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Caliment A, Van Reeth O, Hougardy C, Dahan K, Niel O. A step-by-step, multidisciplinary strategy to maximize the yield of genetic testing in pediatric patients with chronic kidney diseases. Pediatr Nephrol 2024; 39:2733-2740. [PMID: 38316682 DOI: 10.1007/s00467-024-06299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND The use of genetic testing in pediatric patients with chronic kidney diseases (CKD) has increased exponentially in the past few years, particularly with the emergence of novel sequencing techniques. However, the genetic yield remains unexpectedly low in nephrology, with an impact on diagnosis, prognosis and treatment. Moreover, the increasing diversity of genetic testing possibilities can be seen as an obstacle by clinicians, in the absence of a strong background in genetics. Here, we propose a step-by-step, multidisciplinary strategy for the diagnostic evaluation of pediatric patients with CKD, and appropriate genetic test selection to maximize the yield of genetic testing. METHODS A total of 126 pediatric patients were enrolled in a retrospective file analysis. Genetic testing techniques used included phenotype-associated next-generation panel sequencing (N = 41), Sanger and SNaPshot sequencing (N = 3) and/or whole exome sequencing (N = 2). RESULTS Overall genetic yield reached 63% and genetic testing significantly impacted patient management in 70%. The distribution of kidney diseases among patients was balanced and matched previously described pediatric cohorts in terms of glomerulopathies, tubulopathies and ciliopathies. Genetic analyses led to significant treatment modifications, kidney biopsy sparing and personalized nephroprotection, as well as tailored genetic counseling. Of note, the evaluation of Human Phenotype Ontology term accuracy in the cohort showed that causal mutations were precisely identified in 85% of the patients at most. CONCLUSION Here we suggest a step-by-step, multidisciplinary strategy to maximize the yield of genetic testing in pediatric patients with CKD. This approach optimizes patient care while avoiding unnecessary treatments or procedures.
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Affiliation(s)
- Ancuta Caliment
- Pediatric Nephrology, Centre Hospitalier de Luxembourg, 4 Rue Barblé, L1210, Luxembourg, Luxembourg.
| | - Olil Van Reeth
- Pediatric Nephrology, Centre Hospitalier de Luxembourg, 4 Rue Barblé, L1210, Luxembourg, Luxembourg
| | - Charlotte Hougardy
- Center of Human Genetics, Institut de Pathologie Et de Génétique, Gosselies, Belgium
| | - Karin Dahan
- Center of Human Genetics, Institut de Pathologie Et de Génétique, Gosselies, Belgium
- Laboratoire National de Santé, 1 Rue Louis Rech, L3555, Dudelange, Luxembourg
| | - Olivier Niel
- Pediatric Nephrology, Centre Hospitalier de Luxembourg, 4 Rue Barblé, L1210, Luxembourg, Luxembourg
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Blasco M, Quiroga B, García-Aznar JM, Castro-Alonso C, Fernández-Granados SJ, Luna E, Fernández Fresnedo G, Ossorio M, Izquierdo MJ, Sanchez-Ospina D, Castañeda-Infante L, Mouzo R, Cao M, Besada-Cerecedo ML, Pan-Lizcano R, Torra R, Ortiz A, de Sequera P. Genetic Characterization of Kidney Failure of Unknown Etiology in Spain: Findings From the GENSEN Study. Am J Kidney Dis 2024:S0272-6386(24)00844-8. [PMID: 38972501 DOI: 10.1053/j.ajkd.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 07/09/2024]
Abstract
RATIONALE & OBJECTIVE Chronic kidney disease of unknown etiology (CKDUE) is one of the main global causes of kidney failure. Genetic studies may identify an etiology in these patients, but few studies have implemented genetic testing of CKDUE in a population-based series of patients, which was the focus of the GENSEN Study. STUDY DESIGN Case series. SETTINGS & PARTICIPANTS 818 patients aged≤45 years at 51 Spanish centers with CKDUE, and either an estimated glomerular filtration rate of<15mL/min/1.73m2 or treatment with maintenance dialysis or transplantation. OBSERVATIONS Genetic testing for 529 genes associated with inherited nephropathies using high-throughput sequencing (HTS). Pathogenic and/or likely pathogenic (P/LP) gene variants concordant with the inheritance pattern were detected in 203 patients (24.8%). Variants in type IV collagen genes were the most frequent (COL4A5, COL4A4, COL4A3; 35% of total gene variants), followed by NPHP1, PAX2, UMOD, MUC1, and INF2 (7.3%, 5.9%, 2.5%, 2.5%, and 2.5%, respectively). Overall, 87 novel variants classified as P/LP were identified. The top 5 most common previously undiagnosed diseases were Alport syndrome spectrum (35% of total positive reports), genetic podocytopathies (19%), nephronophthisis (11%), autosomal dominant tubulointerstitial kidney disease (7%), and congenital anomalies of the kidney and urinary tract (CAKUT, 5%). A family history of kidney disease was reported by 191 participants (23.3%) and by 65 of 203 patients (32.0%) with P/LP variants. LIMITATIONS Missing data, and selection bias resulting from voluntary enrollment. CONCLUSIONS Genomic testing with HTS identified a genetic cause of kidney disease in approximately one quarter of young patients with CKDUE and advanced kidney disease. These findings suggest that genetic studies are a potentially useful tool for the evaluation of people with CKDUE. PLAIN-LANGUAGE SUMMARY The cause of kidney disease is unknown for 1 in 5 patients requiring kidney replacement therapy, reflecting possible prior missed treatment opportunities. We assessed the diagnostic utility of genetic testing in children and adults aged≤45 years with either an estimated glomerular filtration rate of<15mL/min/1.73m2 or treatment with maintenance dialysis or transplantation. Genetic testing identified the cause of kidney disease in approximately 1 in 4 patients without a previously known cause of kidney disease, suggesting that genetic studies are a potentially useful tool for the evaluation of these patients.
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Affiliation(s)
- Miquel Blasco
- Nephrology and Kidney Transplant Department, National Reference Center for Complex Glomerular Diseases, Hospital Clínic, Barcelona University, Barcelona; Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona; RICORS2040, Universidad Autónoma de Madrid, Madrid
| | - Borja Quiroga
- IIS-La Princesa, Servicio de Nefrología, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid; RICORS2040, Universidad Autónoma de Madrid, Madrid
| | - José M García-Aznar
- Clinical Area of Genetic Diagnostic in Nephrology and Immunology, Health in Code, A Coruña
| | - Cristina Castro-Alonso
- Department of Nephrology, Doctor Peset University Hospital, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia
| | - Saulo J Fernández-Granados
- Hospital Universitario Insular de Gran Canaria, Nephrology Service, Las Palmas de Gran Canaria, Las Palmas
| | - Enrique Luna
- Complejo Hospitalario Universitario de Badajoz, Unidad Enfermedades Genéticas Renales, Servicio de Nefrologia, Badajoz
| | - Gema Fernández Fresnedo
- Nephrology Department, Hospital Marqués de Valdecilla-Grupo de Inmunopatología IDIVAL, Santander
| | - Marta Ossorio
- Nephrology Department, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid
| | | | | | | | - Ricardo Mouzo
- Nephrology Department, Hospital El Bierzo, Ponferrada, Spain
| | - Mercedes Cao
- Nephrology Department, Complexo Hospitalario Universitario A Coruña, A Coruña
| | | | | | - Roser Torra
- Inherited Kidney Diseases, Nephrology Department, Fundació Puigvert, Institut de Recerca Sant Pau, Medicine Department, Universitat Autònoma de Barcelona, Barcelona; RICORS2040, Universidad Autónoma de Madrid, Madrid
| | - Alberto Ortiz
- RICORS2040, Universidad Autónoma de Madrid, Madrid; Nephrology and Hypertension Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid; Medicine Department, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid.
| | - Patricia de Sequera
- Nephrology Department, Hospital Universitario Infanta Leonor, Universidad Autónoma de Madrid, Madrid; RICORS2040, Universidad Autónoma de Madrid, Madrid; Universidad Complutense de Madrid, Universidad Autónoma de Madrid, Madrid.
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Mallawaarachchi AC, Fowles L, Wardrop L, Wood A, O'Shea R, Biros E, Harris T, Alexander SI, Bodek S, Boudville N, Burke J, Burnett L, Casauria S, Chadban S, Chakera A, Crafter S, Dai P, De Fazio P, Faull R, Honda A, Huntley V, Jahan S, Jayasinghe K, Jose M, Leaver A, MacShane M, Madelli EO, Nicholls K, Pawlowski R, Rangan G, Snelling P, Soraru J, Sundaram M, Tchan M, Valente G, Wallis M, Wedd L, Welland M, Whitlam J, Wilkins EJ, McCarthy H, Simons C, Quinlan C, Patel C, Stark Z, Mallett AJ. Genomic Testing in Patients with Kidney Failure of an Unknown Cause: A National Australian Study. Clin J Am Soc Nephrol 2024; 19:887-897. [PMID: 38861662 PMCID: PMC11254024 DOI: 10.2215/cjn.0000000000000464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/25/2024] [Indexed: 06/13/2024]
Abstract
Key Points Twenty-five percent of those with unexplained kidney failure have a monogenic cause. Whole genome sequencing with broad gene panel analysis is a feasible diagnostic approach in nephrology. Background The cause of kidney failure is unknown in approximately 10% of patients with stage 5 chronic kidney disease (CKD). For those who first present to nephrology care with kidney failure, standard investigations of serology, imaging, urinalysis, and kidney biopsy are limited differentiators of etiology. We aimed to determine the diagnostic utility of whole genome sequencing (WGS) with analysis of a broad kidney gene panel in patients with kidney failure of unknown cause. Methods We prospectively recruited 100 participants who reached CKD stage 5 at the age of ≤50 years and had an unknown cause of kidney failure after standard investigation. Clinically accredited WGS was performed in this national cohort after genetic counseling. The primary analysis was targeted to 388 kidney-related genes with second-tier, genome-wide, and mitochondrial analysis. Results The cohort was 61% male and the average age of participants at stage 5 CKD was 32 years (9 months to 50 years). A genetic diagnosis was made in 25% of participants. Disease-causing variants were identified across autosomal dominant tubulointerstitial kidney disease (6), glomerular disorders (4), ciliopathies (3), tubular disorders (2), Alport syndrome (4), and mitochondrial disease (1). Most diagnoses (80%) were in autosomal dominant, X-linked, or mitochondrial conditions (UMOD ; COL4A5 ; INF2 ; CLCN5 ; TRPC6 ; COL4A4 ; EYA1 ; HNF1B ; WT1 ; NBEA ; m.3243A>G ). Participants with a family history of CKD were more likely to have a positive result (odds ratio, 3.29; 95% confidence interval, 1.10 to 11.29). Thirteen percent of participants without a CKD family history had a positive result. In those who first presented in stage 5 CKD, WGS with broad analysis of a curated kidney disease gene panel was diagnostically more informative than kidney biopsy, with biopsy being inconclusive in 24 of the 25 participants. Conclusions In this prospectively ascertained Australian cohort, we identified a genetic diagnosis in 25% of patients with kidney failure of unknown cause.
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Affiliation(s)
- Amali C. Mallawaarachchi
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Genomic and Inherited Diseases Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Lindsay Fowles
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Louise Wardrop
- KidGen Collaborative, Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alasdair Wood
- KidGen Collaborative, Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Rosie O'Shea
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Erik Biros
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Queensland, Australia
- Townsville University Hospital, Townsville, Queensland, Australia
| | - Trudie Harris
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Townsville University Hospital, Townsville, Queensland, Australia
| | - Stephen I. Alexander
- Centre for Kidney Research at the Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Department of Nephrology, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Bodek
- Clinical Genetics Service, Austin Health, Melbourne, Victoria, Australia
| | - Neil Boudville
- Medical School, University of Western Australia, Crawley, Western Australia, Australia
| | - Jo Burke
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Leslie Burnett
- Genomic and Inherited Diseases Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia
- St Vincent's Healthcare Clinical Campus, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sarah Casauria
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Steve Chadban
- Renal Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Aron Chakera
- Harry Perkins Institute for Medical Research, University of Western Australia, Crawley, Western Australia, Australia
- Renal Unit, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Sam Crafter
- The Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Pei Dai
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Paul De Fazio
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Randall Faull
- Renal Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew Honda
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Vanessa Huntley
- Adult Genetics Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Sadia Jahan
- The Central and Northern Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Kushani Jayasinghe
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
- Department of Nephrology, Monash Health, Melbourne, Victoria, Australia
- Melbourne Health, Melbourne, Victoria, Australia
| | - Matthew Jose
- Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Anna Leaver
- Clinical Genetics Service, Austin Health, Melbourne, Victoria, Australia
| | - Mandi MacShane
- Genetic Services of WA, KEMH, Subiaco, Western Australia, Australia
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | | | - Kathy Nicholls
- Nephrology Unit, Royal Melbourne Hospital, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Rhonda Pawlowski
- Anatomical Pathology, Monash Health, Melbourne, Victoria, Australia
| | - Gopi Rangan
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
- Michael Stern Laboratory for Polycystic Kidney Disease, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Paul Snelling
- Renal Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Jacqueline Soraru
- Department of Nephrology and Hypertension, Perth Children's Hospital, Nedlands, Western Australia, Australia
- Department of Nephrology and Renal Transplantation, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | | | - Michel Tchan
- Genetic Medicine, Westmead Hospital, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Giulia Valente
- Clinical Genetics Service, Austin Health, Melbourne, Victoria, Australia
| | - Mathew Wallis
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, Tasmania, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Laura Wedd
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
| | - Matthew Welland
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Whitlam
- Department of Nephrology, Austin Health, Melbourne, Victoria, Australia
| | - Ella J. Wilkins
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hugh McCarthy
- Centre for Kidney Research at the Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Department of Nephrology, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Catherine Quinlan
- Department of Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Nephrology, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew J. Mallett
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Townsville University Hospital, Townsville, Queensland, Australia
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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4
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Stevens PE, Ahmed SB, Carrero JJ, Foster B, Francis A, Hall RK, Herrington WG, Hill G, Inker LA, Kazancıoğlu R, Lamb E, Lin P, Madero M, McIntyre N, Morrow K, Roberts G, Sabanayagam D, Schaeffner E, Shlipak M, Shroff R, Tangri N, Thanachayanont T, Ulasi I, Wong G, Yang CW, Zhang L, Levin A. KDIGO 2024 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease. Kidney Int 2024; 105:S117-S314. [PMID: 38490803 DOI: 10.1016/j.kint.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 03/17/2024]
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5
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Lee BK, Thomas CP. Genetic testing in the evaluation of recipient candidates and living kidney donors. Curr Opin Nephrol Hypertens 2024; 33:4-12. [PMID: 37823847 DOI: 10.1097/mnh.0000000000000934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
PURPOSE OF REVIEW The aim of this study is to provide an overview of the role of genetic testing in the evaluation of kidney transplant candidates and living donors who may be at risk for heritable kidney disease. We focus our discussion on monogenic diseases, excluding renal diseases that have complex polygenic influences. Adoption of new technologies such as next-generation sequencing (NGS) with comprehensive gene panels has greatly enabled access to genetic testing recently; yet transplant professionals rarely receive adequate training in clinical genetics. In addition to a broad discussion of genetic testing, we hope to illustrate the thought processes and resources used in clinical genetic evaluation of recipient candidates and donors. RECENT FINDINGS Targeted renal genetic panels, whole exome and genome sequencing have greatly expanded our ability to test for pathogenic variants. Testing methods, analytic tools and the subsequent interpretation by the testing laboratory and treating physician impacts patient management and clinicians may lack the resources to practice in this new era of genomic medicine. SUMMARY The expansion of genomics into transplant medicine can provide improved diagnosis in transplant candidates and potentially disease prediction in living donors. Transplant professionals need to be familiar with emerging trends, promises and limitations of NGS-based testing.
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Affiliation(s)
- Brian K Lee
- Kidney/Pancreas Transplant Center, Dell Seton Medical Center, University of Texas at Austin, Austin, Texas
| | - Christie P Thomas
- Department of Internal Medicine and Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City
- VA Medical Center, Iowa City, Iowa, USA
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Robert T, Raymond L, Dancer M, Torrents J, Jourde-Chiche N, Burtey S, Béroud C, Mesnard L. Beyond the kidney biopsy: genomic approach to undetermined kidney diseases. Clin Kidney J 2024; 17:sfad099. [PMID: 38186885 PMCID: PMC10765093 DOI: 10.1093/ckj/sfad099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Indexed: 01/09/2024] Open
Abstract
Background According to data from large national registries, almost 20%-25% of patients with end-stage kidney disease have an undetermined kidney disease (UKD). Recent data have shown that monogenic disease-causing variants are under-diagnosed. We performed exome sequencing (ES) on UKD patients in our center to improve the diagnosis rate. Methods ES was proposed in routine practice for patients with UKD including kidney biopsy from January 2019 to December 2021. Mutations were detected using a targeted bioinformatic customized kidney gene panel (675 genes). The pathogenicity was assessed using American College of Medical Genetics guidelines. Results We included 230 adult patients, median age 47.5 years. Consanguinity was reported by 25 patients. A family history of kidney disease was documented in 115 patients (50%). Kidney biopsies were either inconclusive in 69 patients (30.1%) or impossible in 71 (30.9%). We detected 28 monogenic renal disorders in 75 (32.6%) patients. Collagenopathies was the most common genetic kidney diagnosis (46.7%), with COL4A3 and COL4A4 accounting for 80% of these diagnoses. Tubulopathies (16%) and ciliopathies (14.7%) yielded, respectively, the second and third genetic kidney diagnosis category and UMOD-associated nephropathy as the main genetic findings for tubulopathies (7/11). Ten of the 22 patients having ES "first" eventually received a positive diagnosis, thereby avoiding 11 biopsies. Among the 44 patients with glomerular, tubulo-interstitial or vascular nephropathy, 13 (29.5%) were phenocopies. The diagnostic yield of ES was higher in female patients (P = .02) and in patients with a family history of kidney disease (P < .0001), reaching 56.8% when the patient had both first- and second-degree family history of renal disease. Conclusion Genetic diagnosis has provided new clinical insights by clarifying or reclassifying kidney disease etiology in over a third of UKD patients. Exome "first" may have a significant positive diagnostic yield, thus avoiding invasive kidney biopsy; moreover, the diagnostic yield remains elevated even when biopsy is impossible or inconclusive. ES provides a clinical benefit for routine nephrological healthcare in patients with UKD.
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Affiliation(s)
- Thomas Robert
- Centre of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Marseille Medical Genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Marine Dancer
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Julia Torrents
- Department of Renal Pathology, CHU Timone, AP-HM, Marseille, France
| | - Noémie Jourde-Chiche
- Centre of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Stéphane Burtey
- Centre of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Christophe Béroud
- Marseille Medical Genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Laurent Mesnard
- Urgences Néphrologiques et Transplantation Rénale, Sorbonne Université, APHP, Hôpital Tenon, Paris, France
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7
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Budde K, Rostaing L. A first small step toward personalized immunosuppression. Kidney Int 2023; 104:652-654. [PMID: 37739615 DOI: 10.1016/j.kint.2023.06.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 09/24/2023]
Abstract
Lloberas et al. provide further evidence for the benefits of an individualized tacrolimus dosing algorithm based on population pharmacokinetics and pharmacogenetics. Better tacrolimus dosing could prevent underexposure and overexposure and potentially save costs. Most important, this could be the start of precision medicine in kidney transplantation, incorporating improved immunologic and donor quality assessments, advanced biopsy readouts, innovative pharmacogenomics for drug safety, and novel diagnostic and outcome algorithms to guide a truly personalized therapy.
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Affiliation(s)
- Klemens Budde
- Department of Nephrology and Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Lionel Rostaing
- Department of Nephrology, Hemodialysis, Apheresis, and Transplantation, CHU Grenoble-Alpes, Grenoble, France
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8
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Cirillo L, De Chiara L, Innocenti S, Errichiello C, Romagnani P, Becherucci F. Chronic kidney disease in children: an update. Clin Kidney J 2023; 16:1600-1611. [PMID: 37779846 PMCID: PMC10539214 DOI: 10.1093/ckj/sfad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Indexed: 10/03/2023] Open
Abstract
Chronic kidney disease (CKD) is a major healthcare issue worldwide. However, the prevalence of pediatric CKD has never been systematically assessed and consistent information is lacking in this population. The current definition of CKD is based on glomerular filtration rate (GFR) and the extent of albuminuria. Given the physiological age-related modification of GFR in the first years of life, the definition of CKD is challenging per se in the pediatric population, resulting in high risk of underdiagnosis in this population, treatment delays and untailored clinical management. The advent and spreading of massive-parallel sequencing technology has prompted a profound revision of the epidemiology and the causes of CKD in children, supporting the hypothesis that CKD is much more frequent than currently reported in children and adolescents. This acquired knowledge will eventually converge in the identification of the molecular pathways and cellular response to damage, with new specific therapeutic targets to control disease progression and clinical features of children with CKD. In this review, we will focus on recent innovations in the field of pediatric CKD and in particular those where advances in knowledge have become available in the last years, with the aim of providing a new perspective on CKD in children and adolescents.
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Affiliation(s)
- Luigi Cirillo
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Letizia De Chiara
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Samantha Innocenti
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Carmela Errichiello
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Paola Romagnani
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Francesca Becherucci
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
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Robert T, greillier S, Torrents J, Raymond L, Dancer M, Jourde-Chiche N, Halimi JM, Burtey S, Béroud C, Mesnard L. Diagnosis of Kidney Diseases of Unknown Etiology Through Biopsy-Genetic Analysis. Kidney Int Rep 2023; 8:2077-2087. [PMID: 37850010 PMCID: PMC10577324 DOI: 10.1016/j.ekir.2023.07.003] [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: 03/14/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Previous studies have suggested that genetic kidney diseases in adults are often overlooked, representing up to 10% of all cases of chronic kidney disease (CKD). We present data obtained from exome sequencing (ES) analysis of patients with biopsy-proven undetermined kidney disease (UKD). Methods ES was proposed during routine clinical care in patients with UKD from January 2020 to December 2021. We used in silico custom kidney genes panel analysis to detect pathological variations using American College of Medical Genetics guidelines in 52 patients with biopsy-proven UKD with histological finding reassessment. Results We detected 12 monogenic renal disorders in 21 (40.4%) patients. The most common diagnoses were collagenopathies (8/21,38.1%), COL4A3 and COL4A4 accounting for 80% of these diagnoses, and ciliopathies (5/21, 23.8%). The diagnostic yield of ES was higher in female patients and patients with a family history of kidney disease (57.1% and 71%, respectively). Clinical nephropathy categories matched with the final genetic diagnoses in 72.7% of cases, whereas histological renal lesions matched with the final diagnoses in 92.3% of cases. The genetics diagnoses and histopathological findings were in complete agreement for both glomerular and tubulointerstitial cases. Interstitial inflammation without tubulitis was only observed in tubulopathies or ciliopathies. Isolated CKD, CKD with proteinuria or hematuria, and isolated proteinuria or hematuria yielded the highest diagnostic yields (54.6%, 52.6%, and 42.9%, respectively). Conclusion ES done in patients with biopsy-proven UKD should be considered as a first-line tool for CKD patients with a family history of kidney disease. Combination of ES and kidney biopsy may have major impacts on kidney disease ontology.
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Affiliation(s)
- Thomas Robert
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Marseille medical genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Sophie greillier
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
| | - Julia Torrents
- Department of Renal Pathology, CHU Timone, AP-HM, Marseille, France
| | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Marine Dancer
- Department of Renal Pathology, CHU Timone, AP-HM, Marseille, France
| | - Noémie Jourde-Chiche
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Jean-Michel Halimi
- Néphrologie-Immunologie Clinique, Hôpital Bretonneau, CHU Tours, Tours, France
| | - Stéphane Burtey
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Christophe Béroud
- Marseille medical genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Laurent Mesnard
- Soins Intensifs Néphrologiques et Rein Aigu (SINRA), Sorbonne Université, APHP, Hôpital Tenon, Paris, France
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10
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Sharma A, Lanktree MB, Liskowich S, Dokouhaki P, Prasad B. Basic Research Protocol: Exome Sequencing in Adults With Loin Pain Hematuria Syndrome: A Pilot Study. Can J Kidney Health Dis 2023; 10:20543581231183856. [PMID: 37426491 PMCID: PMC10328052 DOI: 10.1177/20543581231183856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/18/2023] [Indexed: 07/11/2023] Open
Abstract
Background Loin pain hematuria syndrome (LPHS) is a poorly understood clinical syndrome characterized by hematuria and either unilateral or bilateral severe kidney pain in the absence of identifiable urological disease. Loin pain hematuria syndrome imposes a significant health and economic impact with a loss of productivity and quality of life in a young population. Owing to an incomplete understanding of its pathophysiology, treatment has been limited to nonspecific pain management. Nearly 60 years after its initial description, we are no further ahead in understanding the molecular pathways involved in LPHS. Objective To outline the study design for exome sequencing in adults with LPHS and their families. Methods In this single-center case series, 24 patients with LPHS and 2 additional first-degree family members per participant will be recruited. DNA extracted from venous blood samples will undergo exome sequencing on the Illumina NovaSeq 6000 System at 100× depth and will be assessed for pathogenic variants in genes associated with hematuria (number of genes in: glomerular endothelium [n = 10] and basement membrane [n = 8]), and pain pathways (number of genes in: pain transduction [n = 17], conduction [n = 8], synaptic transmission [n = 37], and modulation [n = 27]). We will further examine identified potentially pathogenic variants that co-segregate with LPHS features among affected families. Conclusions This pilot study may identify new directions for an investigation into the molecular mechanisms underlying LPHS.
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Affiliation(s)
- Aditi Sharma
- Dr. T. Bhanu Prasad Med Prof Corp, Regina, SK, Canada
| | - Matthew B. Lanktree
- Departments of Medicine and Health Research Methodology, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
- Division of Nephrology, St Joseph’s Healthcare Hamilton, ON, Canada
| | - Sarah Liskowich
- Department of Academic Family Medicine, College of Medicine, University of Saskatchewan, Regina, Canada
| | - Pouneh Dokouhaki
- Department of Pathology and Lab Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Bhanu Prasad
- Section of Nephrology, Department of Medicine, Regina General Hospital, SK, Canada
- College of Medicine, University of Saskatchewan, Regina, Canada
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11
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de Haan A, van Eerde AM, Eijgelsheim M, Rump P, van der Zwaag B, Hennekam E, Živná M, Kmoch S, Bleyer AJ, Kidd K, Vogt L, Knoers NVAM, de Borst MH. Novel MUC1 variant identified by massively parallel sequencing explains interstitial kidney disease in a large Dutch family. Kidney Int 2023; 103:986-989. [PMID: 37085259 DOI: 10.1016/j.kint.2023.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 04/23/2023]
Affiliation(s)
- Amber de Haan
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mark Eijgelsheim
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Patrick Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Eric Hennekam
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Martina Živná
- Research Unit of Rare Disease, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine Charles University, Prague, Czech Republic
| | - Stanislav Kmoch
- Research Unit of Rare Disease, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Anthony J Bleyer
- Research Unit of Rare Disease, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Kendrah Kidd
- Research Unit of Rare Disease, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine Charles University, Prague, Czech Republic; Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Liffert Vogt
- Department of Internal Medicine, Section Nephrology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Nine V A M Knoers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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12
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Thomas CP, Daloul R, Lentine KL, Gohh R, Anand PM, Rasouly HM, Sharfuddin AA, Schlondorff JS, Rodig NM, Freese ME, Garg N, Lee BK, Caliskan Y. Genetic evaluation of living kidney donor candidates: A review and recommendations for best practices. Am J Transplant 2023; 23:597-607. [PMID: 36868514 DOI: 10.1016/j.ajt.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023]
Abstract
The growing accessibility and falling costs of genetic sequencing techniques has expanded the utilization of genetic testing in clinical practice. For living kidney donation, genetic evaluation has been increasingly used to identify genetic kidney disease in potential candidates, especially in those of younger ages. However, genetic testing on asymptomatic living kidney donors remains fraught with many challenges and uncertainties. Not all transplant practitioners are aware of the limitations of genetic testing, are comfortable with selecting testing methods, comprehending test results, or providing counsel, and many do not have access to a renal genetic counselor or a clinical geneticist. Although genetic testing can be a valuable tool in living kidney donor evaluation, its overall benefit in donor evaluation has not been demonstrated and it can also lead to confusion, inappropriate donor exclusion, or misleading reassurance. Until more published data become available, this practice resource should provide guidance for centers and transplant practitioners on the responsible use of genetic testing in the evaluation of living kidney donor candidates.
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Affiliation(s)
- Christie P Thomas
- Department of of Internal Medicine and Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA; VA Medical Center, Iowa City, Iowa, USA.
| | - Reem Daloul
- Division of Nephrology, Department of Internal Medicine, Allegheny General Hospital, Pittsburgh, Pennsylvania, USA
| | - Krista L Lentine
- Saint Louis University Transplant Center, SSM Health Saint Louis University Hospital, St. Louis, Missouri, USA
| | - Reginald Gohh
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Prince M Anand
- Mid-Carolinas Transplant Center, Medical University of South Carolina, Lancaster, South Carolina, USA
| | - Hila Milo Rasouly
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York City, New York, USA
| | - Asif A Sharfuddin
- Division of Nephrology and Transplant, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Johannes S Schlondorff
- Department of Internal Medicine, Ohio State University Medical Center, Columbus, Ohio, USA
| | - Nancy M Rodig
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Margaret E Freese
- Department of of Internal Medicine and Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Neetika Garg
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Brian K Lee
- Kidney/Pancreas Transplant Center, Dell Seton Medical Center, University of Texas at Austin, Austin, Texas, USA
| | - Yasar Caliskan
- Saint Louis University Transplant Center, SSM Health Saint Louis University Hospital, St. Louis, Missouri, USA
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13
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Trac N, Ashraf A, Giblin J, Prakash S, Mitragotri S, Chung EJ. Spotlight on Genetic Kidney Diseases: A Call for Drug Delivery and Nanomedicine Solutions. ACS NANO 2023; 17:6165-6177. [PMID: 36988207 PMCID: PMC10145694 DOI: 10.1021/acsnano.2c12140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Nanoparticles as drug delivery carriers have benefited diseases, including cancer, since the 1990s, and more recently, their promise to quickly and efficiently be mobilized to fight against global diseases such as in the COVID-19 pandemic have been proven. Despite these success stories, there are limited nanomedicine efforts for chronic kidney diseases (CKDs), which affect 844 million people worldwide and can be linked to a variety of genetic kidney diseases. In this Perspective, we provide a brief overview of the clinical status of genetic kidney diseases, background on kidney physiology and a summary of nanoparticle design that enable kidney access and targeting, and emerging technological strategies that can be applied for genetic kidney diseases, including rare and congenital kidney diseases. Finally, we conclude by discussing gaps in knowledge remaining in both genetic kidney diseases and kidney nanomedicine and collective efforts that are needed to bring together stakeholders from diverse expertise and industries to enable the development of the most relevant drug delivery strategies that can make an impact in the clinic.
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Affiliation(s)
- Noah Trac
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
| | - Anisa Ashraf
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
| | - Joshua Giblin
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
| | - Supriya Prakash
- John
A. Paulson School of Engineering & Applied Sciences, Harvard University, Allston, Massachusetts 02134, United States
- Wyss
Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Samir Mitragotri
- John
A. Paulson School of Engineering & Applied Sciences, Harvard University, Allston, Massachusetts 02134, United States
- Wyss
Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Eun Ji Chung
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
- Division
of Nephrology and Hypertension, Department of Medicine, Keck School
of Medicine, University of Southern California, Los Angeles, California 90033, United States
- Norris
Comprehensive Cancer Center, University
of Southern California, Los Angeles, California 90033, United States
- Eli and Edythe
Broad Center for Regenerative Medicine and Stem Cell Research, Keck
School of Medicine, University of Southern
California, Los Angeles, California 90033, United States
- Division
of Vascular Surgery and Endovascular Therapy, Department of Surgery,
Keck School of Medicine, University of Southern
California, Los Angeles, California 90033, United States
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
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14
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Becherucci F, Landini S, Palazzo V, Cirillo L, Raglianti V, Lugli G, Tiberi L, Dirupo E, Bellelli S, Mazzierli T, Lomi J, Ravaglia F, Sansavini G, Allinovi M, Giannese D, Somma C, Spatoliatore G, Vergani D, Artuso R, Rosati A, Cirami C, Dattolo PC, Campolo G, De Chiara L, Papi L, Vaglio A, Lazzeri E, Anders HJ, Mazzinghi B, Romagnani P. A Clinical Workflow for Cost-Saving High-Rate Diagnosis of Genetic Kidney Diseases. J Am Soc Nephrol 2023; 34:706-720. [PMID: 36753701 PMCID: PMC10103218 DOI: 10.1681/asn.0000000000000076] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/19/2022] [Indexed: 01/22/2023] Open
Abstract
SIGNIFICANCE STATEMENT To optimize the diagnosis of genetic kidney disorders in a cost-effective manner, we developed a workflow based on referral criteria for in-person evaluation at a tertiary center, whole-exome sequencing, reverse phenotyping, and multidisciplinary board analysis. This workflow reached a diagnostic rate of 67%, with 48% confirming and 19% modifying the suspected clinical diagnosis. We obtained a genetic diagnosis in 64% of children and 70% of adults. A modeled cost analysis demonstrated that early genetic testing saves 20% of costs per patient. Real cost analysis on a representative sample of 66 patients demonstrated an actual cost reduction of 41%. This workflow demonstrates feasibility, performance, and economic effect for the diagnosis of genetic kidney diseases in a real-world setting. BACKGROUND Whole-exome sequencing (WES) increases the diagnostic rate of genetic kidney disorders, but accessibility, interpretation of results, and costs limit use in daily practice. METHODS Univariable analysis of a historical cohort of 392 patients who underwent WES for kidney diseases showed that resistance to treatments, familial history of kidney disease, extrarenal involvement, congenital abnormalities of the kidney and urinary tract and CKD stage ≥G2, two or more cysts per kidney on ultrasound, persistent hyperechoic kidneys or nephrocalcinosis on ultrasound, and persistent metabolic abnormalities were most predictive for genetic diagnosis. We prospectively applied these criteria to select patients in a network of nephrology centers, followed by centralized genetic diagnosis by WES, reverse phenotyping, and multidisciplinary board discussion. RESULTS We applied this multistep workflow to 476 patients with eight clinical categories (podocytopathies, collagenopathies, CKD of unknown origin, tubulopathies, ciliopathies, congenital anomalies of the kidney and urinary tract, syndromic CKD, metabolic kidney disorders), obtaining genetic diagnosis for 319 of 476 patients (67.0%) (95% in 21 patients with disease onset during the fetal period or at birth, 64% in 298 pediatric patients, and 70% in 156 adult patients). The suspected clinical diagnosis was confirmed in 48% of the 476 patients and modified in 19%. A modeled cost analysis showed that application of this workflow saved 20% of costs per patient when performed at the beginning of the diagnostic process. Real cost analysis of 66 patients randomly selected from all categories showed actual cost reduction of 41%. CONCLUSIONS A diagnostic workflow for genetic kidney diseases that includes WES is cost-saving, especially if implemented early, and is feasible in a real-world setting.
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Affiliation(s)
- Francesca Becherucci
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Samuela Landini
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Viviana Palazzo
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Luigi Cirillo
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Valentina Raglianti
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Gianmarco Lugli
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Lucia Tiberi
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Elia Dirupo
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | | | - Tommaso Mazzierli
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Jacopo Lomi
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | | | - Giulia Sansavini
- Nephrology and Dialysis Unit, Santo Stefano Hospital, Prato, Italy
| | - Marco Allinovi
- Nephrology, Dialysis and Transplantation Unit, Careggi University Hospital, Florence, Italy
| | | | - Chiara Somma
- Nephrology Unit Florence 1, Santa Maria Annunziata Hospital, Bagno a Ripoli, Florence, Italy
| | - Giuseppe Spatoliatore
- Nephrology and Dialysis Unit, San Giovanni di Dio Hospital, AUSL Toscana Centro, Florence, Italy
| | - Debora Vergani
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Rosangela Artuso
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Alberto Rosati
- Nephrology and Dialysis Unit, San Giovanni di Dio Hospital, AUSL Toscana Centro, Florence, Italy
| | - Calogero Cirami
- Nephrology, Dialysis and Transplantation Unit, Careggi University Hospital, Florence, Italy
| | - Pietro Claudio Dattolo
- Nephrology Unit Florence 1, Santa Maria Annunziata Hospital, Bagno a Ripoli, Florence, Italy
| | - Gesualdo Campolo
- Nephrology and Dialysis Unit, Santo Stefano Hospital, Prato, Italy
| | - Letizia De Chiara
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Laura Papi
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Augusto Vaglio
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Elena Lazzeri
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Hans-Joachim Anders
- Division of Nephrology, Medizinische Klinik and Poliklinik IV, Klinikum der LMU München, Munich, Germany
| | - Benedetta Mazzinghi
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Paola Romagnani
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
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15
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Peek JL, Wilson MH. Cell and gene therapy for kidney disease. Nat Rev Nephrol 2023:10.1038/s41581-023-00702-3. [PMID: 36973494 DOI: 10.1038/s41581-023-00702-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2023] [Indexed: 03/29/2023]
Abstract
Kidney disease is a leading cause of morbidity and mortality across the globe. Current interventions for kidney disease include dialysis and renal transplantation, which have limited efficacy or availability and are often associated with complications such as cardiovascular disease and immunosuppression. There is therefore a pressing need for novel therapies for kidney disease. Notably, as many as 30% of kidney disease cases are caused by monogenic disease and are thus potentially amenable to genetic medicine, such as cell and gene therapy. Systemic disease that affects the kidney, such as diabetes and hypertension, might also be targetable by cell and gene therapy. However, although there are now several approved gene and cell therapies for inherited diseases that affect other organs, none targets the kidney. Promising recent advances in cell and gene therapy have been made, including in the kidney research field, suggesting that this form of therapy might represent a potential solution for kidney disease in the future. In this Review, we describe the potential for cell and gene therapy in treating kidney disease, focusing on recent genetic studies, key advances and emerging technologies, and we describe several crucial considerations for renal genetic and cell therapies.
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Affiliation(s)
- Jennifer L Peek
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Matthew H Wilson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN, USA.
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16
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Schlevogt B, Schlieper V, Krader J, Schröter R, Wagner T, Weiand M, Zibert A, Schmidt HH, Bergmann C, Nedvetsky PI, Krahn MP. A SEC61A1 variant is associated with autosomal dominant polycystic liver disease. Liver Int 2023; 43:401-412. [PMID: 36478640 DOI: 10.1111/liv.15493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/28/2022] [Accepted: 11/12/2022] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND AIMS Autosomal dominant polycystic liver and kidney disease is a spectrum of hereditary diseases, which display disturbed function of primary cilia leading to cyst formation. In autosomal dominant polycystic kidney disease a genetic cause can be determined in almost all cases. However, in isolated polycystic liver disease (PLD) about half of all cases remain genetically unsolved, suggesting more, so far unidentified genes to be implicated in this disease. METHODS Customized next-generation sequencing was used to identify the underlying pathogenesis in two related patients with PLD. A variant identified in SEC61A1 was further analysed in immortalized patients' urine sediment cells and in an epithelial cell model. RESULTS In both patients, a heterozygous missense change (c.706C>T/p.Arg236Cys) was found in SEC61A1, which encodes for a subunit of the translocation machinery of protein biosynthesis at the endoplasmic reticulum (ER). While kidney disease is absent in the proposita, her mother displays an atypical polycystic kidney phenotype with severe renal failure. In immortalized urine sediment cells, mutant SEC61A1 is expressed at reduced levels, resulting in decreased levels of polycystin-2 (PC2). In an epithelial cell culture model, we found the proteasomal degradation of mutant SEC61A1 to be increased, whereas its localization to the ER is not affected. CONCLUSIONS Our data expand the allelic and clinical spectrum for SEC61A1, adding PLD as a new and the major phenotypic trait in the family described. We further demonstrate that mutant SEC61A1 results in enhanced proteasomal degradation and impaired biosynthesis of PC2.
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Affiliation(s)
- Bernhard Schlevogt
- Department of Medicine B, University Hospital Muenster, Muenster, Germany
| | - Vincent Schlieper
- Department of Medicine D, University Hospital Muenster, Muenster, Germany
| | - Jana Krader
- Department of Medicine D, University Hospital Muenster, Muenster, Germany
| | - Rita Schröter
- Department of Medicine D, University Hospital Muenster, Muenster, Germany
| | - Thomas Wagner
- Department of Medicine D, University Hospital Muenster, Muenster, Germany
| | - Matthias Weiand
- Department of Medicine B, University Hospital Muenster, Muenster, Germany
| | - Andree Zibert
- Department of Medicine B, University Hospital Muenster, Muenster, Germany
| | - Hartmut H Schmidt
- Department of Medicine B, University Hospital Muenster, Muenster, Germany.,Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Carsten Bergmann
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.,Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Pavel I Nedvetsky
- Department of Medicine D, University Hospital Muenster, Muenster, Germany
| | - Michael P Krahn
- Department of Medicine D, University Hospital Muenster, Muenster, Germany
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17
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Claus LR, Snoek R, Knoers NVAM, van Eerde AM. Review of genetic testing in kidney disease patients: Diagnostic yield of single nucleotide variants and copy number variations evaluated across and within kidney phenotype groups. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:358-376. [PMID: 36161467 PMCID: PMC9828643 DOI: 10.1002/ajmg.c.31995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/02/2022] [Accepted: 08/18/2022] [Indexed: 01/29/2023]
Abstract
Genetic kidney disease comprises a diverse group of disorders. These can roughly be divided in the phenotype groups congenital anomalies of the kidney and urinary tract, ciliopathies, glomerulopathies, stone disorders, tubulointerstitial kidney disease, and tubulopathies. Many etiologies can lead to chronic kidney disease that can progress to end-stage kidney disease. Despite each individual disease being rare, together these genetic disorders account for a large proportion of kidney disease cases. With the introduction of massively parallel sequencing, genetic testing has become more accessible, but a comprehensive analysis of the diagnostic yield is lacking. This review gives an overview of the diagnostic yield of genetic testing across and within the full range of kidney disease phenotypes through a systematic literature search that resulted in 115 included articles. Patient, test, and cohort characteristics that can influence the diagnostic yield are highlighted. Detection of copy number variations and their contribution to the diagnostic yield is described for all phenotype groups. Also, the impact of a genetic diagnosis for a patient and family members, which can be diagnostic, therapeutic, and prognostic, is shown through the included articles. This review will allow clinicians to estimate an a priori probability of finding a genetic cause for the kidney disease in their patients.
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Affiliation(s)
- Laura R. Claus
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Rozemarijn Snoek
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nine V. A. M. Knoers
- Department of GeneticsUniversity Medical Center GroningenGroningenThe Netherlands
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18
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A multidisciplinary nephrogenetic referral clinic for children and adults-diagnostic achievements and insights. Pediatr Nephrol 2022; 37:1623-1646. [PMID: 34993602 DOI: 10.1007/s00467-021-05374-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Genetic kidney diseases contribute a significant portion of kidney diseases in children and young adults. Nephrogenetics is a rapidly evolving subspecialty; however, in the clinical setting, increased use of genetic testing poses implementation challenges. Consequently, we established a national nephrogenetics clinic to apply a multidisciplinary model. METHODS Patients were referred from different pediatric or adult nephrology units across the country if their primary nephrologist suspected an undiagnosed genetic kidney disease. We determined the diagnostic rate and observed the effect of diagnosis on medical care. We also discuss the requirements of a nephrogenetics clinic in terms of logistics, recommended indications for referral, and building a multidisciplinary team. RESULTS Over 24 months, genetic evaluation was completed for a total of 74 unrelated probands, with an age range of 10 days to 72 years. The most common phenotypes included congenital anomalies of the kidneys and urinary tract, nephrotic syndrome or unexplained proteinuria, nephrocalcinosis/nephrolithiasis, tubulopathies, and unexplained kidney failure. Over 80% of patients were referred due to clinical suspicion of an undetermined underlying genetic diagnosis. A molecular diagnosis was reached in 42/74 probands, yielding a diagnostic rate of 57%. Of these, over 71% of diagnoses were made via next generation sequencing (gene panel or exome sequencing). CONCLUSIONS We identified a substantial fraction of genetic kidney etiologies among previously undiagnosed individuals which influenced subsequent clinical management. Our results support that nephrogenetics, a rapidly evolving field, may benefit from well-defined multidisciplinary co-management administered by a designated team of nephrologist, geneticist, and bioinformatician. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Soraru J, Jahan S, Quinlan C, Simons C, Wardrop L, O'Shea R, Wood A, Mallawaarachchi A, Patel C, Stark Z, Mallett AJ. The HIDDEN Protocol: An Australian Prospective Cohort Study to Determine the Utility of Whole Genome Sequencing in Kidney Failure of Unknown Aetiology. Front Med (Lausanne) 2022; 9:891223. [PMID: 35721054 PMCID: PMC9204488 DOI: 10.3389/fmed.2022.891223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
Early identification of genetic kidney disease allows personalised management, clarification of risk for relatives, and guidance for family planning. Genetic disease is underdiagnosed, and recognition of genetic disease is particularly challenging in patients with kidney failure without distinguishing diagnostic features. To address this challenge, the primary aim of this study is to determine the proportion of genetic diagnoses amongst patients with kidney failure of unknown aetiology, using whole genome sequencing (WGS). A cohort of up to 100 Australian patients with kidney failure of unknown aetiology, with onset <50 years old and approved by a panel of study investigators will be recruited via 18 centres nationally. Clinically accredited WGS will be undertaken with analysis targeted to a priority list of ∼388 genes associated with genetic kidney disease. The primary outcome will be the proportion of patients who receive a molecular diagnosis (diagnostic rate) via WGS compared with usual -care (no further diagnostic investigation). Participant surveys will be undertaken at consent, after test result return and 1 year subsequently. Where there is no or an uncertain diagnosis, future research genomics will be considered to identify candidate genes and new pathogenic variants in known genes. All results will be relayed to participants via the recruiting clinician and/or kidney genetics clinic. The study is ethically approved (HREC/16/MH/251) with local site governance approvals in place. The future results of this study will be disseminated and inform practical understanding of the potential monogenic contribution to kidney failure of unknown aetiology. These findings are anticipated to impact clinical practice and healthcare policy.
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Affiliation(s)
- Jacqueline Soraru
- Department of Nephrology and Hypertension, Perth Children's Hospital, Perth, WA, Australia
| | - Sadia Jahan
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.,Faculty of Medicine, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Catherine Quinlan
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Cas Simons
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Louise Wardrop
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rosie O'Shea
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Alasdair Wood
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amali Mallawaarachchi
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Chirag Patel
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew John Mallett
- Faculty of Medicine, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.,Townsville University Hospital, Townsville, QLD, Australia.,College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
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20
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Bergmann C. [Polycystic kidneys: Genetic testing and correct classification clinically and therapeutically of increasing significance]. Dtsch Med Wochenschr 2022; 147:710-717. [PMID: 35636423 DOI: 10.1055/a-1337-1828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cystic kidney disease is a clinically and genetically diverse group of diseases, with more than 100 genes known to date. One in 500 is affected worldwide, mostly due to a malfunction of cilia. New genes have been identified recently for the most common form autosomal dominant polycystic kidney disease (ADPKD). Every fourth ADPKD patient is lacking a positive family history (mostly due to a de novo mutation); in these cases remaining family members can be relieved. Differentiation of entities just based on clinical and imaging data is often most challenging. However, an accurate classification is significant for the patient and family. Associated comorbidities and cross-organ complications can be detected early and targeted screening and monitoring can be facilitated. Relatives also benefit from an accurate and early diagnosis. Precise genetic counselling with indication of risks is only possible by knowing the concise disease genotype. Genetic diagnostics is becoming increasingly important in this context and in terms of risk stratification and drug-therapeutic options. The understanding of genotype-phenotype correlations has improved significantly in recent years. Wet and dry lab processes as well as the interpretation of genetic data for ADPKD require a high level of expertise. Differential diagnoses with mutations in other genes underlie patients with "ADPKD" or ADPKD-like phenotypes much more frequently than usually assumed. Due to the number and complexity of genes that need to be considered, a tailored NGS (Next Generation Sequencing) approach using a customized, well-balanced multi-gene panel is cost-effective and currently the method of choice. Differences in the quality of laboratories must be taken into account. With this, the genetic etiology and underlying mutation(s) can be found in most cases.
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21
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Devane J, Ott E, Olinger EG, Epting D, Decker E, Friedrich A, Bachmann N, Renschler G, Eisenberger T, Briem-Richter A, Grabhorn EF, Powell L, Wilson IJ, Rice SJ, Miles CG, Wood K, Trivedi P, Hirschfield G, Pietrobattista A, Wohler E, Mezina A, Sobreira N, Agolini E, Maggiore G, Dahmer-Heath M, Yilmaz A, Boerries M, Metzger P, Schell C, Grünewald I, Konrad M, König J, Schlevogt B, Sayer JA, Bergmann C. Progressive liver, kidney, and heart degeneration in children and adults affected by TULP3 mutations. Am J Hum Genet 2022; 109:928-943. [PMID: 35397207 PMCID: PMC9118107 DOI: 10.1016/j.ajhg.2022.03.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/22/2022] [Indexed: 12/31/2022] Open
Abstract
Organ fibrosis is a shared endpoint of many diseases, yet underlying mechanisms are not well understood. Several pathways governed by the primary cilium, a sensory antenna present on most vertebrate cells, have been linked with fibrosis. Ciliopathies usually start early in life and represent a considerable disease burden. We performed massively parallel sequencing by using cohorts of genetically unsolved individuals with unexplained liver and kidney failure and correlated this with clinical, imaging, and histopathological analyses. Mechanistic studies were conducted with a vertebrate model and primary cells. We detected bi-allelic deleterious variants in TULP3, encoding a critical adaptor protein for ciliary trafficking, in a total of 15 mostly adult individuals, originating from eight unrelated families, with progressive degenerative liver fibrosis, fibrocystic kidney disease, and hypertrophic cardiomyopathy with atypical fibrotic patterns on histopathology. We recapitulated the human phenotype in adult zebrafish and confirmed disruption of critical ciliary cargo composition in several primary cell lines derived from affected individuals. Further, we show interaction between TULP3 and the nuclear deacetylase SIRT1, with roles in DNA damage repair and fibrosis, and report increased DNA damage ex vivo. Transcriptomic studies demonstrated upregulation of profibrotic pathways with gene clusters for hypertrophic cardiomyopathy and WNT and TGF-β signaling. These findings identify variants in TULP3 as a monogenic cause for progressive degenerative disease of major organs in which affected individuals benefit from early detection and improved clinical management. Elucidation of mechanisms crucial for DNA damage repair and tissue maintenance will guide novel therapeutic avenues for this and similar genetic and non-genomic diseases.
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Affiliation(s)
- John Devane
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Elisabeth Ott
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Eric G Olinger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Daniel Epting
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Eva Decker
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | - Anja Friedrich
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | - Nadine Bachmann
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | - Gina Renschler
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | | | - Andrea Briem-Richter
- University Medical Center Hamburg-Eppendorf, Department of Pediatrics, 20251 Hamburg, Germany
| | - Enke Freya Grabhorn
- University Medical Center Hamburg-Eppendorf, Department of Pediatrics, 20251 Hamburg, Germany
| | - Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Ian J Wilson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Sarah J Rice
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Colin G Miles
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Katrina Wood
- Histopathology Department, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Palak Trivedi
- NIHR Birmingham BRC, Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK; Liver Unit, University Hospitals Birmingham, Birmingham B15 2GW, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK; Institute of Applied Health Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Gideon Hirschfield
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M6H 3M1, Canada
| | - Andrea Pietrobattista
- Hepatogastroenterology and Liver Transplant Unit and Medical Genetics Laboratory, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anya Mezina
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emanuele Agolini
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Giuseppe Maggiore
- Hepatogastroenterology and Liver Transplant Unit and Medical Genetics Laboratory, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Mareike Dahmer-Heath
- Department of General Pediatrics, University Hospital Münster, 48149 Münster, Germany
| | - Ali Yilmaz
- Department of Cardiology I, University Hospital Münster, 48149 Münster, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine Medical Center - University of Freiburg, Medical Faculty, University of Freiburg, 79110 Freiburg, Germany; The German Cancer Consortium, Partner Site Freiburg and Cancer Research Center, 69120 Heidelberg, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine Medical Center - University of Freiburg, Medical Faculty, University of Freiburg, 79110 Freiburg, Germany
| | - Christoph Schell
- Institute for Pathology, Medical Center - University of Freiburg, Medical Faculty, University of Freiburg, 79002 Freiburg, Germany
| | - Inga Grünewald
- Institute for Pathology, University Hospital Münster, 48149 Münster, Germany
| | - Martin Konrad
- Department of General Pediatrics, University Hospital Münster, 48149 Münster, Germany
| | - Jens König
- Department of General Pediatrics, University Hospital Münster, 48149 Münster, Germany
| | - Bernhard Schlevogt
- Department of Internal Medicine B, Gastroenterology, University Hospital Münster, 48149 Münster, Germany
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK; Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK; Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne NE4 5PL, UK.
| | - Carsten Bergmann
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany; Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany.
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22
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Soraru J, Chakera A, Isbel N, Mallawaarachichi A, Rogers N, Trnka P, Patel C, Mallett A. The evolving role of diagnostic genomics in kidney transplantation. Kidney Int Rep 2022; 7:1758-1771. [PMID: 35967121 PMCID: PMC9366366 DOI: 10.1016/j.ekir.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/06/2022] Open
Abstract
Monogenic forms of heritable kidney disease account for a significant proportion of chronic kidney disease (CKD) across both pediatric and adult patient populations and up to 11% of patients under 40 years reaching end-stage kidney failure (KF) and awaiting kidney transplant. Diagnostic genomics in the field of nephrology is ever evolving and now plays an important role in assessment and management of kidney transplant recipients and their related donor pairs. Genomic testing can help identify the cause of KF in kidney transplant recipients and assist in prognostication around graft survival and rate of recurrence of primary kidney disease. If a gene variant has been identified in the recipient, at-risk related donors can be assessed for the same and excluded if affected. This paper aims to address the indications for genomic testing in the context for kidney transplantation, the technologies available for testing, the conditions and groups in which testing should be most often considered, and the role for the renal genetics multidisciplinary team in this process.
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23
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Chen X, Faviez C, Vincent M, Briseño-Roa L, Faour H, Annereau JP, Lyonnet S, Zaidan M, Saunier S, Garcelon N, Burgun A. Patient-Patient Similarity-Based Screening of a Clinical Data Warehouse to Support Ciliopathy Diagnosis. Front Pharmacol 2022; 13:786710. [PMID: 35401179 PMCID: PMC8993144 DOI: 10.3389/fphar.2022.786710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
A timely diagnosis is a key challenge for many rare diseases. As an expanding group of rare and severe monogenic disorders with a broad spectrum of clinical manifestations, ciliopathies, notably renal ciliopathies, suffer from important underdiagnosis issues. Our objective is to develop an approach for screening large-scale clinical data warehouses and detecting patients with similar clinical manifestations to those from diagnosed ciliopathy patients. We expect that the top-ranked similar patients will benefit from genetic testing for an early diagnosis. The dependence and relatedness between phenotypes were taken into account in our similarity model through medical concept embedding. The relevance of each phenotype to each patient was also considered by adjusted aggregation of phenotype similarity into patient similarity. A ranking model based on the best-subtype-average similarity was proposed to address the phenotypic overlapping and heterogeneity of ciliopathies. Our results showed that using less than one-tenth of learning sources, our language and center specific embedding provided comparable or better performances than other existing medical concept embeddings. Combined with the best-subtype-average ranking model, our patient-patient similarity-based screening approach was demonstrated effective in two large scale unbalanced datasets containing approximately 10,000 and 60,000 controls with kidney manifestations in the clinical data warehouse (about 2 and 0.4% of prevalence, respectively). Our approach will offer the opportunity to identify candidate patients who could go through genetic testing for ciliopathy. Earlier diagnosis, before irreversible end-stage kidney disease, will enable these patients to benefit from appropriate follow-up and novel treatments that could alleviate kidney dysfunction.
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Affiliation(s)
- Xiaoyi Chen
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France.,HeKA, Inria, Paris, France.,Data Science Platform, Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France
| | - Carole Faviez
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France.,HeKA, Inria, Paris, France
| | - Marc Vincent
- Data Science Platform, Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France
| | | | - Hassan Faour
- Data Science Platform, Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France
| | | | | | - Mohamad Zaidan
- Service de Néphrologie, Hôpital Universitaire Bicêtre, Kremlin Bicêtre, France
| | - Sophie Saunier
- Laboratory of Renal Hereditary Diseases, Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France
| | - Nicolas Garcelon
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France.,HeKA, Inria, Paris, France.,Data Science Platform, Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France
| | - Anita Burgun
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France.,HeKA, Inria, Paris, France.,Department of Medical Informatics, Hôpital Necker-Enfant Malades, AP-HP, Paris, France
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Abstract
PURPOSE OF REVIEW The aim of this study was to summarize recent findings in kidney gene therapy while proposing cystinuria as a model kidney disease target for genome engineering therapeutics. RECENT FINDINGS Despite the advances of gene therapy for treating diseases of other organs, the kidney lags behind. Kidney-targeted gene delivery remains an obstacle to gene therapy of kidney disease. Nanoparticle and adeno-associated viral vector technologies offer emerging hope for kidney gene therapy. Cystinuria represents a model potential target for kidney gene therapy due to its known genetic and molecular basis, targetability, and capacity for phenotypic rescue. SUMMARY Although gene therapy for kidney disease remains a major challenge, new and evolving technologies may actualize treatment for cystinuria and other kidney diseases.
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Affiliation(s)
- Jennifer L. Peek
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232
| | - Matthew H. Wilson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN, 37212
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25
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Choi M, Rübsam A, Schulz M, Decker E, Friedrich A, Schrezenmeier E, Halleck F, Eckardt KU, Bergmann C. Interstitial nephritis - A Change in Diagnosis with Next Generation Sequencing. Kidney Int Rep 2022; 7:1128-1130. [PMID: 35571004 PMCID: PMC9091579 DOI: 10.1016/j.ekir.2022.01.1061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 10/25/2022] Open
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26
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2295-2306. [DOI: 10.1093/hmg/ddac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
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Detection of DZIP1L mutations by whole-exome sequencing in consanguineous families with polycystic kidney disease. Pediatr Nephrol 2022; 37:2657-2665. [PMID: 35211789 PMCID: PMC9489574 DOI: 10.1007/s00467-022-05441-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 12/02/2021] [Accepted: 12/21/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND Autosomal recessive polycystic kidney disease is a cystic kidney disease with early onset and clinically characterized by enlarged echogenic kidneys, hypertension, varying degrees of kidney dysfunction, and liver fibrosis. It is most frequently caused by sequence variants in the PKHD1 gene, encoding fibrocystin. In more rare cases, sequence variants in DZIP1L are seen, encoding the basal body protein DAZ interacting protein 1-like protein (DZIP1L). So far, only four different DZIP1L variants have been reported. METHODS Four children from three consanguineous families presenting with polycystic kidney disease were selected for targeted or untargeted exome sequencing. RESULTS We identified two different, previously not reported homozygous DZIP1L sequence variants: c.193 T > C; p.(Cys65Arg), and c.216C > G; p.(Cys72Trp). Functional analyses of the c.216C > G; p.(Cys72Trp) variant indicated mislocalization of mutant DZIP1L. CONCLUSIONS In line with published data, our results suggest a critical role of the N-terminal domain for proper protein function. Although patients with PKHD1-associated autosomal recessive polycystic kidney disease often have liver abnormalities, none of the present four patients showed any clinically relevant liver involvement. Our data demonstrate the power and efficiency of next-generation sequencing-based approaches. While DZIP1L-related polycystic kidney disease certainly represents a rare form of the disease, our results emphasize the importance of including DZIP1L in multigene panels and in the data analysis of whole-exome sequencing for cystic kidney diseases. A higher resolution version of the Graphical abstract is available as Supplementary information.
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