York Pei
- Division of Nephrology, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada.
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5
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Qiu J, Germino GG, Menezes LF. Mechanisms of Cyst Development in Polycystic Kidney Disease. ADVANCES IN KIDNEY DISEASE AND HEALTH 2023; 30:209-219. [PMID: 37088523 PMCID: PMC10289784 DOI: 10.1053/j.akdh.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Autosomal dominant polycystic kidney disease is the most common inherited cause of end-stage kidney disease worldwide. Most cases result from mutation of either of 2 genes, PKD1 and PKD2, which encode proteins that form a probable receptor/channel complex. Studies suggest that a loss of function of the complex below an indeterminate threshold triggers cyst initiation, which ultimately results in dysregulation of multiple metabolic processes and downstream pathways and subsequent cyst growth. Noncell autonomous factors may also promote cyst growth. In this report, we focus primarily on the process of early cyst formation and factors that contribute to its variability with brief consideration of how new studies suggest this process may be reversible.
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Affiliation(s)
- Jiahe Qiu
- Polycystic Kidney Disease Section, Kidney Disease Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | - Gregory G Germino
- Polycystic Kidney Disease Section, Kidney Disease Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD.
| | - Luis F Menezes
- Polycystic Kidney Disease Section, Kidney Disease Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD.
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6
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Sanz AB, Sanchez-Niño MD, Ramos AM, Ortiz A. Regulated cell death pathways in kidney disease. Nat Rev Nephrol 2023; 19:281-299. [PMID: 36959481 PMCID: PMC10035496 DOI: 10.1038/s41581-023-00694-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 03/25/2023]
Abstract
Disorders of cell number that result from an imbalance between the death of parenchymal cells and the proliferation or recruitment of maladaptive cells contributes to the pathogenesis of kidney disease. Acute kidney injury can result from an acute loss of kidney epithelial cells. In chronic kidney disease, loss of kidney epithelial cells leads to glomerulosclerosis and tubular atrophy, whereas interstitial inflammation and fibrosis result from an excess of leukocytes and myofibroblasts. Other conditions, such as acquired cystic disease and kidney cancer, are characterized by excess numbers of cyst wall and malignant cells, respectively. Cell death modalities act to clear unwanted cells, but disproportionate responses can contribute to the detrimental loss of kidney cells. Indeed, pathways of regulated cell death - including apoptosis and necrosis - have emerged as central events in the pathogenesis of various kidney diseases that may be amenable to therapeutic intervention. Modes of regulated necrosis, such as ferroptosis, necroptosis and pyroptosis may cause kidney injury directly or through the recruitment of immune cells and stimulation of inflammatory responses. Importantly, multiple layers of interconnections exist between different modalities of regulated cell death, including shared triggers, molecular components and protective mechanisms.
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Affiliation(s)
- Ana B Sanz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
| | - Maria Dolores Sanchez-Niño
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Adrian M Ramos
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain.
- RICORS2040, Madrid, Spain.
- Departamento de Farmacología, Universidad Autonoma de Madrid, Madrid, Spain.
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7
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Zhang Z, Blumenfeld J, Ramnauth A, Barash I, Zhou P, Levine D, Parker T, Rennert H. A common intronic single nucleotide variant modifies PKD1 expression level. Clin Genet 2022; 102:483-493. [PMID: 36029107 PMCID: PMC10947153 DOI: 10.1111/cge.14214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/26/2022]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), caused by mutations in PKD1 and PKD2 (PKD1/2), has unexplained phenotypic variability likely affected by environmental and other genetic factors. Approximately 10% of individuals with ADPKD phenotype have no causal mutation detected, possibly due to unrecognized risk variants of PKD1/2. This study was designed to identify risk variants of PKD genes through population genetic analyses. We used Wright's F-statistics (Fst) to evaluate common single nucleotide variants (SNVs) potentially favored by positive natural selection in PKD1 from 1000 Genomes Project (1KG) and genotyped 388 subjects from the Rogosin Institute ADPKD Data Repository. The variants with >90th percentile Fst scores underwent further investigation by in silico analysis and molecular genetics analyses. We identified a deep intronic SNV, rs3874648G> A, located in a conserved binding site of the splicing regulator Tra2-β in PKD1 intron 30. Reverse-transcription PCR (RT-PCR) of peripheral blood leukocytes (PBL) from an ADPKD patient homozygous for rs3874648-A identified an atypical PKD1 splice form. Functional analyses demonstrated that rs3874648-A allele increased Tra2-β binding affinity and activated a cryptic acceptor splice-site, causing a frameshift that introduced a premature stop codon in mRNA, thereby decreasing PKD1 full-length transcript level. PKD1 transcript levels were lower in PBL from rs3874648-G/A carriers than in rs3874648-G/G homozygotes in a small cohort of normal individuals and patients with PKD2 inactivating mutations. Our findings indicate that rs3874648G > A is a PKD1 expression modifier attenuating PKD1 expression through Tra2-β, while the derived G allele advantageously maintains PKD1 expression and is predominant in all subpopulations.
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Affiliation(s)
- Zhengmao Zhang
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Jon Blumenfeld
- Department of Medicine, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Andrew Ramnauth
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Irina Barash
- Department of Medicine, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Pengbo Zhou
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Daniel Levine
- Department of Biochemistry, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Thomas Parker
- Department of Biochemistry, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Hanna Rennert
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
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8
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Lemoine H, Raud L, Foulquier F, Sayer JA, Lambert B, Olinger E, Lefèvre S, Knebelmann B, Harris PC, Trouvé P, Desprès A, Duneau G, Matignon M, Poyet A, Jourde-Chiche N, Guerrot D, Lemoine S, Seret G, Barroso-Gil M, Bingham C, Gilbert R, Le Meur Y, Audrézet MP, Cornec-Le Gall E. Monoallelic pathogenic ALG5 variants cause atypical polycystic kidney disease and interstitial fibrosis. Am J Hum Genet 2022; 109:1484-1499. [PMID: 35896117 PMCID: PMC9388391 DOI: 10.1016/j.ajhg.2022.06.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
Disorders of the autosomal dominant polycystic kidney disease (ADPKD) spectrum are characterized by the development of kidney cysts and progressive kidney function decline. PKD1 and PKD2, encoding polycystin (PC)1 and 2, are the two major genes associated with ADPKD; other genes include IFT140, GANAB, DNAJB11, and ALG9. Genetic testing remains inconclusive in ∼7% of the families. We performed whole-exome sequencing in a large multiplex genetically unresolved (GUR) family affected by ADPKD-like symptoms and identified a monoallelic frameshift variant (c.703_704delCA) in ALG5. ALG5 encodes an endoplasmic-reticulum-resident enzyme required for addition of glucose molecules to the assembling N-glycan precursors. To identify additional families, we screened a cohort of 1,213 families with ADPKD-like and/or autosomal-dominant tubulointerstitial kidney diseases (ADTKD), GUR (n = 137) or naive to genetic testing (n = 1,076), by targeted massively parallel sequencing, and we accessed Genomics England 100,000 Genomes Project data. Four additional families with pathogenic variants in ALG5 were identified. Clinical presentation was consistent in the 23 affected members, with non-enlarged cystic kidneys and few or no liver cysts; 8 subjects reached end-stage kidney disease from 62 to 91 years of age. We demonstrate that ALG5 haploinsufficiency is sufficient to alter the synthesis of the N-glycan chain in renal epithelial cells. We also show that ALG5 is required for PC1 maturation and membrane and ciliary localization and that heterozygous loss of ALG5 affects PC1 maturation. Overall, our results indicate that monoallelic variants of ALG5 lead to a disorder of the ADPKD-spectrum characterized by multiple small kidney cysts, progressive interstitial fibrosis, and kidney function decline.
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Affiliation(s)
- Hugo Lemoine
- Univ. Brest, Inserm, UMR 1078, GGB, 29200 Brest, France
| | - Loann Raud
- Univ. Brest, Inserm, UMR 1078, GGB, 29200 Brest, France
| | - François Foulquier
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE1 3BZ, UK; The Newcastle upon Tyne Hospitals NHS Foundation Trust, Renal Services, Freeman Road, Newcastle Upon Tyne NE7 7DN, UK; NIHR Newcastle Biomedical Research Centre, Newcastle University, Newcastle Upon Tyne NE4 5PL, UK
| | - Baptiste Lambert
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Eric Olinger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE1 3BZ, UK
| | - Siriane Lefèvre
- Univ. Brest, Inserm, UMR 1078, GGB, 29200 Brest, France; Service de Néphrologie, Hôpital de Lorient, 56322 Lorient, France
| | - Bertrand Knebelmann
- Service de Néphrologie et Transplantation rénale, Hôpital Necker, APHP, Université de Paris, Paris, France
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Pascal Trouvé
- Univ. Brest, Inserm, UMR 1078, GGB, 29200 Brest, France
| | - Aurore Desprès
- Service de Génétique moléculaire, CHRU Brest, 29609 Brest, France
| | | | - Marie Matignon
- University Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Henri Mondor, Service de Néphrologie et Transplantation, Fédération Hospitalo-Universitaire "Innovative Therapy for Immune Disorders", Créteil, France
| | - Anais Poyet
- Association Régionale d'Aide aux Urémiques du Centre Ouest (ARAUCO), Bourges, France
| | - Noémie Jourde-Chiche
- Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception (APHM), Marseille, France
| | - Dominique Guerrot
- Service de Néphrologie, Dialyse et Transplantation, CHU de Rouen, Rouen, France
| | - Sandrine Lemoine
- Néphrologie, Dialyse, Hypertension artérielle et Exploration Fonctionnelle rénale, Groupement Hospitalier Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | | | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE1 3BZ, UK
| | - Coralie Bingham
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Rodney Gilbert
- Southampton Children's Hospital, University of Southampton, Southampton SO16 6YD, UK
| | - Yannick Le Meur
- Univ Brest, UMR 1227, LBAI, Labex IGO, 29200 Brest, France; Service de Néphrologie, Hémodialyse et Transplantation rénale, CHRU Brest, 29609 Brest, France
| | - Marie-Pierre Audrézet
- Univ. Brest, Inserm, UMR 1078, GGB, 29200 Brest, France; Service de Génétique moléculaire, CHRU Brest, 29609 Brest, France
| | - Emilie Cornec-Le Gall
- Univ. Brest, Inserm, UMR 1078, GGB, 29200 Brest, France; Service de Néphrologie, Hémodialyse et Transplantation rénale, CHRU Brest, 29609 Brest, France.
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Identification of Genetic Risk Factors of Severe COVID-19 Using Extensive Phenotypic Data: A Proof-of-Concept Study in a Cohort of Russian Patients. Genes (Basel) 2022; 13:genes13030534. [PMID: 35328087 PMCID: PMC8949130 DOI: 10.3390/genes13030534] [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: 02/01/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
The COVID-19 pandemic has drawn the attention of many researchers to the interaction between pathogen and host genomes. Over the last two years, numerous studies have been conducted to identify the genetic risk factors that predict COVID-19 severity and outcome. However, such an analysis might be complicated in cohorts of limited size and/or in case of limited breadth of genome coverage. In this work, we tried to circumvent these challenges by searching for candidate genes and genetic variants associated with a variety of quantitative and binary traits in a cohort of 840 COVID-19 patients from Russia. While we found no gene- or pathway-level associations with the disease severity and outcome, we discovered eleven independent candidate loci associated with quantitative traits in COVID-19 patients. Out of these, the most significant associations correspond to rs1651553 in MYH14p = 1.4 × 10-7), rs11243705 in SETX (p = 8.2 × 10-6), and rs16885 in ATXN1 (p = 1.3 × 10-5). One of the identified variants, rs33985936 in SCN11A, was successfully replicated in an independent study, and three of the variants were found to be associated with blood-related quantitative traits according to the UK Biobank data (rs33985936 in SCN11A, rs16885 in ATXN1, and rs4747194 in CDH23). Moreover, we show that a risk score based on these variants can predict the severity and outcome of hospitalization in our cohort of patients. Given these findings, we believe that our work may serve as proof-of-concept study demonstrating the utility of quantitative traits and extensive phenotyping for identification of genetic risk factors of severe COVID-19.
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10
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Caplan MJ. AMPK and Polycystic Kidney Disease Drug Development: An Interesting Off-Target Target. Front Med (Lausanne) 2022; 9:753418. [PMID: 35174190 PMCID: PMC8841847 DOI: 10.3389/fmed.2022.753418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/10/2022] [Indexed: 11/20/2022] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease is a genetic disease that causes dramatic perturbations of both renal tissue architecture and of a multitude of cellular signaling pathways. The relationship between the products of the genes whose mutations cause polycystic kidney disease and these signaling pathways remains difficult to determine. It is clear, however, that cellular metabolism is dramatically altered in cells that are affected by polycystic kidney disease mutations. Adenosine monophosphate-stimulated protein kinase is a master regulator of cellular energy use and generation pathways whose activity appears to be perturbed in cells affected by polycystic kidney disease. Furthermore, modulation of this enzyme's activity may constitute a promising approach for the development of new therapeutics for polycystic kidney disease.
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11
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Bowden SA, Rodger EJ, Chatterjee A, Eccles MR, Stayner C. Recent Discoveries in Epigenetic Modifications of Polycystic Kidney Disease. Int J Mol Sci 2021; 22:ijms222413327. [PMID: 34948126 PMCID: PMC8708269 DOI: 10.3390/ijms222413327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a heritable renal disease that results in end-stage kidney disease, due to the uncontrolled bilateral growth of cysts throughout the kidneys. While it is known that a mutation within a PKD-causing gene is required for the development of ADPKD, the underlying mechanism(s) causing cystogenesis and progression of the disease are not well understood. Limited therapeutic options are currently available to slow the rate of cystic growth. Epigenetic modifications, including DNA methylation, are known to be altered in neoplasia, and several FDA-approved therapeutics target these disease-specific changes. As there are many similarities between ADPKD and neoplasia, we (and others) have postulated that ADPKD kidneys contain alterations to their epigenetic landscape that could be exploited for future therapeutic discovery. Here we summarise the current understanding of epigenetic changes that are associated with ADPKD, with a particular focus on the burgeoning field of ADPKD-specific alterations in DNA methylation.
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Affiliation(s)
- Sarah A. Bowden
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; (S.A.B.); (E.J.R.); (A.C.); (M.R.E.)
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; (S.A.B.); (E.J.R.); (A.C.); (M.R.E.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; (S.A.B.); (E.J.R.); (A.C.); (M.R.E.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; (S.A.B.); (E.J.R.); (A.C.); (M.R.E.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Cherie Stayner
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; (S.A.B.); (E.J.R.); (A.C.); (M.R.E.)
- Correspondence: ; Tel.: +64-3-479-5060; Fax: +64-3-479-7136
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