201
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Chen J, Lin F, Zhai Y, Wang C, Wu B, Ma D, Rao J, Liu J, Liu J, Yu M, Shen Q, Xu H. Diagnostic and clinical utility of genetic testing in children with kidney failure. Pediatr Nephrol 2021; 36:3653-3662. [PMID: 34031707 DOI: 10.1007/s00467-021-05141-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genetic kidney disease is well established as an important cause of pediatric kidney failure, and genetic testing might increase diagnostic accuracy, but evidence is limited. This study was conducted to determine the diagnostic yield and clinical impact of genetic testing for children with kidney failure. METHODS Patients who were diagnosed with kidney failure before 19 years of age at Children's Hospital of Fudan University from 2009 to 2018 and received next-generation sequencing (NGS) were enrolled. The results for likely pathogenic variants in genes known to cause chronic kidney disease (CKD) were analyzed. RESULTS A molecular diagnosis was identified in 39.9% (75/188) of children with kidney failure. Specific subtype of clinical category was discerned in 54 (72.0%) patients, kidney disease was reclassified in 7 (9.3%) patients, the unknown etiology of 5 (6.7%) patients was molecularly diagnosed, and the clinical diagnoses of the other 9 (12.0%) patients were confirmed. In addition, genetic diagnosis was considered to have contributed to clinical management, including negating the need for kidney biopsy (26/75, 34.7%), avoiding immunosuppressive therapy (24/75, 32.0%), changing surveillance (48/75, 64.0%), guiding specific treatment (21/75, 28.0%), and guiding peri-transplant management and options for kidney transplantation (12/75, 16.0%). Furthermore, cascade testing was subsequently offered to 34.7% (26/75) of families. CONCLUSIONS Genetic testing identified a molecular diagnosis in nearly 40% of children with kidney failure. Our results confirm that in children with kidney failure, genetic testing can not only establish a specific molecular diagnosis, but has a significant impact on clinical management.
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Affiliation(s)
- Jing Chen
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Fang Lin
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yihui Zhai
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Chunyan Wang
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Bingbing Wu
- Clinical Genetic Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Jiaojiao Liu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Jialu Liu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Minghui Yu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Qian Shen
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.
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202
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Elliott MD, James LC, Simms EL, Sharma P, Girard LP, Cheema K, Elliott MJ, Lauzon JL, Chun J. Mainstreaming Genetic Testing for Adult Patients With Autosomal Dominant Polycystic Kidney Disease. Can J Kidney Health Dis 2021; 8:20543581211055001. [PMID: 34733539 PMCID: PMC8558595 DOI: 10.1177/20543581211055001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/28/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Genetic testing results are currently obtained approximately 1 year after referral to a medical genetics team for autosomal dominant polycystic kidney disease (ADPKD). We evaluated a mainstream genetic testing (MGT) pathway whereby the nephrology team provided pre-test counseling and selection of patients with suspected ADPKD for genetic testing prior to direct patient interaction by a medical geneticist. SOURCES OF INFORMATION A multidisciplinary team of nephrologists, genetic counselors, and medical geneticists developed an MGT pathway for ADPKD using current testing criteria for adult patient with suspected ADPKD and literature from MGT in oncology. METHODS An MGT pathway was assessed using a prospective cohort and compared to a retrospective cohort of 56 patients with ADPKD who received genetic testing using the standard, traditional pathway prior to implementing the MGT for ADPKD. The mainstream pathway was evaluated using time to diagnosis, diagnostic yield, and a patient survey to assess patient perceptions of the MGT pathway. KEY FINDINGS We assessed 26 patients with ADPKD using the MGT and 18 underwent genetic testing with return of results. Of them, 52 patients had data available for analysis in the traditional control cohort. The time for return of results using our MGT pathway was significantly shorter with a median time to results of 6 months compared to 12 months for the traditional pathway. We identified causative variants in 61% of patients, variants of uncertain significance in 28%, and 10% had negative testing which is in line with expectations from the literature. The patient surveys showed high satisfaction rates with the MGT pathway. LIMITATIONS This report is an evaluation of a new genetic testing pathway restricted to a single, publicly funded health care center. The MGT pathway involved a prospective collection of a limited number of patients with ADPKD with comparison to a retrospective cohort of patients with ADPKD evaluated by standard testing. IMPLICATIONS A MGT pathway using clearly defined criteria and commercially available gene panels for ADPKD can be successfully implemented in a publicly funded health care system to reduce the time required to obtain genetic results.
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Affiliation(s)
- Mark D. Elliott
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Leslie C. James
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, AB, Canada
| | - Emily L. Simms
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Priyana Sharma
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, AB, Canada
| | - Louis P. Girard
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Kim Cheema
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Meghan J. Elliott
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Julie L. Lauzon
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, AB, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Justin Chun
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, AB, Canada
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203
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Haydock L, Garneau AP, Tremblay L, Yen HY, Gao H, Harrisson R, Isenring P. Genetic abnormalities in biopsy-proven, adult-onset hemolytic uremic syndrome and C3 glomerulopathy. J Mol Med (Berl) 2021; 100:269-284. [PMID: 34714369 PMCID: PMC8770394 DOI: 10.1007/s00109-021-02102-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/25/2022]
Abstract
Abstract Atypical hemolytic uremic syndrome (aHUS) and C3 glomerulopathy (C3G) have been linked to mutations in many of the proteins that are involved in alternative complement pathway activation. Age and etiology confounded, the prevalence of such mutations has been reported to be over 30 to 50% in these diseases. However, the cohorts studied included many children or individuals with a familial history of complement-related disorders and genetic tests were usually limited to exome sequencing of known causative or risk-associated genes. In this study, a retrospective adult cohort of 35 patients with biopsy-proven thrombotic microangiopathy (the largest in Canada) and 10 patients with C3 glomerulopathy was tested through an extended exome panel to identify causative defects in associated or candidate genes including those of the alternative and terminal complement pathways. A variant of unknown significance was also analyzed for pathogenicity through in vitro studies. To our surprise, the prevalence of known causative or risk-associated variants in either of these cohorts was found to be less than ~ 15% overall. However, the panel used and analyses carried out allowed to identify novel variants of potential clinical significance and a number of candidate genes. The prevalence of known genetic defects in adult-onset aHUS and C3G is thus probably much lower than 30 to 50%. Our results also point towards the importance of investigating diseases of the alternative complement pathway through extended exome panels and in vitro analyses. Key messages The alternative complement pathway plays a major role in the pathogenesis of hemolytic uremic syndrome and C3 glomerulopathy. Based on previous studies, both disorders have been commonly linked to variants in the various intermediates that sustain or regulate this pathway. The prevalence of such mutations in the adult-onset and sporadic forms of these diseases is probably much lower than expected based on larger series. The sporadic forms of complementopathies are likely to involve additional genes that are yet to be uncovered.
Supplementary information The online version contains supplementary material available at 10.1007/s00109-021-02102-1.
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Affiliation(s)
- Ludwig Haydock
- Nephrology Research Group, L'Hôtel-Dieu de Québec Research Center, Department of Medicine, Faculty of Medicine, Laval University, Quebec, QC, G1R2J6, Canada
| | - Alexandre P Garneau
- Nephrology Research Group, L'Hôtel-Dieu de Québec Research Center, Department of Medicine, Faculty of Medicine, Laval University, Quebec, QC, G1R2J6, Canada.,Cardiometabolic Axis, School of Kinesiology and Physical Activity Sciences, Faculty of Medicine, University of Montréal, 900, rue Saint-Denis, Montreal, QC, H2X 0A9, Canada
| | - Laurence Tremblay
- Nephrology Research Group, L'Hôtel-Dieu de Québec Research Center, Department of Medicine, Faculty of Medicine, Laval University, Quebec, QC, G1R2J6, Canada
| | - Hai-Yun Yen
- Fulgent Genetics, Temple City, CA, 91780, USA
| | - Hanlin Gao
- Fulgent Genetics, Temple City, CA, 91780, USA
| | - Raphaël Harrisson
- Nephrology Research Group, L'Hôtel-Dieu de Québec Research Center, Department of Medicine, Faculty of Medicine, Laval University, Quebec, QC, G1R2J6, Canada
| | - Paul Isenring
- Nephrology Research Group, L'Hôtel-Dieu de Québec Research Center, Department of Medicine, Faculty of Medicine, Laval University, Quebec, QC, G1R2J6, Canada.
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204
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Martínez-Pulleiro R, García-Murias M, Fidalgo-Díaz M, García-González MÁ. Molecular Basis, Diagnostic Challenges and Therapeutic Approaches of Alport Syndrome: A Primer for Clinicians. Int J Mol Sci 2021; 22:ijms222011063. [PMID: 34681722 PMCID: PMC8541626 DOI: 10.3390/ijms222011063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/20/2022] Open
Abstract
Alport syndrome is a genetic and hereditary disease, caused by mutations in the type IV collagen genes COL4A3, COL4A4 and COL4A5, that affects the glomerular basement membrane of the kidney. It is a rare disease with an underestimated prevalence. Genetic analysis of population cohorts has revealed that it is the second most common inherited kidney disease after polycystic kidney disease. Renal involvement is the main manifestation, although it may have associated extrarenal manifestations such as hearing loss or ocular problems. The degree of expression of the disease changes according to the gene affected and other factors, known or yet to be known. The pathophysiology is not yet fully understood, although some receptors, pathways or molecules are known to be linked to the disease. There is also no specific treatment for Alport syndrome; the most commonly used are renin–angiotensin–aldosterone system inhibitors. In recent years, diagnosis has come a long way, thanks to advances in DNA sequencing technologies such as next-generation sequencing (NGS). Further research at the genetic and molecular levels in the future will complete the partial vision of the pathophysiological mechanism that we have, and will allow us to better understand what is happening and how to solve it.
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Affiliation(s)
- Raquel Martínez-Pulleiro
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (R.M.-P.); (M.G.-M.)
- Grupo de Medicina Xenómica (GMX), 15706 Santiago de Compostela, Spain
| | - María García-Murias
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (R.M.-P.); (M.G.-M.)
- Grupo de Medicina Xenómica (GMX), 15706 Santiago de Compostela, Spain
| | - Manuel Fidalgo-Díaz
- Departamento de Nefrología, Complexo Hospitalario Universitario de Santiago (CHUS), 15706 Santiago de Compostela, Spain;
| | - Miguel Ángel García-González
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (R.M.-P.); (M.G.-M.)
- Grupo de Medicina Xenómica (GMX), 15706 Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
- Correspondence: ; Tel.: +34-981-555-197
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205
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Thomas CP, Gupta S, Freese ME, Chouhan KK, Dantuma MI, Holanda DG, Katz DA, Darbro BW, Mansilla MA, Smith RJ. Sequential genetic testing of living-related donors for inherited renal disease to promote informed choice and enhance safety of living donation. Transpl Int 2021; 34:2696-2705. [PMID: 34632641 DOI: 10.1111/tri.14133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/09/2023]
Abstract
Living kidney donors (LKDs) with a family history of renal disease are at risk of kidney disease as compared to LKDs without such history suggesting that some LKDs may be pre-symptomatic for monogenic kidney disease. LKDs with related transplant candidates whose kidney disease was considered genetic in origin were selected for genetic testing. In each case, the transplant candidate was first tested to verify the genetic diagnosis. A genetic diagnosis was confirmed in 12 of 24 transplant candidates (ADPKD-PKD1: 6, ALPORT-COL4A3: 2, ALPORT-COL4A5: 1: nephronophthisis-SDCCAG8: 1; CAKUT-HNF1B and ADTKD-MUC1: 1 each) and 2 had variants of unknown significance (VUS) in phenotype-relevant genes. Focused genetic testing was then done in 20 of 34 LKDs. 12 LKDs screened negative for the familial variant and were permitted to donate; seven screened positive and were counseled against donation. One, the heterozygous carrier of a recessive disorder was also cleared. Six of seven LKDs with a family history of ADPKD were under 30 years and in 5, by excluding ADPKD, allowed donation to safely proceed. The inclusion of genetic testing clarified the diagnosis in recipient candidates, improving safety or informed decision-making in LKDs.
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Affiliation(s)
- Christie P Thomas
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.,Department of Pediatrics, University of Iowa, Iowa City, IA, USA.,Veterans Affairs Medical Center, Iowa City, IA, USA
| | - Sonali Gupta
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Margaret E Freese
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | | | - Maisie I Dantuma
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | | | - Daniel A Katz
- Department of Surgery, University of Iowa, Iowa City, IA, USA
| | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Maria A Mansilla
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Richard J Smith
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.,Department of Pediatrics, University of Iowa, Iowa City, IA, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
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206
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Domingo-Gallego A, Pybus M, Madariaga L, Piñero-Fernández JA, González-Pastor S, López-González M, Simarro-Rueda E, Quintanilla-Mata ML, Matoses-Ruipérez ML, Ejarque-Vila L, Gall ECL, Guirado L, Torra R, Ariceta G, Ars E. Clinical and genetic characterization of a cohort of proteinuric patients with biallelic CUBN variants. Nephrol Dial Transplant 2021; 37:1906-1915. [PMID: 34610128 DOI: 10.1093/ndt/gfab285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Proteinuria is a well-known risk factor for progressive kidney impairment. Recently, C-terminal cubilin (CUBN) variants have been associated with isolated proteinuria without progression of kidney disease. METHODS Genetic testing of 347 families with proteinuria of suspected monogenic cause was performed by next-generation sequencing of a custom-designed kidney disease gene panel. Families with CUBN biallelic proteinuria-causing variants were studied at the clinical, genetic, laboratory, and pathologic levels. RESULTS Twelve families (15 patients) bearing homozygous or compound heterozygous proteinuria-causing variants in the C-terminal CUBN gene were identified, representing 3.5% of the total cohort. We identified 14 different sequence variants, five of which were novel. The median age at diagnosis of proteinuria was 4 years (range 9 months to 44 years), and in most cases proteinuria was detected incidentally. Thirteen patients had moderate-severe proteinuria at diagnosis without nephrotic syndrome. These patients showed lack of response to angiotensin-converting enzyme inhibitor (ACEi) and angiotensin receptor blocker (ARB) treatment, normal kidney biopsy, and preservation of normal kidney function over time. The two remaining patients presented a more severe phenotype, likely caused by associated comorbidities. CONCLUSIONS Identification of C-terminal pathogenic CUBN variants is diagnostic of an entity characterized by glomerular proteinuria, normal kidney histology, and lack of response to ACEi/ARB treatment. This study adds evidence and increases awareness about albuminuria caused by C-terminal variants in the CUBN gene, which is a benign condition usually diagnosed in childhood with preserved renal function until adulthood.
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Affiliation(s)
- Andrea Domingo-Gallego
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Barcelona, Catalonia, Spain.,Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Medicine Department, REDinREN, Barcelona, Catalonia, Spain
| | - Marc Pybus
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Barcelona, Catalonia, Spain.,Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Medicine Department, REDinREN, Barcelona, Catalonia, Spain
| | - Leire Madariaga
- Pediatric Nephrology Department, Cruces University Hospital, Instituto de Investigación Sanitaria Biocruces-Bizkaia, CIBERER, CIBERDEM, Universidad del País Vasco UPV/EHU, Barakaldo, Spain
| | | | - Sara González-Pastor
- Pediatric Nephrology Department, Hospital Universitario Germans Trias i Pujol, Barcelona, Catalonia, Spain
| | - Mercedes López-González
- Pediatric Nephrology Department, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Esther Simarro-Rueda
- Clinical Analysis Department, Hospital General Universitario de Albacete, Castilla-La Mancha, Spain
| | | | | | - Laia Ejarque-Vila
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Barcelona, Catalonia, Spain
| | - Emilie Cornec-Le Gall
- Service de Néphrologie, Hémodialyse et Transplantation Rénale, Centre Hospitalier Universitaire, Brest, France; UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, INSERM, Université de Brest, Brest, France; Université de Bretagne Occidentale, Brest, France
| | - Lluís Guirado
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Medicine Department, REDinREN, Barcelona, Catalonia, Spain
| | - Roser Torra
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Medicine Department, REDinREN, Barcelona, Catalonia, Spain
| | - Gema Ariceta
- Pediatric Nephrology Department, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Barcelona, Catalonia, Spain.,Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Medicine Department, REDinREN, Barcelona, Catalonia, Spain
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207
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Lenain R, Maanaoui M, Hamroun A, Larrue R, Van Der Hauwaert C, Gibier JB, Gnemmi V, Gomis S, Labalette M, Broly F, Hennart B, Pottier N, Hazzan M, Cauffiez C, Glowacki F. Impact of Tacrolimus Daily Dose Limitation in Renal Transplant Recipients Expressing CYP3A5: A Retrospective Study. J Pers Med 2021; 11:jpm11101002. [PMID: 34683143 PMCID: PMC8539387 DOI: 10.3390/jpm11101002] [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: 07/28/2021] [Revised: 09/25/2021] [Accepted: 09/30/2021] [Indexed: 11/24/2022] Open
Abstract
The pharmacokinetic variability of tacrolimus can be partly explained by CYP3A5 activity. Our objective was to evaluate a tacrolimus sparing policy on renal graft outcome according to CYP3A5 6986A>G genetic polymorphism. This retrospective study included 1114 recipients with a median follow-up of 6.3 years. Genotyping of the 6986A>G allelic variant corresponding to CYP3A5*3 was systematically performed. One year after transplantation, tacrolimus blood trough concentration (C0) target range was 5–7 ng/mL. However, daily dose was capped to 0.10 mg/kg/day regardless of the CYP3A5 genotype. A total 208 CYP3A5*1/- patients were included. Despite a higher daily dose, CYP3A5*1/- recipients exhibited lower C0 during follow-up (p < 0.01). Multivariate analysis did not show any significant influence of CYP3A5*1/- genotype (HR = 0.70, 0.46–1.07, p = 0.10) on patient-graft survival. Glomerular Filtration Rate (GFR) decline was significantly lower for the CYP3A5*1/- group (p = 0.02). The CYP3A5*1/- genotype did not significantly impact the risk of biopsy-proven acute rejection (BPAR) (HR = 1.01, 0.68–1.49, p = 0.97) despite significantly lower C0. Based on our experience, a strategy of tacrolimus capping is associated with a better GFR evolution in CYP3A5*1/- recipients without any significant increase of BPAR incidence. Our study raised some issues about specific therapeutic tacrolimus C0 targets for CYP3A5*1/- patients and suggests to set up randomized control studies in this specific population.
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Affiliation(s)
- Rémi Lenain
- CHU Lille, Service de Néphrologie, F-59000 Lille, France; (R.L.); (M.M.); (A.H.); (S.G.); (M.H.); (F.G.)
| | - Mehdi Maanaoui
- CHU Lille, Service de Néphrologie, F-59000 Lille, France; (R.L.); (M.M.); (A.H.); (S.G.); (M.H.); (F.G.)
| | - Aghilès Hamroun
- CHU Lille, Service de Néphrologie, F-59000 Lille, France; (R.L.); (M.M.); (A.H.); (S.G.); (M.H.); (F.G.)
| | - Romain Larrue
- UMR9020-U1277—CANTHER—Cancer Heterogeneity, Plasticity and Resistance to Therapies, University Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (R.L.); (C.V.D.H.); (N.P.)
- CHU Lille, Service de Toxicologie et Génopathies, F-59000 Lille, France; (F.B.); (B.H.)
| | - Cynthia Van Der Hauwaert
- UMR9020-U1277—CANTHER—Cancer Heterogeneity, Plasticity and Resistance to Therapies, University Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (R.L.); (C.V.D.H.); (N.P.)
- CHU Lille, Département de la Recherche en Santé, F-59000 Lille, France
| | - Jean-Baptiste Gibier
- CHU Lille, Service d’Anatomo-Pathologie, F-59000 Lille, France; (J.-B.G.); (V.G.)
| | - Viviane Gnemmi
- CHU Lille, Service d’Anatomo-Pathologie, F-59000 Lille, France; (J.-B.G.); (V.G.)
| | - Sébastien Gomis
- CHU Lille, Service de Néphrologie, F-59000 Lille, France; (R.L.); (M.M.); (A.H.); (S.G.); (M.H.); (F.G.)
| | - Myriam Labalette
- CHU de Lille, Institut D’Immunologie-HLA, F-59000 Lille, France;
| | - Franck Broly
- CHU Lille, Service de Toxicologie et Génopathies, F-59000 Lille, France; (F.B.); (B.H.)
| | - Benjamin Hennart
- CHU Lille, Service de Toxicologie et Génopathies, F-59000 Lille, France; (F.B.); (B.H.)
| | - Nicolas Pottier
- UMR9020-U1277—CANTHER—Cancer Heterogeneity, Plasticity and Resistance to Therapies, University Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (R.L.); (C.V.D.H.); (N.P.)
- CHU Lille, Service de Toxicologie et Génopathies, F-59000 Lille, France; (F.B.); (B.H.)
| | - Marc Hazzan
- CHU Lille, Service de Néphrologie, F-59000 Lille, France; (R.L.); (M.M.); (A.H.); (S.G.); (M.H.); (F.G.)
| | - Christelle Cauffiez
- UMR9020-U1277—CANTHER—Cancer Heterogeneity, Plasticity and Resistance to Therapies, University Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (R.L.); (C.V.D.H.); (N.P.)
- Correspondence:
| | - François Glowacki
- CHU Lille, Service de Néphrologie, F-59000 Lille, France; (R.L.); (M.M.); (A.H.); (S.G.); (M.H.); (F.G.)
- UMR9020-U1277—CANTHER—Cancer Heterogeneity, Plasticity and Resistance to Therapies, University Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (R.L.); (C.V.D.H.); (N.P.)
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208
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Olinger E, Al Alawi I, Al Riyami MS, Al Salmi I, Molinari E, Faqeih EA, Al Hamed M, Barroso-Gil M, Powell L, Al-Hussaini AA, Rahim KA, Almontashiri N, Miles C, Shril S, Hildebrandt F, Wilson IJ, Sayer JA. A discarded synonymous variant in NPHP3 explains nephronophthisis and congenital hepatic fibrosis in several families. Hum Mutat 2021; 42:1221-1228. [PMID: 34212438 PMCID: PMC8434971 DOI: 10.1002/humu.24251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 02/05/2023]
Abstract
Half of patients with a ciliopathy syndrome remain unsolved after initial analysis of whole exome sequencing (WES) data, highlighting the need for improved variant filtering and annotation. By candidate gene curation of WES data, combined with homozygosity mapping, we detected a homozygous predicted synonymous allele in NPHP3 in two children with hepatorenal fibrocystic disease from a consanguineous family. Analyses on patient-derived RNA shows activation of a cryptic mid-exon splice donor leading to frameshift. Remarkably, the same rare variant was detected in four additional families with hepatorenal disease from UK, US, and Saudi patient cohorts and in addition, another synonymous NPHP3 variant was identified in an unsolved case from the Genomics England 100,000 Genomes data set. We conclude that synonymous NPHP3 variants, not reported before and discarded by pathogenicity pipelines, solved several families with a ciliopathy syndrome. These findings prompt careful reassessment of synonymous variants, especially if they are rare and located in candidate genes.
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Affiliation(s)
- Eric Olinger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Intisar Al Alawi
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
- National Genetic Center, Ministry of Health, Oman
| | | | - Isa Al Salmi
- National Genetic Center, Ministry of Health, Oman
| | - Elisa Molinari
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Eissa Ali Faqeih
- Department of Medical Genetics, Children’s Specialist Hospital, King Fahad Medical City, Riyadh Saudi Arabia
| | - Mohamed Al Hamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Abdulrahman A. Al-Hussaini
- Department of Medical Genetics, Children’s Specialist Hospital, King Fahad Medical City, Riyadh Saudi Arabia
| | - Khawla A. Rahim
- Department of Medical Genetics, Children’s Specialist Hospital, King Fahad Medical City, Riyadh Saudi Arabia
| | - Naif Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Colin Miles
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ian J. Wilson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - John A. Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
- Renal Services, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, United Kingdom
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, NE4 5PL, United Kingdom
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209
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Abstract
A huge array of data in nephrology is collected through patient registries, large epidemiological studies, electronic health records, administrative claims, clinical trial repositories, mobile health devices and molecular databases. Application of these big data, particularly using machine-learning algorithms, provides a unique opportunity to obtain novel insights into kidney diseases, facilitate personalized medicine and improve patient care. Efforts to make large volumes of data freely accessible to the scientific community, increased awareness of the importance of data sharing and the availability of advanced computing algorithms will facilitate the use of big data in nephrology. However, challenges exist in accessing, harmonizing and integrating datasets in different formats from disparate sources, improving data quality and ensuring that data are secure and the rights and privacy of patients and research participants are protected. In addition, the optimism for data-driven breakthroughs in medicine is tempered by scepticism about the accuracy of calibration and prediction from in silico techniques. Machine-learning algorithms designed to study kidney health and diseases must be able to handle the nuances of this specialty, must adapt as medical practice continually evolves, and must have global and prospective applicability for external and future datasets.
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210
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Ortiz A, Roger M, Jiménez VM, Perez JCR, Furlano M, Atxer LS, Zurro DG, Casabona CMR, Zurro DG, Gómez CG, Bermúdez PP, Armisen MA, López SA, Porras IG, Ruiz JG, Orgaz JMM, Barón MM, Ortiz PDS, Fuente GDADL, Gili BQ, Fresnedo GF, Cabrera SS, Contreras JP, Pelicano MB, Blanca AM, Portillo MR, Álvarez JES, Romeo MJS, Pérez MG, Diezhandino MG, Marrero DH, Campo CF, García EM, Carmona DGC, Ramírez AT, Bellvis LM, Haym MB, Gómez MB, Martínez JMC, Garrit JMC, Garrido RSJ, Delgado JB, Marimont MB, Muñoz MOV, Villares JMP, Velázquez ÁS, Bonet LA, Bravo MÁG, Mateos FJM, Amador MM, Blanca AM, Miñano JAP, Belmonte AA, Jover AS, Rituerto DC, Sánchez FP, Arenas MD, Hernández RM, Serrano BM, Arduan AO, Sanz AB, Ramos AM, Córdoba-David G, García-Jiménez J, Fontecha-Barriuso M, Guerrero-Mauvecin J, Lopez-Díaz AM, Sánchez-Niño MD, Valiño-Rivas L, Cuarental L, Ribagorda M, Pintor-Chocano A, Favero C, Alvarez-Llamas G, Catalina MC, Fernández-Fernández B, Pérez-Gómez MV, Montaner ERAD, Prado RF, Rivera JR, Verde AMR, Luis-Lima S, Sánchez-Rodríguez J, Sánchez SP, Ortega MR, Parra EG, Mateos SR, Ortiz PJC, Expósito LM, Tejera-Muñoz A, Marchant V, Tejedor-Santamaria L, Agilar MA, Diekmann F, Genis BB, Salinas FO, Bajo MJR, Maneus EB, Guillen MA, Juárez JR, Rodríguez ML, Vicente IR, Pelicano JMB, Porras LFQ, Aguiar PVA, Font MX, Andujar AM, Cucchiari D, Marrah EM, M J, Piñeiro GJ, Salgado CM, Morales Martín AI, López Hernández FJ, Balboa NE, Vicente MP, Calvo IF, González LR, Vicente LV, Martínez SMS, Casanova Paso AG, Garriel MP, López JJV, Palacios AMC, Saénz DS, García PG, Bonilla JLA, Fernández Rodríguez MA, Galán AD, Marcos EM, Pérez-Aradros JC, José RMS, Zelaya FM, Panadés ES, Molina ÁG, Salido JA, Balcells RT, Criach EA, Encarnación MD, Perich LG, Furlano M, Girol CC, Terroba YA, Oliveras MP, Vila LE, Cabañas NS, Molas CF, Torres IS, Pelaez SL, Serra CR, Torres CC, Fajardo JPT, Lahuerta JIH, Herranz VM, Portillo MR, Malo AM, Cabrera SS, Castañeda JRM, Ortiz MER, Moreno JMM, Bermúdez AIR, Olmo RS, Pavón FG, Peregrin CM, Tejero EA, Villalba IL, Muñoz AC, Mier MVPRD, Martos CMP, Baltanas RL, Haad CR, Bartolomé MF, Valdemoros RL, Serres FEB, Díaz MN, Mariño FJJ, Sole LC, Saborido MIT, Majoral JS, Martínez ML, Calabia ER, Millán JCRS, López-Hoyos M, Benito-Hernández A, Fresnedo GF, Segundo DS, Valero R, García EC, Ona JGD, Llavona EC, Rodríguez FS, Gutiérrez RL, Peña HG, Pérez MG, Marrero DH, López V, Sola E, Cabello M, Caballero A, León M, Ruiz P, Alonso J, Navarro-González J, Mora-Fernández MDC, Donate-Correa J, Martín-Nuñez E, Delgado NP, Gigarrán-Guldris S, Pérez JCR, Teruel JLG, Castelao AM, Revilla JMV, Martínez CM, Stanojevic MB, Boque EC, Rosell MNS, Lamo VMD, Tocados JMD, Carrasco AG, López MB, Enriquez MC, Bardaji AM, Masot ND, Gómez AP, Sanjuan AE, Ortega AO, Fuentes RW, Guindo MDCDG, Fuentes MDCR, Ravassa FO, Molina MC, Tortosa CLR, Garrido RGDM, Romeo MJS, Jacobs-Cachá C, Matamoros OB, Mateos FM, Meneghini MAE, Roig JS, Betsabé IT, Larrea CL, Álvarez BS, Corte MDCD, Rodrigues-Diez RR, Vázquez AL, Rodríguez SG, Castiñeira JRV, Martín CM, Álvarez MLS, Iglesias VC, Borra JM, Rubio MAB, Gilsanz GDP, Cabrera ML, Heffernan JAJ, González MO, González OC, García MEG, Martín CJ, Correa PS, Ramos SA, Oliva ML, Becerra BR, Cabrera CV, Mateo GTG, Villanueva RS, García LÁ, Cannata Andía JB, Díaz MN, Martín JLF, López NC, García SP, Montes CA, García MR, Luengas ILM, Álvarez ES, Arias LM, Carro BM, Virgala JM, González MG, Barreiro JML, Fontan MP, González AO, Barja LMC, Barreiro AS, Arias BP, Hernández ÁA, Pérez MP, Varela JC, Lechuga JA, Rodríguez CD, Murias MG, Iglesia AMBDL, Piñeiro PB, González ÁG, Eijo AC, Cachaza NC, González MV, Garrit JMC, Blanch NL, Martínez AMS, Val MH, BordignonDraibe J, Melilli E, Montero AM, Pérez NM, Oliveras XF, Barrio MC, Santos JP, Barrera CB, Sáez MJP, Pachón MDR, Cabrales CA, Porras AB, García ER, Atxer LS, González VP, Mallol LL, Oliva MR, Puyol DR, Torres MPR, Ongil SL, Basilio LC, Centenera GO, Miguel PMD, Rodríguez LF, Nadah HB, Fernández MP, Chamond MRR, Ortiz PS, Fernández NG, Boillos AB, Cenarruzabeitia NV, Seara MAF, Moreno IDDPM, Lavilla FJ, Torres A, Miranda DM, Hernández APR, Redondo EDB, Porrini E, Caso MDLÁC, Tamajón MLP, Hernández MR, Rebollo MSG, Mallen PD, González AÁ, Rinne AMG, Rodríguez RM, Torres SE, Sosa DÁ, Cabrera BE, Rodríguez NZ, Hernández AF, Gamboa MJR, Caso C, Angeles MDL, Tamajon P, Lourdes M, Hernandez MR, Rebollo G, Sagrario M, Mallen PD, Gonzalez A, Alejandra, Rinne G, Maria A, Rodriguez RM, Torres SE, Sosa DA, Cabrera BE, Rodiguez NZ, Hernandez AF, Gamboa R, Jose M, Bermejo MLG, Lucas MF, Moreno EC, Muñoz LS, Huertas SS, Serrano EMR, Muñoz MER, Toro LC, Agudo CPB, Álvarez CG, Portoles J, Marqués M, Rubio E, Sánchez-Sobrino B, García-Menéndez E, Fernández AL, Diezhandin MG, Benítez PR, González MÁGN, Gallardo ML, Juárez GMF, Martínez EG, Terente MP, Ribera AT, Escribano TC, Fontan FC, Fernández AS, Pérez - Monteoliva NRR, Huerta EL, Rodríguez GG, Hernández SB, Zamorano SM, Gómez JML, Gallego RH. RICORS2040: the need for collaborative research in chronic kidney disease. Clin Kidney J 2021; 15:372-387. [PMID: 35211298 PMCID: PMC8862113 DOI: 10.1093/ckj/sfab170] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 01/17/2023] Open
Abstract
Abstract
Chronic kidney disease (CKD) is a silent and poorly known killer. The current concept of CKD is relatively young and uptake by the public, physicians and health authorities is not widespread. Physicians still confuse CKD with chronic kidney insufficiency or failure. For the wider public and health authorities, CKD evokes kidney replacement therapy (KRT). In Spain, the prevalence of KRT is 0.13%. Thus health authorities may consider CKD a non-issue: very few persons eventually need KRT and, for those in whom kidneys fail, the problem is ‘solved’ by dialysis or kidney transplantation. However, KRT is the tip of the iceberg in the burden of CKD. The main burden of CKD is accelerated ageing and premature death. The cut-off points for kidney function and kidney damage indexes that define CKD also mark an increased risk for all-cause premature death. CKD is the most prevalent risk factor for lethal coronavirus disease 2019 (COVID-19) and the factor that most increases the risk of death in COVID-19, after old age. Men and women undergoing KRT still have an annual mortality that is 10- to 100-fold higher than similar-age peers, and life expectancy is shortened by ~40 years for young persons on dialysis and by 15 years for young persons with a functioning kidney graft. CKD is expected to become the fifth greatest global cause of death by 2040 and the second greatest cause of death in Spain before the end of the century, a time when one in four Spaniards will have CKD. However, by 2022, CKD will become the only top-15 global predicted cause of death that is not supported by a dedicated well-funded Centres for Biomedical Research (CIBER) network structure in Spain. Realizing the underestimation of the CKD burden of disease by health authorities, the Decade of the Kidney initiative for 2020–2030 was launched by the American Association of Kidney Patients and the European Kidney Health Alliance. Leading Spanish kidney researchers grouped in the kidney collaborative research network Red de Investigación Renal have now applied for the Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS) call for collaborative research in Spain with the support of the Spanish Society of Nephrology, Federación Nacional de Asociaciones para la Lucha Contra las Enfermedades del Riñón and ONT: RICORS2040 aims to prevent the dire predictions for the global 2040 burden of CKD from becoming true.
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211
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Jiang L, Mei JP, Zhao YW, Zhang R, Pan HX, Yang Y, Sun QY, Xu Q, Yan XX, Tan JQ, Li JC, Tang BS, Guo JF. Low-frequency and rare coding variants of NUS1 contribute to susceptibility and phenotype of Parkinson's disease. Neurobiol Aging 2021; 110:106-112. [PMID: 34635350 DOI: 10.1016/j.neurobiolaging.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 01/13/2023]
Abstract
NUS1 has been recently identified as a candidate gene for Parkinson's disease (PD). Few studies have examined the association of NUS1 variants with PD susceptibility and phenotypes. In the first cohort, whole-exome sequencing was performed to identify variants in NUS1 exon-coding and exon-intron regions in 1542 cases and 1625 controls. 13 variants were totally detected, of which 10 rare variants and 3 low-frequency variants. Burden analysis showed that rare NUS1 variants significantly enriched in PD (p=0.016). We also performed a meta-analysis based on previous and our studies to correlate NUS1 mutations with PD susceptibility. Integrating our previous cohort (3210 cases and 2807 controls) and the first cohort identified the significant association of rs539668656 with PD risk (odds ratio (OR) = 2.82, p = 0.016). The genotype-phenotype association analysis showed that patients carrying rare variants, or rs539668656 were significantly associated with earlier onset age, depression, emotional impairment and severe disease condition. Our results support the role of NUS1 rare variants and rs539668656 towards PD susceptibility and phenotype.
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Affiliation(s)
- Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun-Pu Mei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qi-Ying Sun
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie-Qiong Tan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jin-Chen Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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212
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Mabillard H, Sayer JA, Olinger E. Clinical and genetic spectra of autosomal dominant tubulointerstitial kidney disease. Nephrol Dial Transplant 2021; 38:271-282. [PMID: 34519781 PMCID: PMC9923703 DOI: 10.1093/ndt/gfab268] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Indexed: 12/23/2022] Open
Abstract
Autosomal dominant tubulointerstitial kidney disease (ADTKD) is a clinical entity defined by interstitial fibrosis with tubular damage, bland urinalysis and progressive kidney disease. Mutations in UMOD and MUC1 are the most common causes of ADTKD but other rarer (REN, SEC61A1), atypical (DNAJB11) or heterogeneous (HNF1B) subtypes have been described. Raised awareness, as well as the implementation of next-generation sequencing approaches, have led to a sharp increase in reported cases. ADTKD is now believed to be one of the most common monogenic forms of kidney disease and overall it probably accounts for ∼5% of all monogenic causes of chronic kidney disease. Through international efforts and systematic analyses of patient cohorts, critical insights into clinical and genetic spectra of ADTKD, genotype-phenotype correlations as well as innovative diagnostic approaches have been amassed during recent years. In addition, intense research efforts are addressed towards deciphering and rescuing the cellular pathways activated in ADTKD. A better understanding of these diseases and of possible commonalities with more common causes of kidney disease may be relevant to understand and target mechanisms leading to fibrotic kidney disease in general. Here we highlight recent advances in our understanding of the different subtypes of ADTKD with an emphasis on the molecular underpinnings and its clinical presentations.
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Affiliation(s)
- Holly Mabillard
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK,Renal Services, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - John A Sayer
- Faculty of Medical Sciences, Translational and Clinical Research Institute, 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
| | - Eric Olinger
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK,Correspondence to: Eric Olinger; E-mail:
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213
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Chaperon JL, Wemmer NM, McKanna TA, Clark DM, Westemeyer MA, Gauthier P, Bai Y, Coleman JM. Preimplantation Genetic Testing for Kidney Disease-Related Genes: A Laboratory's Experience. Am J Nephrol 2021; 52:684-690. [PMID: 34515037 DOI: 10.1159/000518253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/28/2021] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Recent literature highlights the clinical utility of genetic testing for patients with kidney disease. Genetic testing provides significant benefits for reproductive risk counseling, including the option of in vitro fertilization with preimplantation genetic testing for monogenic disease (PGT-M). PGT-M allows for a significant reduction in risk for a pregnancy affected with the familial disease. We aim to summarize our experience with PGT-M for genes with kidney involvement as either a primary or secondary feature of the disease. METHODS All PGT-M tests performed by the reference laboratory between September 2010 and July 2020 were reviewed for clinical indication and cases for which the disease tested included a renal component. Each patient referred for PGT-M had an existing molecular genetic diagnosis themselves or in their family. Frequency of each condition, gene, inheritance pattern, and year over year increase in referral cases was analyzed. RESULTS In the study cohort, the most common disease targeted was autosomal dominant polycystic kidney disease, caused by pathogenic variants in the PKD1 or PKD2 genes, which accounted for 16.5% (64/389) of cases. The 5 most common referral indications accounted for 51.9% (202/389) of the cases. Autosomal recessive inheritance accounted for 52.0% (26/50) of conditions for which PGT-M was performed. The number of PGT-M tests performed for conditions that included either primary or secondary kidney disease increased from 5 cases in 2010 to 47 cases in the 2020 study period. DISCUSSION/CONCLUSION These data suggest that the pursuit of PGT-M by couples at risk for passing on conditions with a kidney component is common and has significantly increased since 2010. With this rising trend of patients undergoing PGT-M and the prerequisite of molecular genetic confirmation in the PGT-M process, this study underscores the importance of the reproductive component to a molecular genetic diagnosis for patients with kidney disease, especially as the accessibility of genetic testing and utilization by nephrologists grows.
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Affiliation(s)
| | | | | | | | | | | | - Yan Bai
- Natera, Inc., San Carlos, California, USA
| | - Jessica M Coleman
- Nephrology and Hypertension Medical Associates, P.C., Beaufort, South Carolina, USA
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214
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Mergnac JP, Wiedemann A, Chery C, Ravel JM, Namour F, Guéant JL, Feillet F, Oussalah A. Diagnostic yield of clinical exome sequencing as a first-tier genetic test for the diagnosis of genetic disorders in pediatric patients: results from a referral center study. Hum Genet 2021; 141:1269-1278. [PMID: 34495415 DOI: 10.1007/s00439-021-02358-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/28/2021] [Indexed: 12/29/2022]
Abstract
The emergence of next-generation sequencing enabled a cost-effective and straightforward diagnostic approach to genetic disorders using clinical exome sequencing (CES) panels. We performed a retrospective observational study to assess the diagnostic yield of CES as a first-tier genetic test in 128 consecutive pediatric patients addressed to a referral center in the North-East of France for a suspected genetic disorder, mainly an inborn error of metabolism between January 2016 and August 2020. CES was performed using the TruSight One (4811 genes) or the TruSight One expanded (6699 genes) panel on an Illumina sequencing platform. The median age was 6.5 years (IQR 2.0-12.0) with 43% of males (55/128), and the median disease duration was 7 months (IQR 1-47). In the whole analysis, the CES diagnostic yield was 55% (70/128). The median test-to-report time was 5 months (IQR 4-7). According to CES indications, the CES diagnostic yields were 81% (21/26) for hyperlipidemia, 75% (6/8) for osteogenesis imperfecta, 64% (25/39) for metabolic disorders, 39% (10/26) for neurological disorders, and 28% (8/29) for the subgroup of patients with miscellaneous conditions. Our results demonstrate the usefulness of a CES-based diagnosis as a first-tier genetic test to establish a molecular diagnosis in pediatric patients with a suspected genetic disorder with a median test-to-report time of 5 months. It highlights the importance of a close interaction between the pediatrician with expertise in genetic disorders and the molecular medicine physician to optimize both CES indication and interpretation. Diagnostic yield of clinical exome sequencing (CES) as a first-tier genetic test for diagnosing genetic disorders in 128 consecutive pediatric patients referred to a reference center in the North-East of France for a suspected genetic disorder, mainly an inborn error of metabolism between January 2016 and August 2020. The CES diagnostic yields are reported in the whole population and patients' subgroups (hyperlipidemia, osteogenesis imperfecta, metabolic diseases, neurological disorders, miscellaneous conditions) (Icons made by Flaticon, flaticon.com; CC-BY-3.0).
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Affiliation(s)
- Jean-Philippe Mergnac
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Department of Pediatrics, University Hospital of Nancy, 54000, Nancy, France
| | - Arnaud Wiedemann
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Pediatric Intensive Care Unit, University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France
| | - Céline Chery
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - Jean-Marie Ravel
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France
| | - Farès Namour
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - Jean-Louis Guéant
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - François Feillet
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Department of Pediatrics, University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France
| | - Abderrahim Oussalah
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France. .,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France. .,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France.
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215
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Vaisitti T, Peritore D, Magistroni P, Ricci A, Lombardini L, Gringeri E, Catalano S, Spada M, Sciveres M, Di Giorgio A, Limongelli G, Varrenti M, Gerosa G, Terzi A, Pace Napoleone C, Amodeo A, Ragni L, Strologo LD, Benetti E, Fontana I, Testa S, Peruzzi L, Mitrotti A, Abbate S, Comai G, Gotti E, Schiavon M, Boffini M, De Angelis D, Bertani A, Pinelli D, Torre M, Poggi C, Deaglio S, Cardillo M, Amoroso A. The frequency of rare and monogenic diseases in pediatric organ transplant recipients in Italy. Orphanet J Rare Dis 2021; 16:374. [PMID: 34481500 PMCID: PMC8418291 DOI: 10.1186/s13023-021-02013-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background Rare diseases are chronic and life-threatening disorders affecting < 1 person every 2,000. For most of them, clinical symptoms and signs can be observed at birth or childhood. Approximately 80% of all rare diseases have a genetic background and most of them are monogenic conditions. In addition, while the majority of these diseases is still incurable, early diagnosis and specific treatment can improve patients’ quality of life. Transplantation is among the therapeutic options and represents the definitive treatment for end-stage organ failure, both in children and adults. The aim of this paper was to analyze, in a large cohort of Italian patients, the main rare genetic diseases that led to organ transplantation, specifically pointing the attention on the pediatric cohort. Results To the purpose of our analysis, we considered heart, lung, liver and kidney transplants included in the Transplant Registry (TR) of the Italian National Transplantation Center in the 2002–2019 timeframe. Overall, 49,404 recipients were enrolled in the cohort, 5.1% of whom in the pediatric age. For 40,909 (82.8%) transplant recipients, a disease diagnosis was available, of which 38,615 in the adult cohort, while 8,495 patients (17.2%) were undiagnosed. There were 128 disease categories, and of these, 117 were listed in the main rare disease databases. In the pediatric cohort, 2,294 (5.6%) patients had a disease diagnosis: of the 2,126 (92.7%) patients affected by a rare disease, 1,402 (61.1%) presented with a monogenic condition. As expected, the frequencies of pathologies leading to organ failure were different between the pediatric and the adult cohort. Moreover, the pediatric group was characterized, compared to the adult one, by an overall better survival of the graft at ten years after transplant, with the only exception of lung transplants. When comparing survival considering rare vs non-rare diseases or rare and monogenic vs rare non-monogenic conditions, no differences were highlighted for kidney and lung transplants, while rare diseases had a better survival in liver as opposed to heart transplants. Conclusions This work represents the first national survey analyzing the main genetic causes and frequencies of rare and/or monogenic diseases leading to organ failure and requiring transplantation both in adults and children. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-02013-x.
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Affiliation(s)
- Tiziana Vaisitti
- Department of Medical Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Daniela Peritore
- National Transplant Center, Istituto Superiore Di Sanità, Roma, Italy
| | - Paola Magistroni
- Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria Città Della Salute E Della Scienza Di Torino, Torino, Italy
| | - Andrea Ricci
- National Transplant Center, Istituto Superiore Di Sanità, Roma, Italy
| | | | - Enrico Gringeri
- Hepatobiliary Surgery and Liver Transplantation Unit, Padova University Hospital, Padova, Italy
| | - Silvia Catalano
- General Surgery 2U - Liver Transplant Center, Azienda Ospedaliera Universitaria Città Della Salute E Della Scienza Di Torino, University of Turin, Torino, Italy
| | - Marco Spada
- Divison of Hepatobiliopancreatic Surgery, Liver and Kidney Transplantation, Research Unit of Clinical Hepatogastroenterology and Transplantation, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Angelo Di Giorgio
- Paediatric Hepatology, Gastroenterology and Transplantation, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Giuseppe Limongelli
- Center for Coordination on rare diseases - Regione Campania, Cardiovascular Rare and Genetic Diseases Unit, Department of Cardiology, Monaldi Hospital, AORN Dei Colli,, Naples, Italy
| | - Marisa Varrenti
- DeGasperis CardioCenter, Niguarda Great Metropolitan Hospital, Milan, Italy
| | - Gino Gerosa
- Heart Transplantation Unit, Cardio-Thoraco-Vascular Sciences and Public Health Department, University Padova Hospital, Padova, Italy
| | - Amedeo Terzi
- UOS Transplantation Surgery, Asst Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Carlo Pace Napoleone
- Pediatric Cardiac Surgery and Congenital Cardiopathies Unit, Regina Margherita Children's Hospital, Azienda Ospedaliera Città Della Salute E Della Scienza Di Torino, Turin, Italy
| | | | - Luca Ragni
- Paediatric Cardiology and ACHD Unit, S. Orsola, Malpighi Hospital, Bologna, Italy
| | - Luca Dello Strologo
- Renal Transplant Unit. Bambino Gesù Children's Research Hospital IRCCS, Rome, Italy
| | - Elisa Benetti
- Pediatric Nephrology, Dialysis and Transplant Unit, Department of Women's and Children's Health, Padua University Hospital, Padua, Italy
| | - Iris Fontana
- Azienda Ospedaliera Universitaria San Martino, Genoa, Italy
| | - Sara Testa
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Licia Peruzzi
- Pediatric Nephrology Unit, Regina Margherita Children's Hospital, Azienda Ospedaliera Universitaria Città Della Salute E Della Scienza Di Torino, Turin, Italy
| | - Adele Mitrotti
- Azienda Ospedaliera, Universitaria Policlinico Di Bari, Bari, Italy
| | | | - Giorgia Comai
- Nephrology, Dialysis and Kidney Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Eliana Gotti
- Unit of Nephrology, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Marco Schiavon
- Thoracic Surgery and Lung Transplant Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University Hospital of Padua, Padua, Italy
| | - Massimo Boffini
- Heart and Lung Transplant Center, Cardiac Surgery Division, Surgical Sciences Department, University of Torino, Torino, Italy
| | | | - Alessandro Bertani
- Division of Thoracic Surgery and Lung Transplantation, Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT, Palermo, Italy
| | - Domenico Pinelli
- Department of Organ Failure and Transplantation, ASST Giovanni XXIII, Bergamo, Italy
| | | | - Camilla Poggi
- Department of Thoracic Surgery, Policlinico Umberto I Hospital, University of Rome Sapienza, Rome, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy. .,Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria Città Della Salute E Della Scienza Di Torino, Torino, Italy.
| | - Massimo Cardillo
- National Transplant Center, Istituto Superiore Di Sanità, Roma, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy.,Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria Città Della Salute E Della Scienza Di Torino, Torino, Italy
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Sheng X, Guan Y, Ma Z, Wu J, Liu H, Qiu C, Vitale S, Miao Z, Seasock MJ, Palmer M, Shin MK, Duffin KL, Pullen SS, Edwards TL, Hellwege JN, Hung AM, Li M, Voight BF, Coffman TM, Brown CD, Susztak K. Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. Nat Genet 2021; 53:1322-1333. [PMID: 34385711 PMCID: PMC9338440 DOI: 10.1038/s41588-021-00909-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The functional interpretation of genome-wide association studies (GWAS) is challenging due to the cell-type-dependent influences of genetic variants. Here, we generated comprehensive maps of expression quantitative trait loci (eQTLs) for 659 microdissected human kidney samples and identified cell-type-eQTLs by mapping interactions between cell type abundances and genotypes. By partitioning heritability using stratified linkage disequilibrium score regression to integrate GWAS with single-cell RNA sequencing and single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing data, we prioritized proximal tubules for kidney function and endothelial cells and distal tubule segments for blood pressure pathogenesis. Bayesian colocalization analysis nominated more than 200 genes for kidney function and hypertension. Our study clarifies the mechanism of commonly used antihypertensive and renal-protective drugs and identifies drug repurposing opportunities for kidney disease.
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Affiliation(s)
- Xin Sheng
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuting Guan
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ziyuan Ma
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Junnan Wu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chengxiang Qiu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Vitale
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhen Miao
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew J Seasock
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Palmer
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Kevin L Duffin
- Eli Lilly and Company Lilly Corporate Center, Indianapolis, IN, USA
| | - Steven S Pullen
- Department of Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adriana M Hung
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingyao Li
- Department of Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F Voight
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas M Coffman
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | | | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA.
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
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217
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Gibson J, Fieldhouse R, Chan MM, Sadeghi-Alavijeh O, Burnett L, Izzi V, Persikov AV, Gale DP, Storey H, Savige J. Prevalence Estimates of Predicted Pathogenic COL4A3-COL4A5 Variants in a Population Sequencing Database and Their Implications for Alport Syndrome. J Am Soc Nephrol 2021; 32:2273-2290. [PMID: 34400539 PMCID: PMC8729840 DOI: 10.1681/asn.2020071065] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 05/05/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The reported prevalence of Alport syndrome varies from one in 5000 to one in 53,000 individuals. This study estimated the frequencies of predicted pathogenic COL4A3-COL4A5 variants in sequencing databases of populations without known kidney disease. METHODS Predicted pathogenic variants were identified using filtering steps based on the ACMG/AMP criteria, which considered collagen IV α3-α5 position 1 Gly to be critical domains. The population frequencies of predicted pathogenic COL4A3-COL4A5 variants were then determined per mean number of sequenced alleles. Population frequencies for compound heterozygous and digenic combinations were calculated from the results for heterozygous variants. RESULTS COL4A3-COL4A5 variants resulting in position 1 Gly substitutions were confirmed to be associated with hematuria (for each, P<0.001). Predicted pathogenic COL4A5 variants were found in at least one in 2320 individuals. p.(Gly624Asp) represented nearly half (16 of 33, 48%) of the variants in Europeans. Most COL4A5 variants (54 of 59, 92%) had a biochemical feature that potentially mitigated the clinical effect. The predicted pathogenic heterozygous COL4A3 and COL4A4 variants affected one in 106 of the population, consistent with the finding of thin basement membrane nephropathy in normal donor kidney biopsy specimens. Predicted pathogenic compound heterozygous variants occurred in one in 88,866 individuals, and digenic variants in at least one in 44,793. CONCLUSIONS The population frequencies for Alport syndrome are suggested by the frequencies of predicted pathogenic COL4A3-COL4A5 variants, but must be adjusted for the disease penetrance of individual variants and for the likelihood of already diagnosed disease and non-Gly substitutions. Disease penetrance may depend on other genetic and environmental factors.
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Affiliation(s)
- Joel Gibson
- The University of Melbourne Department of Medicine, Melbourne Health and Northern Health, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Rachel Fieldhouse
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Melanie M.Y. Chan
- Department of Renal Medicine, University College London, London, United Kingdom,Genomics England, Queen Mary University of London, London, United Kingdom
| | - Omid Sadeghi-Alavijeh
- Department of Renal Medicine, University College London, London, United Kingdom,Genomics England, Queen Mary University of London, London, United Kingdom
| | - Leslie Burnett
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Valerio Izzi
- Center for Cell-Matrix Research and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anton V. Persikov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Daniel P. Gale
- Department of Renal Medicine, University College London, London, United Kingdom,Genomics England, Queen Mary University of London, London, United Kingdom
| | - Helen Storey
- Molecular Genetics, Viapath Laboratories, Guy’s Hospital, London, United Kingdom
| | - Judy Savige
- The University of Melbourne Department of Medicine, Melbourne Health and Northern Health, Royal Melbourne Hospital, Parkville, Victoria, Australia
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218
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Mallett AJ, Knoers N, Sayer J, Stark Z. Clinical versus research genomics in kidney disease. Nat Rev Nephrol 2021; 17:570-571. [PMID: 33958773 DOI: 10.1038/s41581-021-00436-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia. .,College of Medicine and Dentistry, James Cook University, Townsville, Australia. .,Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Australia. .,KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia.
| | - Nine Knoers
- Department of Genetics, University Medical Centre Groningen, Groningen, Netherlands
| | - John Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Renal Services, The Newcastle Upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, UK.,National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
| | - Zornitza Stark
- KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia. .,Murdoch Children's Research Institute, Melbourne, Australia. .,Department of Paediatrics, University of Melbourne, Melbourne, Australia.
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219
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Pinto E Vairo F, Prochnow C, Kemppainen JL, Lisi EC, Steyermark JM, Kruisselbrink TM, Pichurin PN, Dhamija R, Hager MM, Albadri S, Cornell LD, Lazaridis KN, Klee EW, Senum SR, El Ters M, Amer H, Baudhuin LM, Moyer AM, Keddis MT, Zand L, Sas DJ, Erickson SB, Fervenza FC, Lieske JC, Harris PC, Hogan MC. Genomics Integration Into Nephrology Practice. Kidney Med 2021; 3:785-798. [PMID: 34746741 PMCID: PMC8551494 DOI: 10.1016/j.xkme.2021.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RATIONALE & OBJECTIVE The etiology of kidney disease remains unknown in many individuals with chronic kidney disease (CKD). We created the Mayo Clinic Nephrology Genomics Clinic to improve our ability to integrate genomic and clinical data to identify the etiology of unexplained CKD. STUDY DESIGN Retrospective study. SETTING & PARTICIPANTS An essential component of our program is the Nephrology Genomics Board which consists of nephrologists, geneticists, pathologists, translational omics scientists, and trainees who interpret the patient's clinical and genetic data. Since September 2016, the Board has reviewed 163 cases (15 cystic, 100 glomerular, 6 congenital anomalies of kidney and urinary tract (CAKUT), 20 stones, 15 tubulointerstitial, and 13 other). ANALYTICAL APPROACH Testing was performed with targeted panels, single gene analysis, or analysis of kidney-related genes from exome sequencing. Variant classification was obtained based on the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines. RESULTS A definitive genetic diagnosis was achieved for 50 families (30.7%). The highest diagnostic yield was obtained in individuals with tubulointerstitial diseases (53.3%), followed by congenital anomalies of the kidney and urological tract (33.3%), glomerular (31%), cysts (26.7%), stones (25%), and others (15.4%). A further 20 (12.3%) patients had variants of interest, and variant segregation, and research activities (exome, genome, or transcriptome sequencing) are ongoing for 44 (40%) unresolved families. LIMITATIONS Possible overestimation of diagnostic rate due to inclusion of individuals with variants with evidence of pathogenicity but classified as of uncertain significance by the clinical laboratory. CONCLUSIONS Integration of genomic and research testing and multidisciplinary evaluation in a nephrology cohort with CKD of unknown etiology or suspected monogenic disease provided a diagnosis in a third of families. These diagnoses had prognostic implications, and often changes in management were implemented.
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Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Carri Prochnow
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | | | - Emily C Lisi
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Joan M Steyermark
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Rhadika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, Arizona
| | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, Arizona
| | - Sam Albadri
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lynn D Cornell
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Sarah R Senum
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Mireille El Ters
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Hatem Amer
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Linnea M Baudhuin
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ann M Moyer
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mira T Keddis
- Division of Nephrology, Mayo Clinic, Scottsdale, Arizona
| | - Ladan Zand
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - David J Sas
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Stephen B Erickson
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | | | - John C Lieske
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Peter C Harris
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Marie C Hogan
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
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220
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Granhøj J, Tougaard B, Lildballe DL, Rasmussen M. Family History is Important to Identify Patients with Monogenic Causes of Adult-Onset Chronic Kidney Disease. Nephron Clin Pract 2021; 146:49-57. [PMID: 34515170 DOI: 10.1159/000518175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Monogenic causes of chronic kidney disease (CKD) are more prevalent in adults than previously thought, as causative gene variants are found in almost 10% of unselected patients with CKD. Even so, genetic testing in patients with adult-onset CKD is uncommon in clinical practice and the optimal criteria for patient selection remain unclear. A family history of kidney disease emerges as one marker associated with a high diagnostic yield of genetic testing. We present 3 cases of adult-onset CKD with underlying monogenic causes exemplifying different modes of inheritance. Case 1 is a 60-year-old male with slowly progressive CKD initially ascribed to hypertension and diabetes despite a family history with several affected first-degree relatives. A pathogenic MUC1 variant was found, and thus we identified the first Danish family of MUC1-associated autosomal dominant tubulointerstitial kidney disease. Case 2 is a 40-year-old female with nephrocalcinosis, nephrolithiasis, and unexplainable hypercalcemia consistent with vitamin D intoxication. The family history indicated autosomal recessive inheritance, and genetic testing revealed 2 pathogenic CYP24A1 variants in compound heterozygous form associated with idiopathic infantile hypercalcemia. Case 3 is a 50-year-old male with microscopic hematuria, proteinuria, and hearing loss. Electron microscopy of renal biopsy showed thin basal membrane syndrome, and the family history indicated X-linked inheritance. A novel missense variant in COL4A5 was identified, suggesting an atypical late-onset form of X-linked Alport syndrome. This case series illustrates the heterogeneous presentations of monogenic kidney disease in adults and emphasizes the importance of family history for initiating genetic testing to identify underlying monogenic causation. Moreover, we discuss the potential impact of genetic diagnostics on patient management and genetic family counseling.
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Affiliation(s)
- Jeff Granhøj
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Birgitte Tougaard
- Department of Nephrology, Aarhus University Hospital, Aarhus, Denmark
| | - Dorte L Lildballe
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Maria Rasmussen
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
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221
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Boyer O, Dorval G, Servais A. The genetics of steroid-resistant nephrotic syndrome in adults. Nephrol Dial Transplant 2021; 36:1600-1602. [PMID: 32040156 DOI: 10.1093/ndt/gfz257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Olivia Boyer
- Néphrologie Pédiatrique, Centre de référence MARHEA, Hôpital Necker-Enfants Malades, APHP, Paris, France.,Inserm U1163, Institut Imagine, Université de Paris, Paris, France
| | - Guillaume Dorval
- Néphrologie Pédiatrique, Centre de référence MARHEA, Hôpital Necker-Enfants Malades, APHP, Paris, France.,Inserm U1163, Institut Imagine, Université de Paris, Paris, France
| | - Aude Servais
- Inserm U1163, Institut Imagine, Université de Paris, Paris, France.,Néphrologie et Transplantation, Centre de référence MARHEA, Hôpital Necker-Enfants Malades, APHP, Paris, France
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222
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Shamshirgaran Y, Jonebring A, Svensson A, Leefa I, Bohlooly-Y M, Firth M, Woollard KJ, Hofherr A, Rogers IM, Hicks R. Rapid target validation in a Cas9-inducible hiPSC derived kidney model. Sci Rep 2021; 11:16532. [PMID: 34400685 PMCID: PMC8368200 DOI: 10.1038/s41598-021-95986-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 12/24/2022] Open
Abstract
Recent advances in induced pluripotent stem cells (iPSCs), genome editing technologies and 3D organoid model systems highlight opportunities to develop new in vitro human disease models to serve drug discovery programs. An ideal disease model would accurately recapitulate the relevant disease phenotype and provide a scalable platform for drug and genetic screening studies. Kidney organoids offer a high cellular complexity that may provide greater insights than conventional single-cell type cell culture models. However, genetic manipulation of the kidney organoids requires prior generation of genetically modified clonal lines, which is a time and labor consuming procedure. Here, we present a methodology for direct differentiation of the CRISPR-targeted cell pools, using a doxycycline-inducible Cas9 expressing hiPSC line for high efficiency editing to eliminate the laborious clonal line generation steps. We demonstrate the versatile use of genetically engineered kidney organoids by targeting the autosomal dominant polycystic kidney disease (ADPKD) genes: PKD1 and PKD2. Direct differentiation of the respective knockout pool populations into kidney organoids resulted in the formation of cyst-like structures in the tubular compartment. Our findings demonstrated that we can achieve > 80% editing efficiency in the iPSC pool population which resulted in a reliable 3D organoid model of ADPKD. The described methodology may provide a platform for rapid target validation in the context of disease modeling.
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Affiliation(s)
- Yasaman Shamshirgaran
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Jonebring
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Svensson
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Isabelle Leefa
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kevin J Woollard
- Bioscience Renal, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Alexis Hofherr
- Early Clinical Development, Research and Early Development, Cardiovascular, Renal and Metabolic, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ian M Rogers
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Soham & Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, M5G 2C4, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, M5G1E2, Canada
| | - Ryan Hicks
- BioPharmaceuticals R&D Cell Therapy, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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223
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Urine peptidome analysis in cardiorenal syndrome reflects molecular processes. Sci Rep 2021; 11:16219. [PMID: 34376786 PMCID: PMC8355128 DOI: 10.1038/s41598-021-95695-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
The cardiorenal syndrome (CRS) is defined as the confluence of heart-kidney dysfunction. This study investigates the molecular differences at the level of the urinary peptidome between CRS patients and controls and their association to disease pathophysiology. The urinary peptidome of CRS patients (n = 353) was matched for age and sex with controls (n = 356) at a 1:1 ratio. Changes in the CRS peptidome versus controls were identified after applying the Mann-Whitney test, followed by correction for multiple testing. Proteasix tool was applied to investigate predicted proteases involved in CRS-associated peptide generation. Overall, 559 differentially excreted urinary peptides were associated with CRS patients. Of these, 193 peptides were specifically found in CRS when comparing with heart failure and chronic kidney disease urinary peptide profiles. Proteasix predicted 18 proteases involved in > 1% of proteolytic cleavage events including multiple forms of MMPs, proprotein convertases, cathepsins and kallikrein 4. Forty-four percent of the cleavage events were produced by 3 proteases including MMP13, MMP9 and MMP2. Pathway enrichment analysis supported that ECM-related pathways, fibrosis and inflammation were represented. Collectively, our study describes the changes in urinary peptides of CRS patients and potential proteases involved in their generation, laying the basis for further validation.
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224
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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225
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Genetic testing in ambulatory cardiology clinics reveals high rate of findings with clinical management implications. Genet Med 2021; 23:2404-2414. [PMID: 34363016 DOI: 10.1038/s41436-021-01294-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Cardiovascular disease (CVD) is the leading cause of death in adults in the United States, yet the benefits of genetic testing are not universally accepted. METHODS We developed the "HeartCare" panel of genes associated with CVD, evaluating high-penetrance Mendelian conditions, coronary artery disease (CAD) polygenic risk, LPA gene polymorphisms, and specific pharmacogenetic (PGx) variants. We enrolled 709 individuals from cardiology clinics at Baylor College of Medicine, and samples were analyzed in a CAP/CLIA-certified laboratory. Results were returned to the ordering physician and uploaded to the electronic medical record. RESULTS Notably, 32% of patients had a genetic finding with clinical management implications, even after excluding PGx results, including 9% who were molecularly diagnosed with a Mendelian condition. Among surveyed physicians, 84% reported medical management changes based on these results, including specialist referrals, cardiac tests, and medication changes. LPA polymorphisms and high polygenic risk of CAD were found in 20% and 9% of patients, respectively, leading to diet, lifestyle, and other changes. Warfarin and simvastatin pharmacogenetic variants were present in roughly half of the cohort. CONCLUSION Our results support the use of genetic information in routine cardiovascular health management and provide a roadmap for accompanying research.
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226
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Pinto E Vairo F, Kemppainen JL, Lieske JC, Harris PC, Hogan MC. Establishing a nephrology genetic clinic. Kidney Int 2021; 100:254-259. [PMID: 34294204 DOI: 10.1016/j.kint.2021.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA.
| | | | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Marie C Hogan
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
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227
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Wright MB, Varona Santos J, Kemmer C, Maugeais C, Carralot JP, Roever S, Molina J, Ducasa GM, Mitrofanova A, Sloan A, Ahmad A, Pedigo C, Ge M, Pressly J, Barisoni L, Mendez A, Sgrignani J, Cavalli A, Merscher S, Prunotto M, Fornoni A. Compounds targeting OSBPL7 increase ABCA1-dependent cholesterol efflux preserving kidney function in two models of kidney disease. Nat Commun 2021; 12:4662. [PMID: 34341345 PMCID: PMC8329197 DOI: 10.1038/s41467-021-24890-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/06/2021] [Indexed: 02/08/2023] Open
Abstract
Impaired cellular cholesterol efflux is a key factor in the progression of renal, cardiovascular, and autoimmune diseases. Here we describe a class of 5-arylnicotinamide compounds, identified through phenotypic drug discovery, that upregulate ABCA1-dependent cholesterol efflux by targeting Oxysterol Binding Protein Like 7 (OSBPL7). OSBPL7 was identified as the molecular target of these compounds through a chemical biology approach, employing a photoactivatable 5-arylnicotinamide derivative in a cellular cross-linking/immunoprecipitation assay. Further evaluation of two compounds (Cpd A and Cpd G) showed that they induced ABCA1 and cholesterol efflux from podocytes in vitro and normalized proteinuria and prevented renal function decline in mouse models of proteinuric kidney disease: Adriamycin-induced nephropathy and Alport Syndrome. In conclusion, we show that small molecule drugs targeting OSBPL7 reveal an alternative mechanism to upregulate ABCA1, and may represent a promising new therapeutic strategy for the treatment of renal diseases and other disorders of cellular cholesterol homeostasis.
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Affiliation(s)
- Matthew B Wright
- Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Javier Varona Santos
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Christian Kemmer
- Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Cyrille Maugeais
- Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jean-Philippe Carralot
- Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Stephan Roever
- Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Judith Molina
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - G Michelle Ducasa
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Alla Mitrofanova
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Alexis Sloan
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Anis Ahmad
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Christopher Pedigo
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Mengyuan Ge
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jeffrey Pressly
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Laura Barisoni
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Armando Mendez
- Diabetes Research Institute, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandra Merscher
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Marco Prunotto
- Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
| | - Alessia Fornoni
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA.
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA.
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228
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Savige J, Storey H, Watson E, Hertz JM, Deltas C, Renieri A, Mari F, Hilbert P, Plevova P, Byers P, Cerkauskaite A, Gregory M, Cerkauskiene R, Ljubanovic DG, Becherucci F, Errichiello C, Massella L, Aiello V, Lennon R, Hopkinson L, Koziell A, Lungu A, Rothe HM, Hoefele J, Zacchia M, Martic TN, Gupta A, van Eerde A, Gear S, Landini S, Palazzo V, al-Rabadi L, Claes K, Corveleyn A, Van Hoof E, van Geel M, Williams M, Ashton E, Belge H, Ars E, Bierzynska A, Gangemi C, Lipska-Ziętkiewicz BS. Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria. Eur J Hum Genet 2021; 29:1186-1197. [PMID: 33854215 PMCID: PMC8384871 DOI: 10.1038/s41431-021-00858-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/13/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
The recent Chandos House meeting of the Alport Variant Collaborative extended the indications for screening for pathogenic variants in the COL4A5, COL4A3 and COL4A4 genes beyond the classical Alport phenotype (haematuria, renal failure; family history of haematuria or renal failure) to include persistent proteinuria, steroid-resistant nephrotic syndrome, focal and segmental glomerulosclerosis (FSGS), familial IgA glomerulonephritis and end-stage kidney failure without an obvious cause. The meeting refined the ACMG criteria for variant assessment for the Alport genes (COL4A3-5). It identified 'mutational hotspots' (PM1) in the collagen IV α5, α3 and α4 chains including position 1 Glycine residues in the Gly-X-Y repeats in the intermediate collagenous domains; and Cysteine residues in the carboxy non-collagenous domain (PP3). It considered that 'well-established' functional assays (PS3, BS3) were still mainly research tools but sequencing and minigene assays were commonly used to confirm splicing variants. It was not possible to define the Minor Allele Frequency (MAF) threshold above which variants were considered Benign (BA1, BS1), because of the different modes of inheritances of Alport syndrome, and the occurrence of hypomorphic variants (often Glycine adjacent to a non-collagenous interruption) and local founder effects. Heterozygous COL4A3 and COL4A4 variants were common 'incidental' findings also present in normal reference databases. The recognition and interpretation of hypomorphic variants in the COL4A3-COL4A5 genes remains a challenge.
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Affiliation(s)
- Judy Savige
- grid.1008.90000 0001 2179 088XDepartment of Medicine (MH and NH), The University of Melbourne, Parkville, VIC Australia
| | - Helen Storey
- grid.239826.40000 0004 0391 895XMolecular Genetics, Viapath Laboratories, Guy’s Hospital, London, UK
| | - Elizabeth Watson
- Elizabeth Watson, South West Genomic Laboratory Hub, North Bristol Trust, Bristol, UK
| | - Jens Michael Hertz
- grid.7143.10000 0004 0512 5013Jens Michael Hertz, Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Constantinos Deltas
- grid.6603.30000000121167908Center of Excellence in Biobanking and Biomedical Research and Molecule Medicine Center, University of Cyprus, Nicosia, Cyprus
| | - Alessandra Renieri
- grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Institute de Pathologie et de Genetique ASBL, Departement de Biologie Moleculaire, Gosselies, Belgium
| | - Pascale Hilbert
- Institute de Pathologie et de Genetique ASBL, Departement de Biologie Moleculaire, Gosselies, Belgium
| | - Pavlina Plevova
- grid.412727.50000 0004 0609 0692Department of Medical Genetics, and Department of Biomedical Sciences, University Hospital of Ostrava, Ostrava, Czech Republic
| | - Peter Byers
- grid.34477.330000000122986657Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, WA USA
| | - Agne Cerkauskaite
- grid.6441.70000 0001 2243 2806Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Martin Gregory
- grid.223827.e0000 0001 2193 0096Division of Nephrology, Department of Medicine, University of Utah Health, Salt Lake City, UT USA
| | - Rimante Cerkauskiene
- grid.6441.70000 0001 2243 2806Clinic of Pediatrics, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Danica Galesic Ljubanovic
- grid.412095.b0000 0004 0631 385XDepartment of Pathology, University of Zagreb, School of Medicine, Dubrava University Hospital, Zagreb, Croatia
| | - Francesca Becherucci
- grid.411477.00000 0004 1759 0844Nephrology Unit and Meyer Children’s University Hospital, Firenze, Italy
| | - Carmela Errichiello
- grid.411477.00000 0004 1759 0844Nephrology Unit and Meyer Children’s University Hospital, Firenze, Italy
| | - Laura Massella
- grid.414125.70000 0001 0727 6809Division of Nephrology and Dialysis, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Valeria Aiello
- grid.6292.f0000 0004 1757 1758Department of Experimental Diagnostic and Specialty Medicine (DIMES), Nephrology, Dialysis and Renal Transplant Unit, S. Orsola Hospital, University of Bologna, Bologna, Italy
| | - Rachel Lennon
- grid.5379.80000000121662407Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Louise Hopkinson
- grid.5379.80000000121662407Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Ania Koziell
- grid.13097.3c0000 0001 2322 6764School of Immunology and Microbial Sciences, Faculty of Life Sciences, King’s College London, London, UK
| | - Adrian Lungu
- grid.415180.90000 0004 0540 9980Fundeni Clinical Institute, Pediatric Nephrology Department, Bucharest, Romania
| | | | - Julia Hoefele
- grid.6936.a0000000123222966Institute of Human Genetics, Technical University of Munich, München, Germany
| | | | - Tamara Nikuseva Martic
- grid.4808.40000 0001 0657 4636Department of Biology, School of Medicine University of Zagreb, Zagreb, Croatia
| | - Asheeta Gupta
- grid.415246.00000 0004 0399 7272Birmingham Children’s Hospital, Birmingham, UK
| | - Albertien van Eerde
- grid.5477.10000000120346234Departments of Genetics and Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | | | - Samuela Landini
- grid.8404.80000 0004 1757 2304Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Viviana Palazzo
- grid.411477.00000 0004 1759 0844Medical Genetics Unit, Meyer Children’s University Hospital, Florence, Italy
| | - Laith al-Rabadi
- grid.223827.e0000 0001 2193 0096Health Sciences Centre, University of UTAH, Salt Lake City, UT USA
| | - Kathleen Claes
- grid.410569.f0000 0004 0626 3338Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- grid.410569.f0000 0004 0626 3338Center for Human Genetics, University Hospitals and KU Leuven, Leuven, Belgium
| | - Evelien Van Hoof
- grid.410569.f0000 0004 0626 3338Center for Human Genetics, University Hospitals and KU Leuven, Leuven, Belgium
| | - Micheel van Geel
- grid.412966.e0000 0004 0480 1382Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maggie Williams
- grid.416201.00000 0004 0417 1173Bristol Genetics Laboratory Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Emma Ashton
- grid.420468.cNorth East Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Hendica Belge
- grid.10417.330000 0004 0444 9382Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elisabeth Ars
- grid.7080.f0000 0001 2296 0625Inherited Kidney Disorders, Fundacio Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Agnieszka Bierzynska
- grid.5337.20000 0004 1936 7603Bristol Renal Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Concetta Gangemi
- grid.411475.20000 0004 1756 948XDivision of Nephrology and Dialysis, University Hospital of Verona, Verona, Italy
| | - Beata S. Lipska-Ziętkiewicz
- grid.11451.300000 0001 0531 3426Centre for Rare Diseases, and Clinical Genetics Unit, Medical University of Gdansk, Gdansk, Poland
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229
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García-Foncillas J, Argente J, Bujanda L, Cardona V, Casanova B, Fernández-Montes A, Horcajadas JA, Iñiguez A, Ortiz A, Pablos JL, Pérez Gómez MV. Milestones of Precision Medicine: An Innovative, Multidisciplinary Overview. Mol Diagn Ther 2021; 25:563-576. [PMID: 34331269 DOI: 10.1007/s40291-021-00544-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2021] [Indexed: 12/11/2022]
Abstract
Although the concept of precision medicine, in which healthcare is tailored to the molecular and clinical characteristics of each individual, is not new, its implementation in clinical practice has been heterogenous. In some medical specialties, precision medicine has gone from being just a promise to a reality that achieves better patient outcomes. This is a fact if we consider, for example, the great advances made in the genetic diagnosis and subsequent treatment of countless hereditary diseases, such as cystic fibrosis, which have improved the life expectancy of many of the affected children. In the field of oncology, the development of targeted therapies has prolonged the survival of patients with breast, lung, colorectal, melanoma, and hematological malignancies. In other disciplines, clinical milestones are perhaps less well known, but no less important. The current challenge is to expand and generalize the use of technologies that are central to precision medicine, such as massively parallel sequencing, to improve the management (prevention and treatment) of complex conditions such as cardiovascular, kidney, or autoimmune diseases. This process requires investment in specialized expertise, multidisciplinary collaboration, and the nationwide organization of genetic laboratories for diagnosis of specific diseases.
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Affiliation(s)
- Jesús García-Foncillas
- Department of Oncology, Oncohealth Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain. .,Medical Oncology Department, University Hospital Fundación Jiménez Díaz-Universidad Autonoma de Madrid, Madrid, Spain.
| | - Jesús Argente
- Department of Endocrinology, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain.,Department of Pediatrics, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universidad del País Vasco (UPV/EHU), San Sebastian, Spain
| | - Victoria Cardona
- Allergy Section, Department of Internal Medicine, Hospital Vall d'Hebron, Barcelona, Spain.,ARADyAL Research Network, Barcelona, Spain
| | - Bonaventura Casanova
- Neuroimmunology Unit, La Fe University and Polytechnic Hospital, Valencia, Spain.,Department of Medicine, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Ana Fernández-Montes
- Medical Oncology, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | - Andrés Iñiguez
- Department of Cardiology, Hospital Álvaro Cunqueiro-Complejo Hospitalario Universitario, Vigo, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz-UAM, Madrid, Spain
| | - José L Pablos
- Grupo de Enfermedades Inflamatorias y Autoinmunes, Instituto de Investigación Hospital 12 de Octubre, Madrid, Spain.,Servicio de Reumatología, Hospital 12 de Octubre, Universidad Complutense de Madrid, Madrid, Spain
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230
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Leveson J, Oates TM. Exome sequencing as a diagnostic tool in chronic kidney disease: ready for clinical application? Curr Opin Nephrol Hypertens 2021; 29:608-612. [PMID: 32889981 DOI: 10.1097/mnh.0000000000000639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PURPOSE OF REVIEW Patients who develop chronic kidney disease at an early age, or from an uncertain cause, may benefit from genomic sequencing approaches to define causative mutations and inform subsequent management. RECENT FINDINGS Whole-exome sequencing has been used to investigate the molecular genetic variants associated with chronic kidney disease in both specific phenotypes such as steroid-resistant nephrotic syndrome, and in large cohorts of patients not selected for a certain diagnosis. These studies have shown that whole-exome sequencing is able to find a genetic variant in a significant number of patients. Often these variants may reclassify the diagnosis, the variants may have ramifications for the patient's management, and some variants may be previously undescribed in the literature. SUMMARY Whole-exome sequencing is likely to become widely used in the investigation of chronic kidney disease, especially in certain phenotypes.
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Affiliation(s)
- James Leveson
- Departments of Nephrology and General Medicine, Royal London Hospital, Barts Health NHS Trust, London, UK
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231
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Stanzick KJ, Li Y, Schlosser P, Gorski M, Wuttke M, Thomas LF, Rasheed H, Rowan BX, Graham SE, Vanderweff BR, Patil SB, Robinson-Cohen C, Gaziano JM, O'Donnell CJ, Willer CJ, Hallan S, Åsvold BO, Gessner A, Hung AM, Pattaro C, Köttgen A, Stark KJ, Heid IM, Winkler TW. Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals. Nat Commun 2021; 12:4350. [PMID: 34272381 PMCID: PMC8285412 DOI: 10.1038/s41467-021-24491-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
Genes underneath signals from genome-wide association studies (GWAS) for kidney function are promising targets for functional studies, but prioritizing variants and genes is challenging. By GWAS meta-analysis for creatinine-based estimated glomerular filtration rate (eGFR) from the Chronic Kidney Disease Genetics Consortium and UK Biobank (n = 1,201,909), we expand the number of eGFRcrea loci (424 loci, 201 novel; 9.8% eGFRcrea variance explained by 634 independent signal variants). Our increased sample size in fine-mapping (n = 1,004,040, European) more than doubles the number of signals with resolved fine-mapping (99% credible sets down to 1 variant for 44 signals, ≤5 variants for 138 signals). Cystatin-based eGFR and/or blood urea nitrogen association support 348 loci (n = 460,826 and 852,678, respectively). Our customizable tool for Gene PrioritiSation reveals 23 compelling genes including mechanistic insights and enables navigation through genes and variants likely relevant for kidney function in human to help select targets for experimental follow-up.
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Affiliation(s)
- Kira J Stanzick
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Laurent F Thomas
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway
| | - Humaira Rasheed
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Bryce X Rowan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Brett R Vanderweff
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Snehal B Patil
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Cassiane Robinson-Cohen
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Medical Center, Division of Nephrology and Hypertension, Vanderbilt Center for Kidney Disease and Integrated Program for Acute Kidney Injury Research, and Vanderbilt Precision Nephrology Program Nashville, Nashville, TN, USA
| | - John M Gaziano
- Massachusetts Area Veterans Epidemiology Research and Information Center (MAVERIC), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Internal Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stein Hallan
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn Olav Åsvold
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Andre Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Adriana M Hung
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Medical Center, Division of Nephrology and Hypertension, Vanderbilt Center for Kidney Disease and Integrated Program for Acute Kidney Injury Research, and Vanderbilt Precision Nephrology Program Nashville, Nashville, TN, USA
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.
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232
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Knoers N, Antignac C, Bergmann C, Dahan K, Giglio S, Heidet L, Lipska-Ziętkiewicz BS, Noris M, Remuzzi G, Vargas-Poussou R, Schaefer F. Genetic testing in the diagnosis of chronic kidney disease: recommendations for clinical practice. Nephrol Dial Transplant 2021; 37:239-254. [PMID: 34264297 PMCID: PMC8788237 DOI: 10.1093/ndt/gfab218] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 11/20/2022] Open
Abstract
The overall diagnostic yield of massively parallel sequencing–based tests in patients with chronic kidney disease (CKD) is 30% for paediatric cases and 6–30% for adult cases. These figures should encourage nephrologists to frequently use genetic testing as a diagnostic means for their patients. However, in reality, several barriers appear to hinder the implementation of massively parallel sequencing–based diagnostics in routine clinical practice. In this article we aim to support the nephrologist to overcome these barriers. After a detailed discussion of the general items that are important to genetic testing in nephrology, namely genetic testing modalities and their indications, clinical information needed for high-quality interpretation of genetic tests, the clinical benefit of genetic testing and genetic counselling, we describe each of these items more specifically for the different groups of genetic kidney diseases and for CKD of unknown origin.
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Affiliation(s)
- Nine Knoers
- Department of Genetics, University Medical Centre Groningen, The Netherlands
| | - Corinne Antignac
- Institut Imagine (Inserm U1163) et Département de Génétique, 24 bd du Montparnasse, 75015, Paris, France
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany.,Department of Medicine, Nephrology, University Hospital Freiburg, Germany
| | - Karin Dahan
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Avenue Hippocrate, 10, B-1200, Brussels, Belgium.,Center of Human Genetics, Institut de Pathologie et de Génétique, Avenue Lemaître, 25, B-6041, Gosselies, Belgium
| | - Sabrina Giglio
- Unit of Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy.,Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Laurence Heidet
- Service de Néphrologie Pédiatrique, Hôpital Universitaire Necker-Enfants Malades, 149 rue de Sèvres, 75743, Paris, Cedex 15, France
| | - Beata S Lipska-Ziętkiewicz
- BSL-Z - ORCID 0000-0002-4169-9685, Centre for Rare Diseases, Medical University of Gdansk, Gdansk, Poland.,Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Marina Noris
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Aldo & Cele Daccò Clinical Research Center for Rare Diseases, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Aldo & Cele Daccò Clinical Research Center for Rare Diseases, Bergamo, Italy
| | - Rosa Vargas-Poussou
- Département de Génétique, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75908, Paris, Cedex 15, France
| | - Franz Schaefer
- Division of Pediatric Nephrology, Center for Pediatrics and Adolescent Medicine, University of Heidelberg, Germany
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233
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Daehn IS, Duffield JS. The glomerular filtration barrier: a structural target for novel kidney therapies. Nat Rev Drug Discov 2021; 20:770-788. [PMID: 34262140 PMCID: PMC8278373 DOI: 10.1038/s41573-021-00242-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 12/19/2022]
Abstract
Loss of normal kidney function affects more than 10% of the population and contributes to morbidity and mortality. Kidney diseases are currently treated with immunosuppressive agents, antihypertensives and diuretics with partial but limited success. Most kidney disease is characterized by breakdown of the glomerular filtration barrier (GFB). Specialized podocyte cells maintain the GFB, and structure-function experiments and studies of intercellular communication between the podocytes and other GFB cells, combined with advances from genetics and genomics, have laid the groundwork for a new generation of therapies that directly intervene at the GFB. These include inhibitors of apolipoprotein L1 (APOL1), short transient receptor potential channels (TRPCs), soluble fms-like tyrosine kinase 1 (sFLT1; also known as soluble vascular endothelial growth factor receptor 1), roundabout homologue 2 (ROBO2), endothelin receptor A, soluble urokinase plasminogen activator surface receptor (suPAR) and substrate intermediates for coenzyme Q10 (CoQ10). These molecular targets converge on two key components of GFB biology: mitochondrial function and the actin-myosin contractile machinery. This Review discusses therapies and developments focused on maintaining GFB integrity, and the emerging questions in this evolving field.
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Affiliation(s)
- Ilse S Daehn
- Department of Medicine, Division of Nephrology, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jeremy S Duffield
- Research and Development, Prime Medicine, Cambridge, MA, USA. .,Department of Medicine, University of Washington, Seattle, WA, USA. .,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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234
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Savige J, Harraka P. Pathogenic Variants in the Genes Affected in Alport Syndrome (COL4A3-COL4A5) and Their Association With Other Kidney Conditions: A Review. Am J Kidney Dis 2021; 78:857-864. [PMID: 34245817 DOI: 10.1053/j.ajkd.2021.04.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/23/2021] [Indexed: 01/15/2023]
Abstract
Massively Parallel Sequencing identifies pathogenic variants in the genes affected in Alport syndrome (COL4A3 - COL4A5) in up to 30 % of individuals with focal and segmental glomerulosclerosis (FSGS), 10 % of those with kidney failure of unknown cause and 20 % with familial IgA glomerulonephritis. FSGS associated with COL4A3 - COL4A5 variants is usually present by kidney failure onset and may develop because the abnormal glomerular membranes result in podocyte loss and secondary hyperfiltration. The association of COL4A3 - COL4A5 variants with kidney failure or IgA glomerulonephritis may be coincidental and not pathogenic. However, since some of these variants occur more often than they should by chance, some may be pathogenic. COL4A3 - COL4A5 variants are sometimes also found in cystic kidney diseases after autosomal dominant polycystic kidney disease (ADPKD) has been excluded. COL4A3 - COL4A5 variants should be suspected in individuals with FSGS, kidney failure of unknown cause, or familial IgA glomerulonephritis, especially where there is persistent haematuria, and a family history of haematuria or kidney failure.
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Affiliation(s)
- Judy Savige
- The University of Melbourne Department of Medicine, Melbourne Health and Northern Health, Royal Melbourne Hospital, Parkville VIC 3050 AUSTRALIA.
| | - Philip Harraka
- The University of Melbourne Department of Medicine, Melbourne Health and Northern Health, Royal Melbourne Hospital, Parkville VIC 3050 AUSTRALIA
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235
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Wang Z, Xu H, Xiang T, Liu D, Xu F, Zhao L, Feng Y, Xu L, Liu J, Fang Y, Liu H, Li R, Hu X, Guan J, Liu L, Feng G, Shen Q, Xu H, Frishman D, Tang W, Guo J, Rao J, Shang W. An accessible insight into genetic findings for transplantation recipients with suspected genetic kidney disease. NPJ Genom Med 2021; 6:57. [PMID: 34215756 PMCID: PMC8253729 DOI: 10.1038/s41525-021-00219-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Determining the etiology of end-stage renal disease (ESRD) constitutes a great challenge in the context of renal transplantation. Evidence is lacking on the genetic findings for adult renal transplant recipients through exome sequencing (ES). Adult patients on kidney transplant waitlist were recruited from 2017 to 2019. Trio-ES was conducted for the families who had multiple affected individuals with nephropathy or clinical suspicion of a genetic kidney disease owing to early onset or extrarenal features. Pathogenic variants were confirmed in 62 from 115 families post sequencing for 421 individuals including 195 health family members as potential living donors. Seventeen distinct genetic disorders were identified confirming the priori diagnosis in 33 (28.7%) families, modified or reclassified the clinical diagnosis in 27 (23.5%) families, and established a diagnosis in two families with ESRD of unknown etiology. In 14.8% of the families, we detected promising variants of uncertain significance in candidate genes associated with renal development or renal disease. Furthermore, we reported the secondary findings of oncogenes in 4.4% of the patients and known single-nucleotide polymorphisms associated with pharmacokinetics in our cohort to predict the drug levels of tacrolimus and mycophenolate. The diagnostic utility of the genetic findings has provided new clinical insight in most families that help with preplanned renal transplantation.
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Affiliation(s)
- Zhigang Wang
- Department of Kidney Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongen Xu
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Tianchao Xiang
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Danhua Liu
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fei Xu
- Department of Kidney Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lixiang Zhao
- Department of Kidney Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yonghua Feng
- Department of Kidney Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Linan Xu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Jialu Liu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Ye Fang
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Huanfei Liu
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ruijun Li
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xinxin Hu
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jingyuan Guan
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Longshan Liu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guiwen Feng
- Department of Kidney Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qian Shen
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Dmitrij Frishman
- Department of Bioinformatics, Technische Universität München, Freising, Germany
| | - Wenxue Tang
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiancheng Guo
- Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China. .,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China. .,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China. .,Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China. .,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Wenjun Shang
- Department of Kidney Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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236
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Quinlan C, Rheault MN. Genetic Basis of Type IV Collagen Disorders of the Kidney. Clin J Am Soc Nephrol 2021; 16:1101-1109. [PMID: 33849932 PMCID: PMC8425620 DOI: 10.2215/cjn.19171220] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The glomerular basement membrane is a vital component of the filtration barrier of the kidney and is primarily composed of a highly structured matrix of type IV collagen. Specific isoforms of type IV collagen, the α3(IV), α4(IV), and α5(IV) isoforms, assemble into trimers that are required for normal glomerular basement membrane function. Disruption or alteration in these isoforms leads to breakdown of the glomerular basement membrane structure and function and can lead to progressive CKD known as Alport syndrome. However, there is wide variability in phenotype among patients with mutations affecting type IV collagen that depends on a complex interplay of sex, genotype, and X-chromosome inactivation. This article reviews the genetic basis of collagen disorders of the kidney as well as potential treatments for these conditions, including direct alteration of the DNA, RNA therapies, and manipulation of collagen proteins.
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Affiliation(s)
- Catherine Quinlan
- Department of Nephrology, Royal Children’s Hospital, Melbourne, Victoria, Australia,Department of Kidney Regeneration, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle N. Rheault
- Division of Pediatric Nephrology, Department of Pediatrics, University of Minnesota Masonic Children’s Hospital, Minneapolis, Minnesota
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237
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Childhood risk factors for adulthood chronic kidney disease. Pediatr Nephrol 2021; 36:1387-1396. [PMID: 32500249 DOI: 10.1007/s00467-020-04611-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/03/2020] [Accepted: 05/11/2020] [Indexed: 12/25/2022]
Abstract
Chronic kidney disease (CKD) is a major public health challenge, affecting as much as 8 to 18% of the world population. Identifying childhood risk factors for future CKD may help clinicians make early diagnoses and initiation of preventive interventions for CKD and its attendant comorbidities as well as monitoring for complications. The purpose of this review is to describe childhood risk factors that may predict development of overt kidney disease later in life. Currently, there are multiple childhood risk factors associated with future onset and progression of CKD. These risk factors can be grouped into five categories: genetic factors (e.g., monogenic or risk alleles), perinatal factors (e.g., low birth weight and prematurity), childhood kidney diseases (e.g., congenital anomalies, glomerular diseases, and renal cystic ciliopathies), childhood onset of chronic conditions (e.g., cancer, diabetes, hypertension, dyslipidemia, and obesity), and different lifestyle factors (e.g., physical activity, diet, and factors related to socioeconomic status). The available published information suggests that the lifelong risk for CKD can be attributed to multiple factors that appear already during childhood. However, results are conflicting on the effects of childhood physical activity, diet, and dyslipidemia on future renal function. On the other hand, there is consistent evidence to support follow-up of high-risk groups.
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238
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Fang Y, Shi H, Xiang T, Liu J, Liu J, Tang X, Fang X, Chen J, Zhai Y, Shen Q, Li G, Sun L, Bi Y, Wang X, Qian Y, Wu B, Wang H, Zhou W, Ma D, Mao J, Jiang X, Sun S, Shen Y, Liu X, Zhang A, Wang X, Huang W, Li Q, Wang M, Gao X, Wu Y, Deng F, Zhang R, Liu C, Yu L, Zhuang J, Sun Q, Dang X, Bai H, Zhu Y, Lu S, Zhang B, Shao X, Liu X, Han M, Zhao L, Liu Y, Gao J, Bao Y, Zhang D, Ma Q, Zhao L, Xia Z, Lu B, Wang Y, Zhao M, Zhang J, Jian S, He G, Zhang H, Zhao B, LI X, Wang F, Li Y, Zhu H, Luo X, Li J, Rao J, Xu H. Genetic Architecture of Childhood Kidney and Urological Diseases in China. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:91-104. [PMID: 36939782 PMCID: PMC9590557 DOI: 10.1007/s43657-021-00014-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 11/28/2022]
Abstract
Kidney disease is manifested in a wide variety of phenotypes, many of which have an important hereditary component. To delineate the genotypic and phenotypic spectrum of pediatric nephropathy, a multicenter registration system is being implemented based on the Chinese Children Genetic Kidney Disease Database (CCGKDD). In this study, all the patients with kidney and urological diseases were recruited from 2014 to 2020. Genetic analysis was conducted using exome sequencing for families with multiple affected individuals with nephropathy or clinical suspicion of a genetic kidney disease owing to early-onset or extrarenal features. The genetic diagnosis was confirmed in 883 of 2256 (39.1%) patients from 23 provinces in China. Phenotypic profiles showed that the primary diagnosis included steroid-resistant nephrotic syndrome (SRNS, 23.5%), glomerulonephritis (GN, 32.2%), congenital anomalies of the kidney and urinary tract (CAKUT, 21.2%), cystic renal disease (3.9%), renal calcinosis/stone (3.6%), tubulopathy (9.7%), and chronic kidney disease of unknown etiology (CKDu, 5.8%). The pathogenic variants of 105 monogenetic disorders were identified. Ten distinct genomic disorders were identified as pathogenic copy number variants (CNVs) in 11 patients. The diagnostic yield differed by subgroups, and was highest in those with cystic renal disease (66.3%), followed by tubulopathy (58.4%), GN (57.7%), CKDu (43.5%), SRNS (29.2%), renal calcinosis /stone (29.3%) and CAKUT (8.6%). Reverse phenotyping permitted correct identification in 40 cases with clinical reassessment and unexpected genetic conditions. We present the results of the largest cohort of children with kidney disease in China where diagnostic exome sequencing was performed. Our data demonstrate the utility of family-based exome sequencing, and indicate that the combined analysis of genotype and phenotype based on the national patient registry is pivotal to the genetic diagnosis of kidney disease. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-021-00014-1.
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Affiliation(s)
- Ye Fang
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Hua Shi
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Tianchao Xiang
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Jiaojiao Liu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Jialu Liu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Xiaoshan Tang
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Xiaoyan Fang
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Jing Chen
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Yihui Zhai
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Qian Shen
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Guomin Li
- grid.411333.70000 0004 0407 2968Department of Rheumatology, Children’s Hospital of Fudan University, Shanghai, China
| | - Li Sun
- grid.411333.70000 0004 0407 2968Department of Rheumatology, Children’s Hospital of Fudan University, Shanghai, China
| | - Yunli Bi
- grid.411333.70000 0004 0407 2968Department of Urology, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiang Wang
- grid.411333.70000 0004 0407 2968Department of Urology, Children’s Hospital of Fudan University, Shanghai, China
| | - Yanyan Qian
- grid.411333.70000 0004 0407 2968Clinical Genetic Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- grid.411333.70000 0004 0407 2968Clinical Genetic Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- grid.411333.70000 0004 0407 2968Clinical Genetic Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- grid.411333.70000 0004 0407 2968Clinical Genetic Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Duan Ma
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jianhua Mao
- grid.13402.340000 0004 1759 700XThe Children Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyun Jiang
- grid.412615.5The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shuzhen Sun
- grid.460018.b0000 0004 1769 9639Shandong Provincial Hospital, Jinan, China
| | - Ying Shen
- grid.24696.3f0000 0004 0369 153XBejing Children’s Hospital Affiliated to Capital University of Medical Science, Beijing, China
| | - Xiaorong Liu
- grid.24696.3f0000 0004 0369 153XBejing Children’s Hospital Affiliated to Capital University of Medical Science, Beijing, China
| | - Aihua Zhang
- grid.452511.6Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaowen Wang
- grid.33199.310000 0004 0368 7223Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenyan Huang
- grid.16821.3c0000 0004 0368 8293Shanghai Children’s Medical Centre, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiu Li
- grid.488412.3Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Mo Wang
- grid.488412.3Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojie Gao
- grid.452787.b0000 0004 1806 5224Shenzhen Children’s Hospital, Shenzheng, China
| | - Yubin Wu
- grid.412467.20000 0004 1806 3501Shengjing Hospital of China Medical University, Shenyang, Liaoning China
| | - Fang Deng
- grid.489986.2Anhui Provincial Children’s Hospital, Hefei, China
| | - Ruifeng Zhang
- grid.460138.8Xuzhou Children’s Hospital, Xuzhou, China
| | - Cuihua Liu
- Henan Children’s Hospital, Zhengzhou, China
| | - Li Yu
- grid.413432.30000 0004 1798 5993Guangzhou First People’s Hospital, Guangzhou, China
| | - Jieqiu Zhuang
- grid.417384.d0000 0004 1764 2632The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qing Sun
- grid.508137.80000 0004 4914 6107Qingdao Women and Children’s Hospital, Qingdao, China
| | - Xiqiang Dang
- grid.452223.00000 0004 1757 7615Xiangya Hospital Central South University, Changsha, Hunan China
| | - Haitao Bai
- grid.412625.6The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Ying Zhu
- grid.412679.f0000 0004 1771 3402First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Siguang Lu
- Children’s Hospital of Lianyungang, Lianyungang, China
| | - Bili Zhang
- Tianjin Children Hospital, Tianjing, China
| | - Xiaoshan Shao
- The Children’s Hospital of Guiyang City, Guiyang, China
| | - Xuemei Liu
- grid.27255.370000 0004 1761 1174Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Mei Han
- Dalian Children’s Hospital, Dalian, China
| | - Lijun Zhao
- grid.440213.00000 0004 1757 9418Shanxi Children’s Hospital, Taiyuan, China
| | - Yuling Liu
- grid.460171.5Boai Hospital of Zhongshan, Zhongshan, China
| | - Jian Gao
- Weifang Maternal and Child Health Hospital, Weifang, China
| | - Ying Bao
- grid.452902.8Xi’an Children’s Hospital, Xian, China
| | - Dongfeng Zhang
- grid.470210.0Children’s Hospital of Hebei Province, Shijiazhuang, China
| | - Qingshan Ma
- grid.430605.4First Affiliated Hospital of Jilin University, Changchun, China
| | - Liping Zhao
- Wuxi Municipal Children’s Hospital, Wuxi, China
| | - Zhengkun Xia
- grid.89957.3a0000 0000 9255 8984Department of Pediatrics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Biao Lu
- grid.413385.8General Hospital of Ningxia Medical University, Yinchuan, China
| | - Yulong Wang
- grid.452704.0The Second Hospital of Shandong University, Jinan, China
| | - Mengzhun Zhao
- grid.194645.b0000000121742757Shenzhen Hospital of University of Hong Kong, Shenzhen, China
| | - Jianjiang Zhang
- grid.412633.1First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shan Jian
- grid.413106.10000 0000 9889 6335Peking Union Medical College Hospital, Beijing, China
| | - Guohua He
- Child Health Hospital of Foshan, Foshan, Guangdong China
| | - Huifeng Zhang
- grid.452702.60000 0004 1804 3009The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bo Zhao
- grid.415549.8Kunming Children’s Hospital, Kunming, China
| | - Xiaohua LI
- grid.413375.70000 0004 1757 7666Affiliated Hospital of Inner Mongolia Medical University, Hohehot, China
| | - Feiyan Wang
- Urumqi City Children’s Hospital, Urumqi, China
| | - Yufeng Li
- grid.16821.3c0000 0004 0368 8293Xinhua Hospital Affiliated to Medical College of Shanghai Jiaotong University, Shanghai, China
| | - Hongtao Zhu
- grid.13394.3c0000 0004 1799 3993Academy of Pediatrics, Xinjiang Medical University, Urumqi, China
| | - Xinhui Luo
- Xinjiang Uygur Autonomous Region People’s Hospital, Urumqi, China
| | - Jinghai Li
- grid.470082.9Changchun Children’s Hospital, Changchun, China
| | - Jia Rao
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | - Hong Xu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of CHINA, 399 Wanyuan Road, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- grid.411333.70000 0004 0407 2968Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, 201102 China
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239
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Lindenmeyer MT, Alakwaa F, Rose M, Kretzler M. Perspectives in systems nephrology. Cell Tissue Res 2021; 385:475-488. [PMID: 34027630 PMCID: PMC8523456 DOI: 10.1007/s00441-021-03470-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/28/2021] [Indexed: 12/19/2022]
Abstract
Chronic kidney diseases (CKD) are a major health problem affecting approximately 10% of the world’s population and posing increasing challenges to the healthcare system. While CKD encompasses a broad spectrum of pathological processes and diverse etiologies, the classification of kidney disease is currently based on clinical findings or histopathological categorizations. This descriptive classification is agnostic towards the underlying disease mechanisms and has limited progress towards the ability to predict disease prognosis and treatment responses. To gain better insight into the complex and heterogeneous disease pathophysiology of CKD, a systems biology approach can be transformative. Rather than examining one factor or pathway at a time, as in the reductionist approach, with this strategy a broad spectrum of information is integrated, including comprehensive multi-omics data, clinical phenotypic information, and clinicopathological parameters. In recent years, rapid advances in mathematical, statistical, computational, and artificial intelligence methods enable the mapping of diverse big data sets. This holistic approach aims to identify the molecular basis of CKD subtypes as well as individual determinants of disease manifestation in a given patient. The emerging mechanism-based patient stratification and disease classification will lead to improved prognostic and predictive diagnostics and the discovery of novel molecular disease-specific therapies.
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Affiliation(s)
- Maja T Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Fadhl Alakwaa
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael Rose
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
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240
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Vigneau C, Germain DP, Larmet D, Jabbour F, Hourmant M. Screening for Fabry disease in male patients with end-stage renal disease in western France. Nephrol Ther 2021; 17:180-184. [PMID: 33994139 DOI: 10.1016/j.nephro.2021.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 01/05/2023]
Abstract
CONTEXT Fabry disease is a rare X-linked genetic disease due to pathogenic variants in the GLA gene. Classic Fabry disease is characterized by glycosphingolipids accumulation in all organs including the kidney, resulting in end-stage renal disease in a subset of male patients. Fabry disease should therefore be considered in the differential diagnosis of patients with unexplained end-stage renal disease. OBJECTIVE We performed a prospective screening study in Western France to determine the prevalence of Fabry disease in a large population of dialyzed and transplanted patients. PATIENTS AND METHODS Patients meeting the inclusion criteria (males, 18-70 years with end-stage renal disease of unknown or vascular origin) were selected from the REIN® registry and the CRISTAL® database. Screening on filter papers was performed after patient consent was obtained during either a dialysis session or a transplantation follow-up visit. RESULTS One thousand five hundred and sixty-one end-stage renal disease male patients were screened and 819 consented (dialysis: n=242; transplant: n=577). One single patient was found with decreased alpha-galactosidase levels <25%. GLA sequencing identified the p.Phe113Leu variant in favor of an unknown superimposed kidney disease responsible for end-stage renal disease since this GLA pathogenic variant is associated with a later-onset cardiac form of Fabry disease with minimal kidney involvement. Family cascade genotyping revealed a previously undiagnosed affected brother. CONCLUSION The prevalence of Fabry disease in end-stage renal disease patients was 0.12%, questioning the efficacy of this screening strategy with respect to the low prevalence. However, beside the benefit for the patient and his family, the increased awareness of Fabry disease among participating nephrologists may be of interest for future patients.
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Affiliation(s)
- C Vigneau
- Inserm, EHESP, IRSET, UMR_S 1085, University of Rennes, CHU de Rennes, 35000 Rennes, France
| | - D P Germain
- Inserm, EHESP, IRSET, UMR_S 1085, University of Rennes, CHU de Rennes, 35000 Rennes, France; French Referral Center for Fabry disease, Division of Medical Genetics, AP-HP Paris Saclay University, University of Versailles, 2, avenue de la source de la Bièvre, 78180 Montigny, France; Second Department of Internal Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic; Faculty of Medicine, University of Puthisastra, Phnom Penh, Cambodia.
| | - D Larmet
- Department of Nephrology, University of Nantes, 44093 Nantes cedex 01, France
| | - F Jabbour
- French Referral Center for Fabry disease, Division of Medical Genetics, AP-HP Paris Saclay University, University of Versailles, 2, avenue de la source de la Bièvre, 78180 Montigny, France
| | - M Hourmant
- Department of Nephrology, University of Nantes, 44093 Nantes cedex 01, France
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241
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Mansilla MA, Sompallae RR, Nishimura CJ, Kwitek AE, Kimble MJ, Freese ME, Campbell CA, Smith RJ, Thomas CP. Targeted broad-based genetic testing by next-generation sequencing informs diagnosis and facilitates management in patients with kidney diseases. Nephrol Dial Transplant 2021; 36:295-305. [PMID: 31738409 PMCID: PMC7834596 DOI: 10.1093/ndt/gfz173] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background The clinical diagnosis of genetic renal diseases may be limited by the overlapping spectrum of manifestations between diseases or by the advancement of disease where clues to the original process are absent. The objective of this study was to determine whether genetic testing informs diagnosis and facilitates management of kidney disease patients. Methods We developed a comprehensive genetic testing panel (KidneySeq) to evaluate patients with various phenotypes including cystic diseases, congenital anomalies of the kidney and urinary tract (CAKUT), tubulointerstitial diseases, transport disorders and glomerular diseases. We evaluated this panel in 127 consecutive patients ranging in age from newborns to 81 years who had samples sent in for genetic testing. Results The performance of the sequencing pipeline for single-nucleotide variants was validated using CEPH (Centre de’Etude du Polymorphism) controls and for indels using Genome-in-a-Bottle. To test the reliability of the copy number variant (CNV) analysis, positive samples were re-sequenced and analyzed. For patient samples, a multidisciplinary review board interpreted genetic results in the context of clinical data. A genetic diagnosis was made in 54 (43%) patients and ranged from 54% for CAKUT, 53% for ciliopathies/tubulointerstitial diseases, 45% for transport disorders to 33% for glomerulopathies. Pathogenic and likely pathogenic variants included 46% missense, 11% nonsense, 6% splice site variants, 23% insertion–deletions and 14% CNVs. In 13 cases, the genetic result changed the clinical diagnosis. Conclusion Broad genetic testing should be considered in the evaluation of renal patients as it complements other tests and provides insight into the underlying disease and its management.
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Affiliation(s)
- M Adela Mansilla
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | | | - Carla J Nishimura
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Anne E Kwitek
- Physiology, Medical College of Wisconsin, Iowa City, IA, USA
| | - Mycah J Kimble
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | | | - Colleen A Campbell
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Richard J Smith
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA.,Internal Medicine, University of Iowa, Iowa City, IA, USA.,Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Christie P Thomas
- Internal Medicine, University of Iowa, Iowa City, IA, USA.,Pediatrics, University of Iowa, Iowa City, IA, USA.,Veterans Affairs Medical Center, Iowa City, IA, USA
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242
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Molecular genetics of renal ciliopathies. Biochem Soc Trans 2021; 49:1205-1220. [PMID: 33960378 DOI: 10.1042/bst20200791] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022]
Abstract
Renal ciliopathies are a heterogenous group of inherited disorders leading to an array of phenotypes that include cystic kidney disease and renal interstitial fibrosis leading to progressive chronic kidney disease and end-stage kidney disease. The renal tubules are lined with epithelial cells that possess primary cilia that project into the lumen and act as sensory and signalling organelles. Mutations in genes encoding ciliary proteins involved in the structure and function of primary cilia cause ciliopathy syndromes and affect many organ systems including the kidney. Recognised disease phenotypes associated with primary ciliopathies that have a strong renal component include autosomal dominant and recessive polycystic kidney disease and their various mimics, including atypical polycystic kidney disease and nephronophthisis. The molecular investigation of inherited renal ciliopathies often allows a precise diagnosis to be reached where renal histology and other investigations have been unhelpful and can help in determining kidney prognosis. With increasing molecular insights, it is now apparent that renal ciliopathies form a continuum of clinical phenotypes with disease entities that have been classically described as dominant or recessive at both extremes of the spectrum. Gene-dosage effects, hypomorphic alleles, modifier genes and digenic inheritance further contribute to the genetic complexity of these disorders. This review will focus on recent molecular genetic advances in the renal ciliopathy field with a focus on cystic kidney disease phenotypes and the genotypes that lead to them. We discuss recent novel insights into underlying disease mechanisms of renal ciliopathies that might be amenable to therapeutic intervention.
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243
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Zhang JQJ, Saravanabavan S, Cheng KM, Raghubanshi A, Chandra AN, Munt A, Rayner B, Zhang Y, Chau K, Wong ATY, Rangan GK. Long-term dietary nitrate supplementation does not reduce renal cyst growth in experimental autosomal dominant polycystic kidney disease. PLoS One 2021; 16:e0248400. [PMID: 33886581 PMCID: PMC8061912 DOI: 10.1371/journal.pone.0248400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/26/2021] [Indexed: 11/18/2022] Open
Abstract
Augmentation of endogenous nitric oxide (NO) synthesis, either by the classical L-arginine-NO synthase pathway, or the recently discovered entero-salivary nitrate-nitrite-NO system, may slow the progression of autosomal dominant polycystic kidney disease (ADPKD). To test this hypothesis, the expression of NO in human ADPKD cell lines (WT 9–7, WT 9–12), and the effect of L-arginine on an in vitro model of three-dimensional cyst growth using MDCK cells, was examined. In addition, groups of homozygous Pkd1RC/RC mice (a hypomorphic genetic ortholog of ADPKD) received either low, moderate or high dose sodium nitrate (0.1, 1 or 10 mmol/kg/day), or sodium chloride (vehicle; 10 mmol/kg/day), supplemented drinking water from postnatal month 1 to 9 (n = 12 per group). In vitro, intracellular NO, as assessed by DAF-2/DA fluorescence, was reduced by >70% in human ADPKD cell lines, and L-arginine and the NO donor, sodium nitroprusside, both attenuated in vitro cyst growth by up to 18%. In contrast, in Pkd1RC/RC mice, sodium nitrate supplementation increased serum nitrate/nitrite levels by ~25-fold in the high dose group (P<0.001), but kidney enlargement and percentage cyst area was not altered, regardless of dose. In conclusion, L-arginine has mild direct efficacy on reducing renal cyst growth in vitro, whereas long-term sodium nitrate supplementation was ineffective in vivo. These data suggest that the bioconversion of dietary nitrate to NO by the entero-salivary pathway may not be sufficient to influence the progression of renal cyst growth in ADPKD.
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Affiliation(s)
- Jennifer Q. J. Zhang
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Sayanthooran Saravanabavan
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Kai Man Cheng
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Aarya Raghubanshi
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Ashley N. Chandra
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Alexandra Munt
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Benjamin Rayner
- Heart Research Institute, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Yunjia Zhang
- Heart Research Institute, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Katrina Chau
- Department of Renal Medicine and School of Medicine, Western Sydney University at Blacktown Hospital, Sydney, New South Wales, Australia
| | - Annette T. Y. Wong
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Gopala K. Rangan
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
- * E-mail:
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244
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Shang N, Khan A, Polubriaginof F, Zanoni F, Mehl K, Fasel D, Drawz PE, Carrol RJ, Denny JC, Hathcock MA, Arruda-Olson AM, Peissig PL, Dart RA, Brilliant MH, Larson EB, Carrell DS, Pendergrass S, Verma SS, Ritchie MD, Benoit B, Gainer VS, Karlson EW, Gordon AS, Jarvik GP, Stanaway IB, Crosslin DR, Mohan S, Ionita-Laza I, Tatonetti NP, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. NPJ Digit Med 2021; 4:70. [PMID: 33850243 PMCID: PMC8044136 DOI: 10.1038/s41746-021-00428-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Chronic Kidney Disease (CKD) represents a slowly progressive disorder that is typically silent until late stages, but early intervention can significantly delay its progression. We designed a portable and scalable electronic CKD phenotype to facilitate early disease recognition and empower large-scale observational and genetic studies of kidney traits. The algorithm uses a combination of rule-based and machine-learning methods to automatically place patients on the staging grid of albuminuria by glomerular filtration rate ("A-by-G" grid). We manually validated the algorithm by 451 chart reviews across three medical systems, demonstrating overall positive predictive value of 95% for CKD cases and 97% for healthy controls. Independent case-control validation using 2350 patient records demonstrated diagnostic specificity of 97% and sensitivity of 87%. Application of the phenotype to 1.3 million patients demonstrated that over 80% of CKD cases are undetected using ICD codes alone. We also demonstrated several large-scale applications of the phenotype, including identifying stage-specific kidney disease comorbidities, in silico estimation of kidney trait heritability in thousands of pedigrees reconstructed from medical records, and biobank-based multicenter genome-wide and phenome-wide association studies.
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Affiliation(s)
- Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Fernanda Polubriaginof
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Karla Mehl
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - David Fasel
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Paul E Drawz
- Department of Medicine, University of Minnesota, Minnesota, MN, USA
| | - Robert J Carrol
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
- Departments of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | | | | | - Richard A Dart
- Marshfield Clinic Research Institute, Marshfield, WI, USA
| | | | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | | | | | | | | | - Adam S Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ian B Stanaway
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David R Crosslin
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Sumit Mohan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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Floris M, Lepori N, Angioi A, Cabiddu G, Piras D, Loi V, Swaminathan S, Rosner MH, Pani A. Chronic Kidney Disease of Undetermined Etiology around the World. Kidney Blood Press Res 2021; 46:142-151. [PMID: 33845480 DOI: 10.1159/000513014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/12/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Epidemics of chronic kidney disease of uncertain etiology (CKDu) are occurring on the Pacific coast of Central America, in Sri Lankan and Indian agricultural communities, and in other hotspots around the world. CKDu primarily affects male agricultural workers, and traditional risk factors such as diabetes and hypertension are not involved in the pathogenesis. Although a causal factor has not yet been identified, culprits include repeated volume depletion-induced kidney injury, as well as exposure to agrichemicals, heavy metals and nephrotoxins contained in drugs, beverages, and traditional medications. Multiple risk factors may interact in a synergistic fashion thus resulting in chronic kidney damage. The absence of undefined protective factors may amplify the risk. SUMMARY This review focuses on the current understanding of CKDu by analyzing epidemiology, potential risk factors, and clinical and pathological features as well as geographical peculiarities of each disease. We also focus our attention on the etiology of these conditions in which multiple factors may synergistically contribute to the development and progression of the disease. The last part of the manuscript is dedicated to the research agenda and practical recommendations. Key Messages: Since renal replacement therapy is not extensively available in areas where CKDu is widespread, prevention by avoiding all known potential risk factors is crucial. Innovative healthcare solutions and social policies in endemic areas along with collaborative clinical research projects are needed to better identify factors involved in disease promotion and progression.
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Affiliation(s)
- Matteo Floris
- Nephrology and Dialysis, G. Brotzu Hospital, Università degli Studi di Cagliari, Cagliari, Italy
| | - Nicola Lepori
- Nephrology and Dialysis, G. Brotzu Hospital, Università degli Studi di Cagliari, Cagliari, Italy
| | - Andrea Angioi
- Nephrology and Dialysis, G. Brotzu Hospital, Università degli Studi di Cagliari, Cagliari, Italy
| | - Gianfranca Cabiddu
- Nephrology and Dialysis, G. Brotzu Hospital, Università degli Studi di Cagliari, Cagliari, Italy
| | - Doloretta Piras
- Nephrology and Dialysis, G. Brotzu Hospital, Università degli Studi di Cagliari, Cagliari, Italy
| | - Valentina Loi
- Nephrology and Dialysis, G. Brotzu Hospital, Università degli Studi di Cagliari, Cagliari, Italy
| | | | - Mitchell H Rosner
- Division of Nephrology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Antonello Pani
- Nephrology and Dialysis, G. Brotzu Hospital, Università degli Studi di Cagliari, Cagliari, Italy
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Furlano M, Martínez V, Pybus M, Arce Y, Crespí J, Venegas MDP, Bullich G, Domingo A, Ayasreh N, Benito S, Lorente L, Ruíz P, Gonzalez VL, Arlandis R, Cabello E, Torres F, Guirado L, Ars E, Torra R. Clinical and Genetic Features of Autosomal Dominant Alport Syndrome: A Cohort Study. Am J Kidney Dis 2021; 78:560-570.e1. [PMID: 33838161 DOI: 10.1053/j.ajkd.2021.02.326] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 02/14/2021] [Indexed: 12/15/2022]
Abstract
RATIONALE & OBJECTIVE Alport syndrome is a common genetic kidney disease accounting for approximately 2% of patients receiving kidney replacement therapy (KRT). It is caused by pathogenic variants in the gene COL4A3, COL4A4, or COL4A5. The aim of this study was to evaluate the clinical and genetic spectrum of patients with autosomal dominant Alport syndrome (ADAS). STUDY DESIGN Retrospective cohort study. SETTING & PARTICIPANTS 82 families (252 patients) with ADAS were studied. Clinical, genetic, laboratory, and pathology data were collected. OBSERVATIONS A pathogenic DNA variant in COL4A3 was identified in 107 patients (35 families), whereas 133 harbored a pathogenic variant in COL4A4 (43 families). Digenic/complex inheritance was observed in 12 patients. Overall, the median kidney survival was 67 (95% CI, 58-73) years, without significant differences across sex (P=0.8), causative genes (P=0.6), or type of variant (P=0.9). Microhematuria was the most common kidney manifestation (92.1%), and extrarenal features were rare. Findings on kidney biopsies ranged from normal to focal segmental glomerulosclerosis. The slope of estimated glomerular filtration rate change was-1.46 (-1.66 to-1.26) mL/min/1.73m2 per year for the overall group, with no significant differences between ADAS genes (P=0.2). LIMITATIONS The relatively small size of this series from a single country, potentially limiting generalizability. CONCLUSIONS Patients with ADAS have a wide spectrum of clinical presentations, ranging from asymptomatic to kidney failure, a pattern not clearly related to the causative gene or type of variant. The diversity of ADAS phenotypes contributes to its underdiagnosis in clinical practice.
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Affiliation(s)
- Mónica Furlano
- Inherited Kidney Diseases, Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Medicine Department-Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Victor Martínez
- Nephrology Department, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Marc Pybus
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Yolanda Arce
- Department of Pathology, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Jaume Crespí
- Departments of Ophthalmology, Hospital de Sant Pau i la Santa Creu, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain
| | - María Del Prado Venegas
- Otolaryngology-Head and Neck Surgery, Hospital de Sant Pau i la Santa Creu, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Gemma Bullich
- Centre Nacional d'Anàlisi Genómica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Domingo
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Nadia Ayasreh
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Medicine Department-Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Silvia Benito
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Medicine Department-Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Laura Lorente
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Patricia Ruíz
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Vanesa López Gonzalez
- Genetics Laboratory, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Rosa Arlandis
- Nephrology Department, Hospital General de la Palma, Islas Canarias, Spain
| | - Elisa Cabello
- Nephrology Department, Hospital General Universitario de Castellón, Castellón de la Plana, Spain
| | - Ferran Torres
- Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain; Medical Statistics Core Facility, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Lluis Guirado
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Medicine Department-Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain.
| | - Roser Torra
- Inherited Kidney Diseases, Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Medicine Department-Universitat Autónoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain.
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247
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Doreille A, Raymond L, Lebre AS, Linster C, Saraeva Lamri R, Karras A, Khayat R, Michel PA, Buob D, Luque Y, Rafat C, Mesnard L. Nephronophthisis in Young Adults Phenocopying Thrombotic Microangiopathy and Severe Nephrosclerosis. Clin J Am Soc Nephrol 2021; 16:615-617. [PMID: 33268504 PMCID: PMC8092057 DOI: 10.2215/cjn.11890720] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Alice Doreille
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, 4 Rue de la Chine, Assistance Publique–Hôpitaux de Paris, Paris, France,Sorbonne Université, Paris, France
| | | | - Anne-Sophie Lebre
- Centre Hospitalier et Universitaire de Reims, Hôpital Maison Blanche, Pole de biologie, Service de génétique, Reims, France
| | - Charel Linster
- Service de Néphrologie, Hôpital Européen Georges Pompidou, 20 Rue Leblan, Assistance Publique–Hôpitaux de Paris, Paris, France
| | | | - Alexandre Karras
- Service de Néphrologie, Hôpital Européen Georges Pompidou, 20 Rue Leblan, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Rateb Khayat
- Service de Néphrologie et Dialyses, Hôpital Tenon, 4 Rue de la Chine, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Pierre-Antoine Michel
- Service de Néphrologie et Dialyses, Hôpital Tenon, 4 Rue de la Chine, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - David Buob
- Sorbonne Université, Paris, France,Service d'Anatomo-Pathologie, Hôpital Tenon, 4 Rue de la Chine, Assistance Publique–Hôpitaux de Paris, Paris, France,Institut National de la Santé et de la Recherche Médicale UMR_S1155, Hôpital Tenon, 4 Rue de la Chine, 75020, Paris, France
| | - Yosu Luque
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, 4 Rue de la Chine, Assistance Publique–Hôpitaux de Paris, Paris, France,Sorbonne Université, Paris, France,Institut National de la Santé et de la Recherche Médicale UMR_S1155, Hôpital Tenon, 4 Rue de la Chine, 75020, Paris, France
| | - Cédric Rafat
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, 4 Rue de la Chine, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Laurent Mesnard
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, 4 Rue de la Chine, Assistance Publique–Hôpitaux de Paris, Paris, France,Sorbonne Université, Paris, France,Institut National de la Santé et de la Recherche Médicale UMR_S1155, Hôpital Tenon, 4 Rue de la Chine, 75020, Paris, France,Institut des Sciences du Calcul et des Données, Campus Pierre et Marie Curie, Batiment Esclangon, Sorbonne Université, 4 Place Jussieu, Cedex 05, Paris, France
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248
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Robin B, Dagobert J, Isnard P, Rabant M, Duong-Van-Huyen JP. [New technologies for renal pathology: Transcriptomics on paraffin-embedded fixed tissue]. Nephrol Ther 2021; 17S:S54-S59. [PMID: 33910699 DOI: 10.1016/j.nephro.2020.03.004] [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: 02/21/2020] [Accepted: 03/01/2020] [Indexed: 11/19/2022]
Abstract
The development of new high-throughput technologies in genomics and then in transcriptomics has modified clinical approach in nephrology. At the interface between high-throughput technologies (microarray, new generation sequencing «NGS») and few mRNA analysis (reverse transcriptase quantitative PCR [RT-qPCR]), the nCounter® of NanoString® offers a new and complementary approach. Capable of analyzing formalin-fixed paraffin-embedded samples, this technology is a credible candidate for implanting transcriptomics in clinical routine.
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Affiliation(s)
- Blaise Robin
- Paris Translational Research Center for Organ Transplantation, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 56, rue Leblanc, 75015 Paris, France; Inserm U970, 56, rue Leblanc, 75015 Paris, France.
| | - Jessy Dagobert
- Paris Translational Research Center for Organ Transplantation, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 56, rue Leblanc, 75015 Paris, France; Inserm U970, 56, rue Leblanc, 75015 Paris, France
| | - Pierre Isnard
- Service d'anatomie pathologique, hôpital Necker-Enfants-Malades, 149, rue de Sèvres, 75015 Paris, France
| | - Marion Rabant
- Service d'anatomie pathologique, hôpital Necker-Enfants-Malades, 149, rue de Sèvres, 75015 Paris, France
| | - Jean-Paul Duong-Van-Huyen
- Paris Translational Research Center for Organ Transplantation, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 56, rue Leblanc, 75015 Paris, France; Inserm U970, 56, rue Leblanc, 75015 Paris, France; Service d'anatomie pathologique, hôpital Necker-Enfants-Malades, 149, rue de Sèvres, 75015 Paris, France
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Abstract
PURPOSE OF REVIEW Perinatal disorders include stillbirth, congenital structural anomalies, and critical illnesses in neonates. The cause of these is often unknown despite a thorough clinical workup. Genetic diseases cause a significant portion of perinatal disorders. The purpose of this review is to describe recent advances in genetic testing of perinatal disorders of unknown cause and to provide a potential diagnostic strategy. RECENT FINDINGS Exome and genome sequencing (ES and GS) have demonstrated that significant portions of perinatal disorders are caused by genetic disease. However, estimates of the exact proportion have varied widely across fetal and neonatal cohorts and most of the genetic diagnoses found in recent studies have been unique to individual cases. Having a specific genetic diagnosis provides significant clinical utility, including improved prognostication of the outcome, tailored therapy, directed testing for associated syndromic manifestations, referral to appropriate subspecialists, family planning, and redirection of care. SUMMARY Perinatal disorders of unknown cause, with nonspecific presentations, are often caused by genetic diseases best diagnosed by ES or GS. Prompt diagnosis facilitates improved clinical care. Improvements in noninvasive sampling, variant interpretation, and population-level research will further enhance the clinical utility of genetic testing. VIDEO ABSTRACT http://links.lww.com/MOP/A61.
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Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
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250
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Chertow GM, Appel GB, Andreoli S, Bangalore S, Block GA, Chapman AB, Chin MP, Gibson KL, Goldsberry A, Iijima K, Inker LA, Knebelmann B, Mariani LH, Meyer CJ, Nozu K, O'Grady M, Silva AL, Stenvinkel P, Torra R, Warady BA, Pergola PE. Study Design and Baseline Characteristics of the CARDINAL Trial: A Phase 3 Study of Bardoxolone Methyl in Patients with Alport Syndrome. Am J Nephrol 2021; 52:180-189. [PMID: 33789284 DOI: 10.1159/000513777] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Alport syndrome is a rare genetic disorder that affects as many as 60,000 persons in the USA and a total of 103,000 persons (<5 per 10,000) in the European Union [1, 2]. It is the second most common inherited cause of kidney failure and is characterized by progressive loss of kidney function that often leads to end-stage kidney disease. Currently, there are no approved disease-specific agents for therapeutic use. We designed a phase 3 study (CARDINAL; NCT03019185) to evaluate the safety, tolerability, and efficacy of bardoxolone methyl in patients with Alport syndrome. METHODS The CARDINAL phase 3 study is an international, multicenter, double-blind, placebo-controlled, randomized registrational trial. Eligible patients were of ages 12-70 years with confirmed genetic or histologic diagnosis of Alport syndrome, eGFR 30-90 mL/min/1.73 m2, and urinary albumin to creatinine ratio (UACR) ≤3,500 mg/g. Patients with B-type natriuretic peptide values >200 pg/mL at baseline or with significant cardiovascular histories were excluded. Patients were randomized 1:1 to bardoxolone methyl or placebo, with stratification by baseline UACR. RESULTS A total of 371 patients were screened, and 157 patients were randomly assigned to receive bardoxolone methyl (n = 77) or placebo (n = 80). The average age at screening was 39.2 years, and 23 (15%) were <18 years of age. Of the randomized population, 146 (93%) had confirmed genetic diagnosis of Alport syndrome, and 62% of patients had X-linked mode of inheritance. Mean baseline eGFR was 62.7 mL/min/1.73 m2, and the geometric mean UACR was 141.0 mg/g. The average annual rate of eGFR decline prior to enrollment in the study was -4.9 mL/min/1.73 m2 despite 78% of the patient population receiving ACE inhibitor (ACEi) or ARB therapy. DISCUSSION/CONCLUSION CARDINAL is one of the largest interventional, randomized controlled trials in Alport syndrome conducted to date. Despite the use of ACEi or ARB, patients were experiencing significant loss of kidney function prior to study entry.
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Affiliation(s)
- Glenn M Chertow
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Gerald B Appel
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Sharon Andreoli
- Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sripal Bangalore
- Cardiovascular Clinical Research Center, New York University School of Medicine, New York, New York, USA
| | - Geoffrey A Block
- Department of Clinical Research and Medical Affairs, US Renal Care, Inc., Plano, Texas, USA
| | - Arlene B Chapman
- Section of Nephrology, University of Chicago, Chicago, Illinois, USA
| | - Melanie P Chin
- Department of Product Development, Reata Pharmaceuticals, Plano, Texas, USA
| | - Keisha L Gibson
- University of North Carolina Kidney Center at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Angie Goldsberry
- Department of Product Development, Reata Pharmaceuticals, Plano, Texas, USA
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Lesley A Inker
- Division of Nephrology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Bertrand Knebelmann
- Department of Nephrology, Necker Hospital, AP-HP, Université de Paris, Paris, France
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Colin J Meyer
- Department of Product Development, Reata Pharmaceuticals, Plano, Texas, USA
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Megan O'Grady
- Department of Product Development, Reata Pharmaceuticals, Plano, Texas, USA
| | - Arnold L Silva
- Boise Kidney and Hypertension Institute, Meridian, Idaho, USA
| | - Peter Stenvinkel
- Division of Renal Medicine and Baxter Novum, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, Stockholm, Sweden
| | - Roser Torra
- Inherited Kidney Disorders, Nephrology Department, Fundacio Puigvert, Instituto de Investigacion Carlos III, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Bradley A Warady
- Division of Pediatric Nephrology, Children's Mercy Kansas City, Kansas City, Missouri, USA
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