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Coukos A, Saglietti C, Sempoux C, Haubitz M, Greuter T, Mittaz-Crettol L, Maurer F, Mdawar-Bailly E, Moradpour D, Alberio L, Good JM, Baerlocher GM, Fraga M. High prevalence of short telomeres in idiopathic porto-sinusoidal vascular disorder. Hepatol Commun 2024; 8:e0500. [PMID: 39037376 PMCID: PMC11265777 DOI: 10.1097/hc9.0000000000000500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/01/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Telomeres prevent damage to coding DNA as end-nucleotides are lost during mitosis. Mutations in telomere maintenance genes cause excessive telomere shortening, a condition known as short telomere syndrome (STS). One hepatic manifestation documented in STS is porto-sinusoidal vascular disorder (PSVD). METHODS As the etiology of many cases of PSVD remains unknown, this study explored the extent to which short telomeres are present in patients with idiopathic PSVD. RESULTS This monocentric cross-sectional study included patients with histologically defined idiopathic PSVD. Telomere length in 6 peripheral blood leukocyte subpopulations was assessed using fluorescent in situ hybridization and flow cytometry. Variants of telomere-related genes were identified using high-throughput exome sequencing. In total, 22 patients were included, of whom 16 (73%) had short (9/22) or very short (7/22) telomeres according to age-adjusted reference ranges. Fourteen patients (64%) had clinically significant portal hypertension. Shorter telomeres were more frequent in males (p = 0.005) and patients with concomitant interstitial lung disease (p < 0.001), chronic kidney disease (p < 0.001), and erythrocyte macrocytosis (p = 0.007). Portal hypertension (p = 0.021), low serum albumin level (p < 0.001), low platelet count (p = 0.007), and hyperbilirubinemia (p = 0.053) were also associated with shorter telomeres. Variants in known STS-related genes were identified in 4 patients with VSTel and 1 with STel. CONCLUSIONS Short and very short telomeres were highly prevalent in patients with idiopathic PSVD, with 31% presenting with variants in telomere-related genes. Telomere biology may play an important role in vascular liver disease development. Clinicians should consider measuring telomeres in any patient presenting with PSVD.
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Affiliation(s)
- Alexander Coukos
- Divisions of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Chiara Saglietti
- Institute of Pathology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Christine Sempoux
- Institute of Pathology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Monika Haubitz
- Department of Biomedical Research, Laboratory for Hematopoiesis and Molecular Genetics, University of Bern, Bern, Switzerland
| | - Thomas Greuter
- Divisions of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Division of Gastroenterology and Hepatology, Department of Medicine, GZO-Zurich Regional Health Center, Wetzikon, Switzerland
| | - Laureane Mittaz-Crettol
- Genetic Medicine, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fabienne Maurer
- Genetic Medicine, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Elise Mdawar-Bailly
- Divisions of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Darius Moradpour
- Divisions of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Lorenzo Alberio
- Department of Oncology, Hematology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jean-Marc Good
- Genetic Medicine, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gabriela M. Baerlocher
- Department of Biomedical Research, Laboratory for Hematopoiesis and Molecular Genetics, University of Bern, Bern, Switzerland
| | - Montserrat Fraga
- Divisions of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Tarragón B, Peleg Y, Jagannathan G, Sekulic M, Chang JH, Cohen DJ, Crew RJ, Dube GK, Fernandez HE, Husain SA, Mohan S, Morris HK, Appel GB, Jadav P, Santoriello D, Kudose S, Stokes MB, Batal I, Bomback AS. C3 Glomerulopathy Recurs Early after Kidney Transplantation in Serial Biopsies Performed within the First 2 Years after Transplantation. Clin J Am Soc Nephrol 2024; 19:1005-1015. [PMID: 39116277 DOI: 10.2215/cjn.0000000000000474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Background C3 glomerulopathy (C3G), which encompasses C3GN and dense deposit disease (DDD), results from dysregulation of the alternative complement pathway. Data on disease recurrence after kidney transplantation are limited, and details on histologic features of recurrent C3G are scarce. We aimed to evaluate C3G recurrence in the allograft, with a focus on histologic presentation and progression. Methods We retrospectively analyzed 18 patients with native kidney failure attributed to C3G (12 C3GN and six DDD), who received a kidney transplant from January 2016 to January 2023. Demographic, genetic, clinical, and histologic data were studied. The NanoString 770 genes PanCancer Immune Profiling Panel was used for transcriptomic analysis. Disease recurrence was the primary outcome. Results During a median (interquartile range) follow-up period of 37 (18–56) months, C3G recurrence occurred in 16 (89%) patients (11 with C3GN and five with DDD) at a median (interquartile range) of 33 (13–141) days after transplantation. Over a third (38%) of recurrent cases were detected in protocol biopsies, and only 31% of patients presented with >300 mg/g of proteinuria. Recurrence in index biopsies was mainly established through a combination of immunofluorescence and electron microscopy findings, while it showed only subtle histologic alterations and no characteristic transcriptomic signals. Over time, histologic chronicity indices increased, but all the allografts were functioning at the end of follow-up. Patients with recurrence of C3GN and DDD showed overlapping immunofluorescence and electron microscopy findings and had similar recurrence rate and time to recurrence. Conclusions Most of the patients with native kidney failure attributed to C3G developed disease recurrence very early after kidney transplantation, usually with minimal proteinuria, mild histologic alterations, and favorable short-term allograft survival. Immunofluorescence and electron microscopy played a crucial role in detecting early, subclinical recurrence of C3GN and DDD, which showed significant overlapping features.
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Affiliation(s)
- Blanca Tarragón
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Yonatan Peleg
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Geetha Jagannathan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Miroslav Sekulic
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Jae-Hyung Chang
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - David J Cohen
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Russell J Crew
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Geoffrey K Dube
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Hilda E Fernandez
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Syed Ali Husain
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Sumit Mohan
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Heather K Morris
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Gerald B Appel
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Paresh Jadav
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Dominick Santoriello
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Satoru Kudose
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - M Barry Stokes
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Ibrahim Batal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Andrew S Bomback
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
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3
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Mahmoud AH, Talaat IM, Tlili A, Hamoudi R. Congenital anomalies of the kidney and urinary tract. Front Med (Lausanne) 2024; 11:1384676. [PMID: 39076761 PMCID: PMC11284074 DOI: 10.3389/fmed.2024.1384676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 06/19/2024] [Indexed: 07/31/2024] Open
Abstract
Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) refer to a range of conditions that affect the kidney and urinary tract. These anomalies can be severe, such as kidney agenesis, or milder, such as vesicoureteral reflux. CAKUT affects over 1% of live births and accounts for 40-50% of cases of chronic kidney failure in children. The pathogenesis of CAKUT is caused by various environmental, genetic, and epigenetic factors that disrupt normal nephrogenesis. Environmental factors that can lead to CAKUT include maternal diabetes, obesity, malnutrition, alcohol consumption, or medications affecting kidneys development. Genetic factors can cause an imbalance in the metanephros and the ureteric bud interaction. Defects in specific genes such as PAX2, TBX18, NRIP1, REX, SIX2, BMP4, and chromosome 17 cause CAKUT. Over 50 genes have been identified as the root cause of this condition, with monogenetic variants causing up to 20% of all cases. CAKUTs can be diagnosed through fetal ultrasonography, but some anomalies may remain undetected. GWASs, Next Generation Sequencing for targeted and whole exome DNA sequencing may provide additional diagnostic methods. This review article highlights some the leading factors that cause CAKUT, which adversely affects kidney development and urinary tract function.
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Affiliation(s)
- Anfal Hussain Mahmoud
- Research Institute for Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Iman M. Talaat
- Research Institute for Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
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4
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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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Mitrotti A, Giliberti M, Di Leo V, di Bari I, Pontrelli P, Gesualdo L. Hidden genetics behind glomerular scars: an opportunity to understand the heterogeneity of focal segmental glomerulosclerosis? Pediatr Nephrol 2024; 39:1685-1707. [PMID: 37728640 PMCID: PMC11026212 DOI: 10.1007/s00467-023-06046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/02/2023] [Accepted: 05/30/2023] [Indexed: 09/21/2023]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a complex disease which describes different kinds of kidney defects, not exclusively linked with podocyte defects. Since nephrin mutation was first described in association with early-onset nephrotic syndrome (NS), many advancements have been made in understanding genetic patterns associated with FSGS. New genetic causes of FSGS have been discovered, displaying unexpected genotypes, and recognizing possible site of damage. Many recent large-scale sequencing analyses on patients affected by idiopathic chronic kidney disease (CKD), kidney failure (KF) of unknown origin, or classified as FSGS, have revealed collagen alpha IV genes, as one of the most frequent sites of pathogenic mutations. Also, recent interest in complex and systemic lysosomal storage diseases, such as Fabry disease, has highlighted GLA mutations as possible causes of FSGS. Tubulointerstitial disease, recently classified by KDIGO based on genetic subtypes, when associated with UMOD variants, may phenotypically gain FSGS features, as well as ciliopathy genes or others, otherwise leading to completely different phenotypes, but found carrying pathogenic variants with associated FSGS phenotype. Thus, glomerulosclerosis may conceal different heterogeneous conditions. When a kidney biopsy is performed, the principal objective is to provide an accurate diagnosis. The broad spectrum of phenotypic expression and genetic complexity is demonstrating that a combined path of management needs to be applied. Genetic investigation should not be reserved only to selected cases, but rather part of medical management, integrating with clinical and renal pathology records. FSGS heterogeneity should be interpreted as an interesting opportunity to discover new pathways of CKD, requiring prompt genotype-phenotype correlation. In this review, we aim to highlight how FSGS represents a peculiar kidney condition, demanding multidisciplinary management, and in which genetic analysis may solve some otherwise unrevealed idiopathic cases. Unfortunately there is not a uniform correlation between specific mutations and FSGS morphological classes, as the same variants may be identified in familial cases or sporadic FSGS/NS or manifest a variable spectrum of the same disease. These non-specific features make diagnosis challenging. The complexity of FSGS genotypes requires new directions. Old morphological classification does not provide much information about the responsible cause of disease and misdiagnoses may expose patients to immunosuppressive therapy side effects, mistaken genetic counseling, and misguided kidney transplant programs.
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Affiliation(s)
- Adele Mitrotti
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.
| | - Marica Giliberti
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Vincenzo Di Leo
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Ighli di Bari
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Paola Pontrelli
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Loreto Gesualdo
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
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6
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Yu S, Gu X, Zheng Q, Liu Y, Suhas T, Du W, Xie L, Fang Z, Zhao Y, Yang M, Xu J, Wang Y, Lin MH, Pan X, Miner JH, Jin Y, Xie J. Tauroursodeoxycholic acid ameliorates renal injury induced by COL4A3 mutation. Kidney Int 2024:S0085-2538(24)00334-X. [PMID: 38782199 DOI: 10.1016/j.kint.2024.04.015] [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: 09/09/2023] [Revised: 03/17/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
COL4A3/A4/A5 mutations have been identified as critical causes of Alport syndrome and other genetic chronic kidney diseases. However, the underlying pathogenesis remains unclear, and specific treatments are lacking. Here, we constructed a transgenic Alport syndrome mouse model by generating a mutation (Col4a3 p.G799R) identified previously from one large Alport syndrome family into mice. We observed that the mutation caused a pathological decrease in intracellular and secreted collagen IV α3α4α5 heterotrimers. The mutant collagen IV α3 chains abnormally accumulated in the endoplasmic reticulum and exhibited defective secretion, leading to persistent endoplasmic reticulum stress in vivo and in vitro. RNA-seq analysis revealed that the MyD88/p38 MAPK pathway plays key roles in mediating subsequent inflammation and apoptosis signaling activation. Treatment with tauroursodeoxycholic acid, a chemical chaperone drug that functions as an endoplasmic reticulum stress inhibitor, effectively suppressed endoplasmic reticulum stress, promoted secretion of the α3 chains, and inhibited the activation of the MyD88/p38 MAPK pathway. Tauroursodeoxycholic acid treatment significantly improved kidney function in vivo. These results partly clarified the pathogenesis of kidney injuries associated with Alport syndrome, especially in glomeruli, and suggested that tauroursodeoxycholic acid might be useful for the early clinical treatment of Alport syndrome.
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Affiliation(s)
- Shuwen Yu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangchen Gu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Nephrology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qimin Zheng
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunzi Liu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Teija Suhas
- Division of Nephrology, Department of Medicine and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Wen Du
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Xie
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengying Fang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yafei Zhao
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingxin Yang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Xu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yimei Wang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meei-Hua Lin
- Division of Nephrology, Department of Medicine and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xiaoxia Pan
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jeffrey H Miner
- Division of Nephrology, Department of Medicine and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yuanmeng Jin
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jingyuan Xie
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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7
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Tavakolidakhrabadi N, Aulicino F, May CJ, Saleem MA, Berger I, Welsh GI. Genome editing and kidney health. Clin Kidney J 2024; 17:sfae119. [PMID: 38766272 PMCID: PMC11099665 DOI: 10.1093/ckj/sfae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Indexed: 05/22/2024] Open
Abstract
Genome editing technologies, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas in particular, have revolutionized the field of genetic engineering, providing promising avenues for treating various genetic diseases. Chronic kidney disease (CKD), a significant health concern affecting millions of individuals worldwide, can arise from either monogenic or polygenic mutations. With recent advancements in genomic sequencing, valuable insights into disease-causing mutations can be obtained, allowing for the development of new treatments for these genetic disorders. CRISPR-based treatments have emerged as potential therapies, especially for monogenic diseases, offering the ability to correct mutations and eliminate disease phenotypes. Innovations in genome editing have led to enhanced efficiency, specificity and ease of use, surpassing earlier editing tools such as zinc-finger nucleases and transcription activator-like effector nucleases (TALENs). Two prominent advancements in CRISPR-based gene editing are prime editing and base editing. Prime editing allows precise and efficient genome modifications without inducing double-stranded DNA breaks (DSBs), while base editing enables targeted changes to individual nucleotides in both RNA and DNA, promising disease correction in the absence of DSBs. These technologies have the potential to treat genetic kidney diseases through specific correction of disease-causing mutations, such as somatic mutations in PKD1 and PKD2 for polycystic kidney disease; NPHS1, NPHS2 and TRPC6 for focal segmental glomerulosclerosis; COL4A3, COL4A4 and COL4A5 for Alport syndrome; SLC3A1 and SLC7A9 for cystinuria and even VHL for renal cell carcinoma. Apart from editing the DNA sequence, CRISPR-mediated epigenome editing offers a cost-effective method for targeted treatment providing new avenues for therapeutic development, given that epigenetic modifications are associated with the development of various kidney disorders. However, there are challenges to overcome, including developing efficient delivery methods, improving safety and reducing off-target effects. Efforts to improve CRISPR-Cas technologies involve optimizing delivery vectors, employing viral and non-viral approaches and minimizing immunogenicity. With research in animal models providing promising results in rescuing the expression of wild-type podocin in mouse models of nephrotic syndrome and successful clinical trials in the early stages of various disorders, including cancer immunotherapy, there is hope for successful translation of genome editing to kidney diseases.
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Affiliation(s)
| | - Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, Bristol Royal Hospital for Children
| | - Carl J May
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Gavin I Welsh
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
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8
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Jefferis J, Mallett AJ. Exploring the impact and utility of genomic sequencing in established CKD. Clin Kidney J 2024; 17:sfae043. [PMID: 38464959 PMCID: PMC10921391 DOI: 10.1093/ckj/sfae043] [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: 10/09/2023] [Indexed: 03/12/2024] Open
Abstract
Clinical genetics is increasingly recognized as an important area within nephrology care. Clinicians require awareness of genetic kidney disease to recognize clinical phenotypes, consider use of genomics to aid diagnosis, and inform treatment decisions. Understanding the broad spectrum of clinical phenotypes and principles of genomic sequencing is becoming increasingly required in clinical nephrology, with nephrologists requiring education and support to achieve meaningful patient outcomes. Establishment of effective clinical resources, multi-disciplinary teams and education is important to increase application of genomics in clinical care, for the benefit of patients and their families. Novel applications of genomics in chronic kidney disease include pharmacogenomics and clinical translation of polygenic risk scores. This review explores established and emerging impacts and utility of genomics in kidney disease.
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Affiliation(s)
- Julia Jefferis
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Andrew J Mallett
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Department of Renal Medicine, Townsville University Hospital, Douglas, Australia
- College of Medicine and Dentistry, James Cook University, Douglas, Australia
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9
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Mitrotti A, Di Bari I, Giliberti M, Franzin R, Conserva F, Chiusolo A, Gigante M, Accetturo M, Cafiero C, Ricciato L, Stea ED, Forleo C, Gallone A, Rossini M, Fiorentino M, Castellano G, Pontrelli P, Gesualdo L. What Is Hidden in Patients with Unknown Nephropathy? Genetic Screening Could Be the Missing Link in Kidney Transplantation Diagnosis and Management. Int J Mol Sci 2024; 25:1436. [PMID: 38338714 PMCID: PMC10855929 DOI: 10.3390/ijms25031436] [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: 12/21/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Between 15-20% of patients with end stage renal disease (ESRD) do not know the cause of the primary kidney disease and can develop complications after kidney transplantation. We performed a genetic screening in 300 patients with kidney transplantation, or undiagnosed primary renal disease, in order to identify the primary disease cause and discriminate between overlapping phenotypes. We used a custom-made panel for next-generation sequencing (Agilent technology, Santa Clara, CA, USA), including genes associated with Fabry disease, podocytopaties, complement-mediated nephropathies and Alport syndrome-related diseases. We detected candidate diagnostic variants in genes associated with nephrotic syndrome and Focal Segmental Glomerulosclerosis (FSGS) in 29 out of 300 patients, solving about 10% of the probands. We also identified the same genetic cause of the disease (PAX2: c.1266dupC) in three family members with different clinical diagnoses. Interestingly we also found one female patient carrying a novel missense variant, c.1259C>A (p.Thr420Lys), in the GLA gene not previously associated with Fabry disease, which is in silico defined as a likely pathogenic and destabilizing, and associated with a mild alteration in GLA enzymatic activity. The identification of the specific genetic background may provide an opportunity to evaluate the risk of recurrence of the primary disease, especially among patient candidates living with a donor kidney transplant.
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Affiliation(s)
- Adele Mitrotti
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Ighli Di Bari
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Marica Giliberti
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Rossana Franzin
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Francesca Conserva
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Anna Chiusolo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Maddalena Gigante
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Matteo Accetturo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Cesira Cafiero
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Luisa Ricciato
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Emma Diletta Stea
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Cinzia Forleo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Anna Gallone
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70121 Bari, Italy;
| | - Michele Rossini
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Marco Fiorentino
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Giuseppe Castellano
- Department of Clinical Sciences and Community Health, University of Milano, 20122 Milano, Italy;
- Fondazione IRCCS Cà Grande Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Paola Pontrelli
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Loreto Gesualdo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
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10
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Nissaisorakarn P, Fadakar PK, Safa K, Lundquist AL, Riella CV, Riella LV. A pragmatic approach to selective genetic testing in kidney transplant candidates. FRONTIERS IN TRANSPLANTATION 2024; 2:1342471. [PMID: 38993907 PMCID: PMC11235289 DOI: 10.3389/frtra.2023.1342471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/22/2023] [Indexed: 07/13/2024]
Abstract
Introduction Advances in the field of genetic testing have spurred its use in transplantation. Potential benefits of genetic testing in transplant nephrology include diagnosis, treatment, risk stratification of recurrent disease, and risk stratification in potential donors. However, it is unclear how to best apply genetic testing in this population to maximize its yield. We describe our transplant center's approach to selective genetic testing as part of kidney transplant candidate and donor evaluation. Methods Transplant recipient candidates were tested if they had a history of ESRD at age <50, primary FSGS, complement-mediated or unknown etiology of kidney disease, or had a family history of kidney disease. Donors were tested if age <35, were related to their potential recipients with known genetic susceptibility or had a first-degree relative with a history of kidney disease of unknown etiology. A targeted NGS gene panel of 385 genes was used. Clinical implications and downstream effects were monitored. Results Over 30% of recipients tested within the established criteria were positive for a pathogenic variant. The most common pathogenic variants were APOL1 high-risk genotypes as well as collagen 4-alpha-3, -4 and -5. Donor testing done according to our inclusion criteria resulted in about 12% yield. Positive test results in recipients helped with stratification of the risk of recurrent disease. Positive test results in potential donors guided informed decisions on when not to move forward with a donation. Discussion Integrating targeted panel genetic testing into a kidney transplant clinic in conjunction with a selective criteria for testing donors and recipients ensured a reasonable diagnostic yield. The results had implications on clinical management, risk stratification and in some cases were instrumental in directing downstream changes including when to stop the evaluation process. Given the impact on management and transplant decisions, we advocate for the widespread use of genetic testing in selected individuals undergoing transplant evaluation and donation who meet pre-defined criteria.
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Affiliation(s)
- Pitchaphon Nissaisorakarn
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Paul K. Fadakar
- Division of Nephrology, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Kassem Safa
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Andrew L. Lundquist
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Cristian V. Riella
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Leonardo V. Riella
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Center for Transplantation Sciences, Department of Surgery Massachusetts General Hospital, Boston, MA, United States
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11
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Higuchi T, Oka S, Furukawa H, Tohma S. The contributions of deleterious rare alleles in NLRP12 and inflammasome-related genes to polymyalgia rheumatica. Sci Rep 2024; 14:490. [PMID: 38177227 PMCID: PMC10767114 DOI: 10.1038/s41598-024-51320-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024] Open
Abstract
Polymyalgia rheumatica (PMR) is a chronic inflammatory disease characterized by arthralgia and myalgia of the shoulder and hip girdles, and fever. PMR is linked to autoimmune diseases and autoinflammatory disorders. Exome sequencing has revealed the roles of rare variants in some diseases. Causative genes for monogenic autoinflammatory disorders might be candidate genes for the selective exome analysis of PMR. We investigated rare variants in the coding and boundary regions of candidate genes for PMR. Exome sequencing was performed to analyze deleterious rare variants in candidate genes, and the frequencies of the deleterious rare alleles in PMR were compared with those of Japanese population controls. Deleterious rare alleles in the NLRL12 gene were associated with PMR (P = 0.0069, Pc = 0.0415, odds ratio [OR] 4.49, 95% confidence interval [CI] 1.79-11.27). A multigene analysis demonstrated the deleterious rare allele frequency of the candidate genes for autoinflammatory disorders was also increased in PMR (P = 0.0016, OR 3.69, 95%CI 1.81-7.54). The deleterious rare allele frequencies of the candidate genes including NLRP12 were increased in PMR patients, showing links to autoinflammatory disorders in the pathogenesis of PMR.
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Affiliation(s)
- Takashi Higuchi
- Department of Rheumatology, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan
| | - Shomi Oka
- Department of Rheumatology, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan
| | - Hiroshi Furukawa
- Department of Rheumatology, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan.
| | - Shigeto Tohma
- Department of Rheumatology, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan
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12
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Dahl NK, Bloom MS, Chebib FT, Clark D, Westemeyer M, Jandeska S, Zhang Z, Milo-Rasouly H, Kolupaeva V, Marasa M, Broumand V, Fatica RA, Raj DS, Demko ZP, Marshall K, Punj S, Tabriziani H, Bhorade S, Gharavi AG. The Clinical Utility of Genetic Testing in the Diagnosis and Management of Adults with Chronic Kidney Disease. J Am Soc Nephrol 2023; 34:2039-2050. [PMID: 37794564 PMCID: PMC10703084 DOI: 10.1681/asn.0000000000000249] [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: 06/07/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
SIGNIFICANCE STATEMENT Accurate diagnosis of a patient's underlying cause of CKD can influence management and ultimately overall health. The single-arm, interventional, prospective Renasight Clinical Application, Review, and Evaluation study assessed the utility of genetic testing with a 385 gene kidney disease panel on the diagnosis and management of 1623 patients with CKD. Among 20.8% of patients who had positive genetic findings, half resulted in a new or reclassified diagnosis. In addition, a change in management because of genetic testing was reported for 90.7% of patients with positive findings, including treatment changes in 32.9%. These findings demonstrate that genetic testing has a significant effect on both CKD diagnosis and management. BACKGROUND Genetic testing in CKD has recently been shown to have diagnostic utility with many predicted implications for clinical management, but its effect on management has not been prospectively evaluated. METHODS Renasight Clinical Application, Review, and Evaluation RenaCARE (ClinicalTrials.gov NCT05846113 ) is a single-arm, interventional, prospective, multicenter study that evaluated the utility of genetic testing with a broad, 385 gene panel (the Renasight TM test) on the diagnosis and management of adult patients with CKD recruited from 31 US-based community and academic medical centers. Patient medical history and clinical CKD diagnosis were collected at enrollment. Physician responses to questionnaires regarding patient disease categorization and management were collected before genetic testing and 1 month after the return of test results. Changes in CKD diagnosis and management after genetic testing were assessed. RESULTS Of 1623 patients with CKD in 13 predefined clinical disease categories (ages, 18-96; median, 55 years), 20.8% ( n =338) had positive genetic findings spanning 54 genes. Positive genetic findings provided a new diagnosis or reclassified a prior diagnosis in 48.8% of those patients. Physicians reported that genetic results altered the management of 90.7% of patients with a positive genetic finding, including changes in treatment plan, which were reported in 32.9% of these patients. CONCLUSIONS Genetic testing with a CKD-focused 385 gene panel substantially refined clinical diagnoses and had widespread implications for clinical management, including appropriate treatment strategies. These data support the utility of broader integration of panels of genetic tests into the clinical care paradigm for patients with CKD. CLINICAL TRIAL REGISTRY NAME AND REGISTRATION NUMBER ClinicalTrials.gov, NCT05846113 .
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Affiliation(s)
- Neera K. Dahl
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | | | - Fouad T. Chebib
- Division of Nephrology and Hypertension, Mayo Clinic, Jacksonville, Florida
| | | | | | | | | | - Hila Milo-Rasouly
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Victoria Kolupaeva
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | | | | | - Dominic S. Raj
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine and Health Sciences, Washington, DC
| | | | | | | | | | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
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13
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Huang Z, Shen Q, Wu B, Wang H, Dong X, Lu Y, Cheng G, Wang L, Lu W, Chen L, Kang W, Li L, Pan X, Wei Q, Zhuang D, Chen D, Yin Z, Yang L, Ni Q, Liu R, Li G, Zhang P, Qian Y, Peng X, Wang Y, Cao Y, Xu H, Hu L, Yang L, Zhou W. Genetic Spectrum of Congenital Anomalies of the Kidney and Urinary Tract in Chinese Newborn Genome Project. Kidney Int Rep 2023; 8:2376-2384. [PMID: 38025242 PMCID: PMC10658258 DOI: 10.1016/j.ekir.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Congenital anomalies of the kidney and urinary tract (CAKUT) corresponds to a spectrum of defects. Several large-cohort studies have used high-throughput sequencing to investigate the genetic risk of CAKUT during antenatal, childhood, and adulthood period. However, our knowledge of newborns with CAKUT is limited. Methods This multicenter retrospective cohort study explored the genetic spectrum of CAKUT in a Chinese neonatal cohort. Clinical data and whole exome sequencing (WES) data of 330 newborns clinically diagnosed with CAKUT were collected. WES data were analyzed for putative deleterious single nucleotide variants (SNVs) and potential disease-associated copy number variants (CNVs). Results In this study, pathogenic variants were identified in 61 newborns (18.5%, 61/330), including 35 patients (57.4%) with SNVs, 25 patients (41%) with CNVs, and 1 patient with both an SNV and a CNV. Genetic diagnosis rates were significantly higher in patients with extrarenal manifestations (P<0.001), especially in those with cardiovascular malformations (P<0.05). SNVs in genes related to syndromic disorders (CAKUT with extrarenal manifestations) were common, affecting 20 patients (57.1%, 20/35). KMT2D was the most common gene (5 patients) and 17q12 deletion was the most common CNV (4 patients). Patient 110 was detected with both a CNV (17q12 deletion) and an SNV (a homozygous variant of SLC25A13). Among the newborns with positive genetic results, 22 (36.1%, 22/61) patients may benefit from a molecular diagnosis and change in clinical management (including early multidisciplinary treatment, disease-specific follow-up, and familial genetic counseling). Conclusion This study shows the heterogeneous genetic etiologies in a Chinese CAKUT neonatal cohort by using WES. Patients with CAKUT who have extrarenal manifestations are more likely to harbor genetic diagnoses. Kabuki syndrome and 17q12 deletion syndrome were the most common genetic findings. Approximately 36.1% of the patients may benefit from molecular diagnoses and a change in clinical management.
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Affiliation(s)
- Zhelan Huang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Liping Chen
- Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Wenqing Kang
- Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Long Li
- Department of Neonatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xinnian Pan
- Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiufen Wei
- Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | | | - Dongmei Chen
- Quanzhou Women and Children’s Hospital, Quanzhou, China
| | | | - Ling Yang
- Hainan Women and Children’s Medical Center, Haikou, China
| | - Qi Ni
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yao Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
- Xiamen Children’s Hospital, Xiamen, China
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14
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Rheault MN, McLaughlin HM, Mitchell A, Blake LE, Devarajan P, Warady BA, Gibson KL, Lieberman KV. COL4A gene variants are common in children with hematuria and a family history of kidney disease. Pediatr Nephrol 2023; 38:3625-3633. [PMID: 37204491 DOI: 10.1007/s00467-023-05993-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/24/2023] [Accepted: 04/15/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Inherited kidney diseases are a common cause of chronic kidney disease (CKD) in children. Identification of a monogenic cause of CKD is more common in children than in adults. This study evaluated the diagnostic yield and phenotypic spectrum of children who received genetic testing through the KIDNEYCODE sponsored genetic testing program. METHODS Unrelated children < 18 years of age who received panel testing through the KIDNEYCODE sponsored genetic testing program from September 2019 through August 2021 were included (N = 832). Eligible children met at least one of the following clinician-reported criteria: estimated GFR ≤ 90 ml/min/1.73 m2, hematuria, a family history of kidney disease, or suspected or biopsy confirmed Alport syndrome or focal segmental glomerulosclerosis (FSGS) in the tested individual or family member. RESULTS A positive genetic diagnosis was observed in 234 children (28.1%, 95% CI [25.2-31.4%]) in genes associated with Alport syndrome (N = 213), FSGS (N = 9), or other disorders (N = 12). Among children with a family history of kidney disease, 30.8% had a positive genetic diagnosis. Among those with hematuria and a family history of CKD, the genetic diagnostic rate increased to 40.4%. CONCLUSIONS Children with hematuria and a family history of CKD have a high likelihood of being diagnosed with a monogenic cause of kidney disease, identified through KIDNEYCODE panel testing, particularly COL4A variants. Early genetic diagnosis can be valuable in targeting appropriate therapy and identification of other at-risk family members. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Michelle N Rheault
- Masonic Children's Hospital, University of Minnesota, Minneapolis, MN, USA.
| | | | | | | | - Prasad Devarajan
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Bradley A Warady
- Children's Mercy Kansas City, University of Missouri-Kansas City, Kansas City, MO, USA
| | | | - Kenneth V Lieberman
- Joseph M. Sanzari Children's Hospital, Hackensack Meridian School of Medicine, Hackensack, NJ, USA
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15
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Tato AM, Carrera N, García-Murias M, Shabaka A, Ávila A, Mora Mora MT, Rabasco C, Soto K, de la Prada Alvarez FJ, Fernández-Lorente L, Rodríguez-Moreno A, Huerta A, Mon C, García-Carro C, González Cabrera F, Navarro JAM, Romera A, Gutiérrez E, Villacorta J, de Lorenzo A, Avilés B, Garca-González MA, Fernández-Juárez G. Genetic testing in focal segmental glomerulosclerosis: in whom and when? Clin Kidney J 2023; 16:2011-2022. [PMID: 37915894 PMCID: PMC10616495 DOI: 10.1093/ckj/sfad193] [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: 03/09/2023] [Indexed: 11/03/2023] Open
Abstract
Background Genetic causes are increasingly recognized in patients with focal segmental glomerulosclerosis (FSGS), but it remains unclear which patients should undergo genetic study. Our objective was to determine the frequency and distribution of genetic variants in steroid-resistant nephrotic syndrome FSGS (SRNS-FSGS) and in FSGS of undetermined cause (FSGS-UC). Methods We performed targeted exome sequencing of 84 genes associated with glomerulopathy in patients with adult-onset SRNS-FSGS or FSGS-UC after ruling out secondary causes. Results Seventy-six patients met the study criteria; 24 presented with SRNS-FSGS and 52 with FSGS-UC. We detected FSGS-related disease-causing variants in 27/76 patients (35.5%). There were no differences between genetic and non-genetic causes in age, proteinuria, glomerular filtration rate, serum albumin, body mass index, hypertension, diabetes or family history. Hematuria was more prevalent among patients with genetic causes. We found 19 pathogenic variants in COL4A3-5 genes in 16 (29.3%) patients. NPHS2 mutations were identified in 6 (16.2%) patients. The remaining cases had variants affecting INF2, OCRL, ACTN4 genes or APOL1 high-risk alleles. FSGS-related genetic variants were more common in SRNS-FSGS than in FSGS-UC (41.7% vs 32.7%). Four SRNS-FSGS patients presented with NPHS2 disease-causing variants. COL4A variants were the most prevalent finding in FSGS-UC patients, with 12 patients carrying disease-causing variants in these genes. Conclusions FSGS-related variants were detected in a substantial number of patients with SRNS-FSGS or FSGS-UC, regardless of age of onset of disease or the patient's family history. In our experience, genetic testing should be performed in routine clinical practice for the diagnosis of this group of patients.
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Affiliation(s)
- Ana María Tato
- Department of Nephrology, Hospital Universitario Fundación Alcorcón, Alcorcón, Spain
| | - Noa Carrera
- Laboratorio de Nefroloxía (No. 11), Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Instituto de investigación sanitaria de Santiago de Compostela – IDIS, Santiago de Compostela, Spain
| | - Maria García-Murias
- Laboratorio de Nefroloxía (No. 11), Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Instituto de investigación sanitaria de Santiago de Compostela – IDIS, Santiago de Compostela, Spain
| | - Amir Shabaka
- Department of Nephrology, Hospital Universitario Fundación Alcorcón, Alcorcón, Spain
| | - Ana Ávila
- Department of Nephrology, Hospital Universitario Doctor Peset, Valencia, Spain
| | | | - Cristina Rabasco
- Department of Nephrology, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Karina Soto
- Department of Nephrology, Hospital Fernando Fonseca, Lisbon, Portugal
| | | | | | | | - Ana Huerta
- Department of Nephrology, Hospital Universitario Puerta de Hierro, Majadahonda, Spain
| | - Carmen Mon
- Department of Nephrology, Hospital Universitario Severo Ochoa, Leganés, Spain
| | | | - Fayna González Cabrera
- Department of Nephrology, Hospital Universitario de Gran Canaria Doctor Negrín, Gran Canaria, Spain
| | | | - Ana Romera
- Department of Nephrology, Hospital de Ciudad Real, Ciudad Real, Spain
| | - Eduardo Gutiérrez
- Department of Nephrology, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Javier Villacorta
- Department of Nephrology, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Beatriz Avilés
- Department of Nephrology, Hospital Costa del Sol, Marbella, Spain
| | - Miguel Angel Garca-González
- Laboratorio de Nefroloxía (No. 11), Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Instituto de investigación sanitaria de Santiago de Compostela – IDIS, Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Complexo Hospitalario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gema Fernández-Juárez
- Department of Nephrology, Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigación de la Paz (IdIPAZ), Madrid, Spain
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16
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Zheng M, Hakim A, Konkwo C, Deaton AM, Ward LD, Silveira MG, Assis DN, Liapakis A, Jaffe A, Jiang ZG, Curry MP, Lai M, Cho MH, Dykas D, Bale A, Mistry PK, Vilarinho S. Advancing diagnosis and management of liver disease in adults through exome sequencing. EBioMedicine 2023; 95:104747. [PMID: 37566928 PMCID: PMC10433007 DOI: 10.1016/j.ebiom.2023.104747] [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: 02/09/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) is an effective tool for diagnosis in patients who remain undiagnosed despite a comprehensive clinical work-up. While WES is being used increasingly in pediatrics and oncology, it remains underutilized in non-oncological adult medicine, including in patients with liver disease, in part based on the faulty premise that adults are unlikely to harbor rare genetic variants with large effect size. Here, we aim to assess the burden of rare genetic variants underlying liver disease in adults at two major tertiary referral academic medical centers. METHODS WES analysis paired with comprehensive clinical evaluation was performed in fifty-two adult patients with liver disease of unknown etiology evaluated at two US tertiary academic health care centers. FINDINGS Exome analysis uncovered a definitive or presumed diagnosis in 33% of patients (17/52) providing insight into their disease pathogenesis, with most of these patients (12/17) not having a known family history of liver disease. Our data shows that over two-thirds of undiagnosed liver disease patients attaining a genetic diagnosis were being evaluated for cholestasis or hepatic steatosis of unknown etiology. INTERPRETATION This study reveals an underappreciated incidence and spectrum of genetic diseases presenting in adulthood and underscores the clinical value of incorporating exome sequencing in the evaluation and management of adults with liver disease of unknown etiology. FUNDING S.V. is supported by the NIH/NIDDK (K08 DK113109 and R01 DK131033-01A1) and the Doris Duke Charitable Foundation Grant #2019081. This work was supported in part by NIH-funded Yale Liver Center, P30 DK34989.
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Affiliation(s)
- Melanie Zheng
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Aaron Hakim
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Chigoziri Konkwo
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Marina G Silveira
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - David N Assis
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - AnnMarie Liapakis
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Ariel Jaffe
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Z Gordon Jiang
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michael P Curry
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michelle Lai
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Dykas
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Allen Bale
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Pramod K Mistry
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Silvia Vilarinho
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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17
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Cybulsky AV, Cercena L, Goodyer PR, Suri RS. Transition From Pediatric to Adult Nephrology Care: Program Report of a Single-Center Experience. Can J Kidney Health Dis 2023; 10:20543581231191836. [PMID: 37564323 PMCID: PMC10411281 DOI: 10.1177/20543581231191836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/23/2023] [Indexed: 08/12/2023] Open
Abstract
Purpose of program Adolescents and young adults with chronic disease face many personal and systemic barriers that may impede their successful transition from pediatric to adult care, putting them at risk for treatment nonadherence, loss to follow-up, and poor health outcomes. Such barriers include impaired socioemotional functioning, overreliance on adult caregivers, lack of disease-specific knowledge, and poor coordination between pediatric and adult health care services. In 2007, we established a specialized youth to adult nephrology transition clinic at a tertiary care center to address these barriers and provide adolescents and young adults with renal disease followed at the affiliated children's hospital with a seamless transition to adult care. Sources of information The attending clinic nephrologist collected data prospectively for this quality improvement report. Methods The features of this specialized clinic included (1) single point of entry and single triage adult nephrologist, (2) ongoing follow-up with a single adult nephrologist who communicated with the pediatric nephrologists, and (3) a single specialized clinic nurse who provided disease-specific education and helped to ensure ongoing patient engagement and follow-up. Importantly, the transition patients were booked into regular appointment slots in the adult nephrologist's general clinic, which facilitated regular follow-up without additional resources. The salary of the transition clinic nurse was covered by an unrestricted grant. Patient visits were in-person, except between 2020 and 2021 when visits were by telephone due to the pandemic. Key findings A total of 213 patients were referred and assessed in the transition clinic from February 2007 until October 2022. Most referrals were from pediatric nephrologists. Among the patients, 29% had a hereditary kidney disease; in 71%, the disease was acquired. The most common disease was glomerulonephritis and ~30% of the patients suffered from a "rare" disease. Of the 213 patients, 123 (58%) continue to be followed up (mean follow-up: 4.8 years), 27 (13%) were transferred to other physicians, in part to accommodate treatment closer to patients' homes, and 29 (14%) without ongoing care needs were discharged. Only 33 (15%) were lost to follow-up. There were several advantages to the clinic, including the maintenance of accurate records, a process to minimize loss to follow-up, and a "critical mass" of patients with rare diseases, which facilitated development of special expertise in rare disease pathogenesis, diagnosis, treatment, and management of complications. Patients with glomerulonephritis demonstrated a stable serum creatinine over 3 to 15 years, and morbidity (as reflected by emergency room visits and hospitalizations) was low. Limitations Due to the relatively small numbers of patients in the disease categories, it was not possible to determine conclusively whether attendance of patients in the transition clinic reduced the rate of progression of kidney disease or morbidity. Implications A dedicated referral, triage, and follow-up process post-transition with only modest financial resources and personnel can result in accurate tracking of clinic data, as well as consistent and reliable follow-up and expert patient care.
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Affiliation(s)
- Andrey V. Cybulsky
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, QC, Canada
| | - Leonor Cercena
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, QC, Canada
| | - Paul R. Goodyer
- Department of Pediatrics, McGill University Health Centre Research Institute, McGill University, Montreal, QC, Canada
| | - Rita S. Suri
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, QC, Canada
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18
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Saha A, Kapadia SF, Vala KB, Patel HV. Clinical utility of genetic testing in Indian children with kidney diseases. BMC Nephrol 2023; 24:212. [PMID: 37464296 DOI: 10.1186/s12882-023-03240-z] [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: 11/13/2022] [Accepted: 06/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Kidney diseases with genetic etiology in children present with an overlapping spectrum of manifestations. We aimed to analyze the clinical utility of genetic testing in the diagnosis and management of suspected genetic kidney diseases in children. METHODS In this retrospective study, children ≤ 18 years in whom a genetic test was ordered were included. Clinical indications for genetic testing were categorized as Glomerular diseases, nephrolithiasis and/or nephrocalcinoses, tubulopathies, cystic kidney diseases, congenital abnormality of kidney and urinary tract, chronic kidney disease of unknown aetiology and others. Clinical exome sequencing was the test of choice. Other genetic tests ordered were sanger sequencing, gene panel, multiplex ligation-dependent probe amplification and karyotyping. The pathogenicity of the genetic variant was interpreted as per the American College of Medical Genetics classification. RESULTS A total of 86 samples were sent for genetic testing from 76 index children, 8 parents and 2 fetuses. A total of 74 variants were reported in 47 genes. Out of 74 variants, 42 were missense, 9 nonsense, 12 frameshifts, 1 indel, 5 affected the splicing regions and 5 were copy number variants. Thirty-two were homozygous, 36 heterozygous and 6 were hemizygous variants. Twenty-four children (31.6%) had pathogenic and 11 (14.5%) had likely pathogenic variants. Twenty-four children (31.6%) had variants of uncertain significance. No variants were reported in 17 children (22.3%). A genetic diagnosis was made in 35 children with an overall yield of 46%. The diagnostic yield was 29.4% for glomerular diseases, 53.8% for tubular disorders, 81% for nephrolithiasis and/or nephrocalcinoses, 60% for cystic kidney diseases and 50% for chronic kidney disease of unknown etiology. Genetic testing made a new diagnosis or changed the diagnosis in 15 children (19.7%). CONCLUSION Nearly half (46%) of the children tested for a genetic disease had a genetic diagnosis. Genetic testing confirmed the clinical diagnoses, changed the clinical diagnoses or made a new diagnosis which helped in personalized management.
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Affiliation(s)
- Anshuman Saha
- Department of Pediatric Nephrology, Institute of Kidney Diseases and Research Centre, Gujarat University of Transplantation Sciences, Ahmedabad, India.
| | - Shahenaz F Kapadia
- Department of Pediatric Nephrology, Institute of Kidney Diseases and Research Centre, Gujarat University of Transplantation Sciences, Ahmedabad, India
| | - Kinnari B Vala
- Department of Pediatric Nephrology, Institute of Kidney Diseases and Research Centre, Gujarat University of Transplantation Sciences, Ahmedabad, India
| | - Himanshu V Patel
- Department of Pediatric Nephrology, Institute of Kidney Diseases and Research Centre, Gujarat University of Transplantation Sciences, Ahmedabad, India
- Department of Nephrology, Institute of Kidney Diseases and Research Centre, Gujarat University of Transplantation Sciences, Ahmedabad, India
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19
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Nigro E, Amicone M, D'Arco D, Sellitti G, De Marco O, Guarino M, Riccio E, Pisani A, Daniele A. Molecular Diagnosis and Identification of Novel Pathogenic Variants in a Large Cohort of Italian Patients Affected by Polycystic Kidney Diseases. Genes (Basel) 2023; 14:1236. [PMID: 37372416 DOI: 10.3390/genes14061236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Polycystic Kidney Diseases (PKDs) consist of a genetically and phenotypically heterogeneous group of inherited disorders characterized by numerous renal cysts. PKDs include autosomal dominant ADPKD, autosomal recessive ARPKD and atypical forms. Here, we analyzed 255 Italian patients using an NGS panel of 63 genes, plus Sanger sequencing of exon 1 of the PKD1 gene and MPLA (PKD1, PKD2 and PKHD1) analysis. Overall, 167 patients bore pathogenic/likely pathogenic variants in dominant genes, and 5 patients in recessive genes. Four patients were carriers of one pathogenic/likely pathogenic recessive variant. A total of 24 patients had a VUS variant in dominant genes, 8 patients in recessive genes and 15 patients were carriers of one VUS variant in recessive genes. Finally, in 32 patients we could not reveal any variant. Regarding the global diagnostic status, 69% of total patients bore pathogenic/likely pathogenic variants, 18.4% VUS variants and in 12.6% of patients we could not find any. PKD1 and PKD2 resulted to be the most mutated genes; additional genes were UMOD and GANAB. Among recessive genes, PKHD1 was the most mutated gene. An analysis of eGFR values showed that patients with truncating variants had a more severe phenotype. In conclusion, our study confirmed the high degree of genetic complexity at the basis of PKDs and highlighted the crucial role of molecular characterization in patients with suspicious clinical diagnosis. An accurate and early molecular diagnosis is essential to adopt the appropriate therapeutic protocol and represents a predictive factor for family members.
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Affiliation(s)
- Ersilia Nigro
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche, Farmaceutiche, Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Amicone
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Daniela D'Arco
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gina Sellitti
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Oriana De Marco
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Maria Guarino
- Gastroenterology and Hepatology Unit, Department of Clinical Medicine and Surgery, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy
| | - Eleonora Riccio
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Antonio Pisani
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Aurora Daniele
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi "Federico II", Via Pansini 5, 80131 Napoli, Italy
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20
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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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21
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Verbitsky M, Krishnamurthy S, Krithivasan P, Hughes D, Khan A, Marasà M, Vena N, Khosla P, Zhang J, Lim TY, Glessner JT, Weng C, Shang N, Shen Y, Hripcsak G, Hakonarson H, Ionita-Laza I, Levy B, Kenny EE, Loos RJ, Kiryluk K, Sanna-Cherchi S, Crosslin DR, Furth S, Warady BA, Igo RP, Iyengar SK, Wong CS, Parsa A, Feldman HI, Gharavi AG. Genomic Disorders in CKD across the Lifespan. J Am Soc Nephrol 2023; 34:607-618. [PMID: 36302597 PMCID: PMC10103259 DOI: 10.1681/asn.2022060725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
SIGNIFICANCE STATEMENT Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis. BACKGROUND Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility. METHODS We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II ( n =248), Chronic Renal Insufficiency Cohort (CRIC) study ( n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort. RESULTS We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk. CONCLUSION Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Pavan Khosla
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Joseph T. Glessner
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology and Columbia Genome Center, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David R. Crosslin
- Division of Biomedical Informatics and Genomics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Susan Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Gutiérrez E, Trujillo H, Aubert L, Sandino J, Morales E, Auñón P, Cavero T, Morales E, Praga M. Why should genetic testing be incorporated into routine clinical practice in nephrology? The utility of specialized clinics. An emerging need. Nefrologia 2023; 43:161-166. [PMID: 37394295 DOI: 10.1016/j.nefroe.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/15/2022] [Indexed: 07/04/2023] Open
Affiliation(s)
| | | | - Lucía Aubert
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | - Pilar Auñón
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | - Manuel Praga
- Hospital Universitario 12 de Octubre, Madrid, Spain
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23
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Estrella E, Rockowitz S, Thorne M, Smith P, Petit J, Zehnder V, Yu RN, Bauer S, Berde C, Agrawal PB, Beggs AH, Gharavi AG, Kunkel L, Brownstein CA. Mendelian Disorders in an Interstitial Cystitis/Bladder Pain Syndrome Cohort. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200013. [PMID: 36910591 PMCID: PMC10000272 DOI: 10.1002/ggn2.202200013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/03/2022] [Indexed: 11/29/2022]
Abstract
Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic pain disorder causing symptoms of urinary frequency, urgency, and bladder discomfort or pain. Although this condition affects a large population, little is known about its etiology. Genetic analyses of whole exome sequencing are performed on 109 individuals with IC/BPS. One family has a previously reported SIX5 variant (ENST00000317578.6:c.472G>A, p.Ala158Thr), consistent with Branchiootorenal syndrome 2 (BOR2). A likely pathogenic heterozygous variant in ATP2A2 (ENST00000539276.2:c.235G>A, p.Glu79Lys) is identified in two unrelated probands, indicating possible Darier-White disease. Two private heterozygous variants are identified in ATP2C1 (ENST00000393221.4:c.2358A>T, p.Glu786Asp (VUS/Likely Pathogenic) and ENST00000393221.4:c.989C>G, p.Thr330Ser (likely pathogenic)), indicative of Hailey-Hailey Disease. Sequence kernel association test analysis finds an increased burden of rare ATP2C1 variants in the IC/BPS cases versus a control cohort (p = 0.03, OR = 6.76), though does not survive Bonferroni correction. The data suggest that some individuals with IC/BPS may have unrecognized Mendelian syndromes. Comprehensive phenotyping and genotyping aid in understanding the range of diagnoses in the population-based IC/BPS cohort. Conversely, ATP2C1, ATP2A2, and SIX5 may be candidate genes for IC/BPS. Further evaluation with larger numbers is needed. Genetically screening individuals with IC/BPS may help diagnose and treat this painful disorder due to its heterogeneous nature.
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Affiliation(s)
- Elicia Estrella
- Department of NeurologyBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Shira Rockowitz
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- Research ComputingInformation TechnologyBoston Children's HospitalBostonMA02115USA
| | - Marielle Thorne
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Pressley Smith
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Jeanette Petit
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Veronica Zehnder
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Richard N. Yu
- Department of UrologyBoston Children's HospitalBostonMA02115USA
| | - Stuart Bauer
- Department of UrologyBoston Children's HospitalBostonMA02115USA
| | - Charles Berde
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- Department of Anesthesiology, Critical Care and Pain MedicineBoston Children's HospitalBostonMA02115USA
- Department of AnaesthesiaHarvard Medical SchoolBostonMA02115USA
| | - Pankaj B. Agrawal
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- Division of Newborn MedicineBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Alan H. Beggs
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Ali G. Gharavi
- Institute for Genomic MedicineVagelos College of Physicians & SurgeonsColumbia UniversityNew YorkNY10032USA
- Division of NephrologyDepartment of MedicineVagelos College of Physicians & SurgeonsColumbia UniversityNew YorkNY10032USA
- Center for Precision Medicine and GenomicsDepartment of MedicineVagelos College of Physicians & SurgeonsColumbia UniversityNew YorkNY10032USA
| | - Louis Kunkel
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Catherine A. Brownstein
- Division of Genetics and Genomics Boston Children's HospitalHarvard Medical SchoolBostonMA02115USA
- The Manton Center for Orphan disease ResearchBoston Children's HospitalHarvard Medical SchoolBostonMA02115USA
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Murali R, Wanjari UR, Mukherjee AG, Gopalakrishnan AV, Kannampuzha S, Namachivayam A, Madhyastha H, Renu K, Ganesan R. Crosstalk between COVID-19 Infection and Kidney Diseases: A Review on the Metabolomic Approaches. Vaccines (Basel) 2023; 11:vaccines11020489. [PMID: 36851366 PMCID: PMC9959335 DOI: 10.3390/vaccines11020489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a respiratory disorder. Various organ injuries have been reported in response to this virus, including kidney injury and, in particular, kidney tubular injury. It has been discovered that infection with the virus does not only cause new kidney disease but also increases treatment difficulty and mortality rates in people with kidney diseases. In individuals hospitalized with COVID-19, urinary metabolites from several metabolic pathways are used to distinguish between patients with acute kidney injury (AKI) and those without. This review summarizes the pathogenesis, pathophysiology, treatment strategies, and role of metabolomics in relation to AKI in COVID-19 patients. Metabolomics is likely to play a greater role in predicting outcomes for patients with kidney disease and COVID-19 with varying levels of severity in the near future as data on metabolic profiles expand rapidly. Here, we also discuss the correlation between COVID-19 and kidney diseases and the available metabolomics approaches.
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Affiliation(s)
- Reshma Murali
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Correspondence: (A.V.G.); (R.G.)
| | - Sandra Kannampuzha
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kaviyarasi Renu
- Center of Molecular Medicine and Diagnostics (COMMAND), Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Correspondence: (A.V.G.); (R.G.)
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25
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Revy P, Kannengiesser C, Bertuch AA. Genetics of human telomere biology disorders. Nat Rev Genet 2023; 24:86-108. [PMID: 36151328 DOI: 10.1038/s41576-022-00527-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 01/24/2023]
Abstract
Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes that prevent the activation of DNA damage response and repair pathways. Numerous factors localize at telomeres to regulate their length, structure and function, to avert replicative senescence or genome instability and cell death. In humans, Mendelian defects in several of these factors can result in abnormally short or dysfunctional telomeres, causing a group of rare heterogeneous premature-ageing diseases, termed telomeropathies, short-telomere syndromes or telomere biology disorders (TBDs). Here, we review the TBD-causing genes identified so far and describe their main functions associated with telomere biology. We present molecular aspects of TBDs, including genetic anticipation, phenocopy, incomplete penetrance and somatic genetic rescue, which underlie the complexity of these diseases. We also discuss the implications of phenotypic and genetic features of TBDs on fundamental aspects related to human telomere biology, ageing and cancer, as well as on diagnostic, therapeutic and clinical approaches.
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Affiliation(s)
- Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Nationale contre le Cancer, Paris, France.
- Université Paris Cité, Imagine Institute, Paris, France.
| | - Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France
- Inserm U1152, Université Paris Cité, Paris, France
| | - Alison A Bertuch
- Departments of Paediatrics and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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26
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Optimizing Screening for Early Disease Detection in Familial Pulmonary Fibrosis (FLORIS): A Prospective Cohort Study Design. J Clin Med 2023; 12:jcm12020674. [PMID: 36675603 PMCID: PMC9862447 DOI: 10.3390/jcm12020674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Background: Familial pulmonary fibrosis (FPF) can be defined as pulmonary fibrosis in two or more first-degree family members. The first-degree family members of FPF patients are at high risk of developing FPF and are eligible for screening. Reproducible studies investigating risk factors for disease are much needed. Methods: Description of the screening study protocol for a single-center, prospective cohort study; the study will include 200 asymptomatic, first-degree family members of patients with FPF who will undergo three study visits in two years. The primary objective is determining the diagnostic value of parameters for detection of early FPF; the secondary objectives are determining the optimal timing of the screening interval and gaining insight into the natural history of early FPF. The presence of interstitial lung disease (ILD) changes on high-resolution computed tomography of the chest is indicative of preclinical ILD; the changes are determined at baseline. The comparison between the group with and without ILD changes is made for clinical parameters (pulmonary function, presence of digital clubbing, presence of Velcro-like crackles, blood count, liver- and kidney-function testing, patient-reported cough and dyspnea score) and exploratory parameters. Discussion: This study will be the first large-size, prospective, longitudinal cohort study for yearly screening of asymptomatic family members of FPF patients investigating the diagnostic value of parameters, including lung function, to detect early FPF. More effective screening strategies could advance early disease detection.
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27
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Hwang JA, Shin J, Cho E, Ahn SY, Ko GJ, Kwon YJ, Kim JE. Risk factors associated with the discordance in kidney function decline rate in identical twins. PLoS One 2023; 18:e0284154. [PMID: 37053150 PMCID: PMC10101412 DOI: 10.1371/journal.pone.0284154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/26/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND The rate of kidney function decline is different for each individual regardless of any difference in the medical histories. This study set out to identify the risk factors for high discordance in kidney function decline in an identical twin cohort. METHODS This study included 333 identical twins from the Korean Genome and Epidemiology Study who were categorized into two groups according to the estimated glomerular filtration rate (eGFR) decline: the slow and rapid progressor groups. The mean differences of variables were compared between the two groups. We calculated the difference in the annual eGFR change between twins and analyzed the risk factors associated with high discordance in twins who had > 5 mL/min/1.73 m2 /yr of the intra-twin difference in the annual eGFR decline. Identical twins with diabetes and baseline eGFR < 60 mL/min/1.73 m2 were excluded. RESULTS The high discordance twins showed significant differences in body mass index; waist-to-hip ratio; total body fat percentage; and levels of blood hemoglobin, serum fasting glucose, albumin, triglyceride, and uric acid; however, there were no differences in low discordance twins. Multivariable logistic regression showed that blood hemoglobin level is the only significant factor associated with high discordance of eGFR decline in twins. CONCLUSIONS Blood hemoglobin level may play a role in the individual differences in kidney function decline.
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Affiliation(s)
- Jeong Ah Hwang
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jaeun Shin
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Eunjung Cho
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Shin Young Ahn
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Gang-Jee Ko
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Young Joo Kwon
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Eun Kim
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
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28
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Grobe N, Scheiber J, Zhang H, Garbe C, Wang X. Omics and Artificial Intelligence in Kidney Diseases. ADVANCES IN KIDNEY DISEASE AND HEALTH 2023; 30:47-52. [PMID: 36723282 DOI: 10.1053/j.akdh.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 11/16/2022] [Indexed: 01/20/2023]
Abstract
Omics applications in nephrology may have relevance in the future to improve clinical care of kidney disease patients. In a short term, patients will benefit from specific measurement and computational analyses around biomarkers identified at various omics-levels. In mid term and long term, these approaches will need to be integrated into a holistic representation of the kidney and all its influencing factors for individualized patient care. Research demonstrates robust data to justify the application of omics for better understanding, risk stratification, and individualized treatment of kidney disease patients. Despite these advances in the research setting, there is still a lack of evidence showing the combination of omics technologies with artificial intelligence and its application in clinical diagnostics and care of patients with kidney disease.
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Affiliation(s)
| | | | | | - Christian Garbe
- Frankfurter Innovationszentrum Biotechnologie, Frankfurt am Main, Germany
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29
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Wadapurkar RM, Sivaram A, Vyas R. Computational studies reveal co-occurrence of two mutations in IL7R gene of high-grade serous carcinoma patients. J Biomol Struct Dyn 2022; 40:13310-13324. [PMID: 34657565 DOI: 10.1080/07391102.2021.1987326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Major cause of mortality in ovarian cancer can be attributed to a lack of specific and sensitive biomarkers for diagnosis and prognosis of the disease. Uncovering the mutations in genes involved in crucial oncogenic pathways is a key step in discovery and development of novel biomarkers. Whole exome sequencing (WES) is a powerful method for the detection of cancer driver mutations. The present work focuses on identifying functionally damaging mutations in patients with high-grade serous ovarian carcinoma (HGSC) through computational analysis of WES. In this study, WES data of HGSC patients was retrieved from the genomic literature available in sequence read archive, the variants were identified and comprehensive structural and functional analysis was performed. Interestingly, I66T and V138I mutations were found to be co-occurring in the IL7R gene in four out of five HGSC patient samples investigated in this study. The V138I mutation was located in the fibronectin type-3 domain and computationally assessed to be causing disruptive effects on the structure and dynamics of IL7R protein. This mutation was found to be co-occurring with the neutral I66T mutation in the same domain which compensated the disruptive effects of V138I variant. These comprehensive studies point to a hitherto unexplored significant role of the IL7R gene in ovarian carcinoma. It is envisaged that the work will lay the foundation for the development of a novel biomarker with potential application in molecular profiling and in estimation of the disease prognosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study. Eur J Hum Genet 2022; 30:1413-1422. [PMID: 36100708 PMCID: PMC9712573 DOI: 10.1038/s41431-022-01177-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 11/09/2022] Open
Abstract
Hereditary chronic kidney disease (CKD) appears to be more frequent than the clinical perception. Exome sequencing (ES) studies in CKD cohorts could identify pathogenic variants in ~10% of individuals. Tubulointerstitial kidney diseases, showing no typical clinical/histologic finding but tubulointerstitial fibrosis, are particularly difficult to diagnose. We used a targeted panel (29 genes) and MUC1-SNaPshot to sequence 271 DNAs, selected in defined disease entities and age cutoffs from 5217 individuals in the German Chronic Kidney Disease cohort. We identified 33 pathogenic variants. Of these 27 (81.8%) were in COL4A3/4/5, the largest group being 15 COL4A5 variants with nine unrelated individuals carrying c.1871G>A, p.(Gly624Asp). We found three cysteine variants in UMOD, a novel missense and a novel splice variant in HNF1B and the homoplastic MTTF variant m.616T>C. Copy-number analysis identified a heterozygous COL4A5 deletion, and a HNF1B duplication/deletion, respectively. Overall, pathogenic variants were present in 12.5% (34/271) and variants of unknown significance in 9.6% (26/271) of selected individuals. Bioinformatic predictions paired with gold standard diagnostics for MUC1 (SNaPshot) could not identify the typical cytosine duplication ("c.428dupC") in any individual, implying that ADTKD-MUC1 is rare. Our study shows that >10% of selected individuals carry disease-causing variants in genes partly associated with tubulointerstitial kidney diseases. COL4A3/4/5 genes constitute the largest fraction, implying they are regularly overlooked using clinical Alport syndrome criteria and displaying the existence of phenocopies. We identified variants easily missed by some ES pipelines. The clinical filtering criteria applied enriched for an underlying genetic disorder.
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Al-Hamed MH, Hussein MH, Shah Y, Al-Mojalli H, Alsabban E, Alshareef T, Altayyar A, Elshouny S, Ali W, Abduljabbar M, AlOtaibi A, AlShammasi A, Akili R, Abouelhoda M, Sayer JA, Dasouki MJ, Imtiaz F. Exome sequencing unravels genetic variants associated with chronic kidney disease in Saudi Arabian patients. Hum Mutat 2022; 43:e24-e37. [PMID: 36177613 DOI: 10.1002/humu.24480] [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: 01/30/2022] [Revised: 09/10/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023]
Abstract
The use of genetic testing within nephrology is increasing and its diagnostic yield depends on the methods utilized, patient selection criteria, and population characteristics. We performed exome sequencing (ES) analysis on 102 chronic kidney disease (CKD) patients with likely genetic kidney disease. Patients had diverse CKD subtypes with/without consanguinity, positive family history, and possible hereditary renal syndrome with extra-renal abnormalities or progressive kidney disease of unknown etiology. The identified genetic variants associated with the observed kidney phenotypes were then confirmed and reported. End-stage kidney disease was reported in 51% of the cohort and a family history of kidney disease in 59%, while known consanguinity was reported in 54%. Pathogenic/likely pathogenic variants were identified in 43 patients with a diagnostic yield of 42%, and clinically associated variants of unknown significance (VUS) were identified in further 21 CKD patients (21%). A total of eight novel predicted pathogenic variants and eight VUS were detected. The clinical utility of ES within the nephrology clinic was demonstrated allowing patient management to be disease-specific. In this cohort, ES detected a diagnostic molecular abnormality in 42% of patients with CKD phenotypes. Positive family history and high rates of consanguinity likely contributed to this high diagnostic yield.
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Affiliation(s)
- Mohamed H Al-Hamed
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,Saudi Diagnostics Laboratory, KFSH&RC, Riyadh, Saudi Arabia
| | - Maged H Hussein
- Medicine Department, Nephrology Section, KFSH&RC, Riyadh, Saudi Arabia
| | - Yaser Shah
- Organ Transplant Centre of Excellence, Adult Transplant Nephrology, KFSH&RC, Riyadh, Saudi Arabia
| | - Hamad Al-Mojalli
- Organ Transplant Centre of Excellence, Adult Transplant Nephrology, KFSH&RC, Riyadh, Saudi Arabia
| | | | | | - Ali Altayyar
- Medicine Department, Nephrology Section, KFSH&RC, Riyadh, Saudi Arabia
| | - Samir Elshouny
- Medicine Department, Nephrology Section, KFSH&RC, Riyadh, Saudi Arabia
| | - Wafaa Ali
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mai Abduljabbar
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Afaf AlOtaibi
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Amal AlShammasi
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rana Akili
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Majed J Dasouki
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,Saudi Diagnostics Laboratory, KFSH&RC, Riyadh, Saudi Arabia
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Theory Designed Strategies to Support Implementation of Genomics in Nephrology. Genes (Basel) 2022; 13:genes13101919. [PMID: 36292804 PMCID: PMC9601730 DOI: 10.3390/genes13101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Genomic testing is increasingly utilized as a clinical tool; however, its integration into nephrology remains limited. The purpose of this study was to identify barriers and prioritize interventions for the widespread implementation of genomics in nephrology. (2) Methods: Qualitative, semi-structured interviews were conducted with 25 Australian adult nephrologists to determine their perspectives on interventions and models of care to support implementation of genomics in nephrology. Interviews were guided by a validated theoretical framework for the implementation of genomic medicine-the Consolidated Framework of Implementation Research (CFIR). (3) Results: Nephrologists were from 18 hospitals, with 7 having a dedicated multidisciplinary kidney genetics service. Most practiced in the public healthcare system (n = 24), a large number were early-career (n = 13), and few had genomics experience (n = 4). The top three preferred interventions were increased funding, access to genomics champions, and education and training. Where interventions to barriers were not reported, we used the CFIR/Expert Recommendations for Implementing Change matching tool to generate theory-informed approaches. The preferred model of service delivery was a multidisciplinary kidney genetics clinic. (4) Conclusions: This study identified surmountable barriers and practical interventions for the implementation of genomics in nephrology, with multidisciplinary kidney genetics clinics identified as the preferred model of care. The integration of genomics education into nephrology training, secure funding for testing, and counselling along with the identification of genomics champions should be pursued by health services more broadly.
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Aron AW, Dahl NK, Besse W. A Practical Guide to Genetic Testing for Kidney Disorders of Unknown Etiology. KIDNEY360 2022; 3:1640-1651. [PMID: 36245662 PMCID: PMC9528385 DOI: 10.34067/kid.0007552021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/08/2022] [Indexed: 01/18/2023]
Abstract
Genetic testing is increasingly used in the workup and diagnosis of kidney disease and kidney-related disorders of undetermined cause. Out-of-pocket costs for clinical genetic testing have become affordable, and logistical hurdles overcome. The interest in genetic testing may stem from the need to make or confirm a diagnosis, guide management, or the patient's desire to have a more informed explanation or prognosis. This poses a challenge for providers who do not have formal training in the selection, interpretation, and limitations of genetic tests. In this manuscript, we provide detailed discussion of relevant cases in which clinical genetic testing using a kidney gene panel was applied. The cases demonstrate identification of pathogenic variants for monogenic diseases-contrasting them from genetic risk alleles-and bring up diagnostic limitations and diagnostic utility of these tests in nephrology. This review aims to guide clinicians in formulating pretest conversations with their patients, interpreting genetic variant nomenclature, and considering follow-up investigations. Although providers are gaining experience, there is still risk of testing causing more anxiety than benefit. However, with provider education and support, clinical genetic testing applied to otherwise unexplained kidney-related disorders will increasingly serve as a valuable diagnostic tool with the potential to reshape how we consider and treat many kidney-related diagnoses.
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Affiliation(s)
- Abraham W. Aron
- Section of Nephrology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Neera K. Dahl
- Section of Nephrology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Whitney Besse
- Section of Nephrology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
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34
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Yavaş C, Ün C, Çelebi E, Gezdirici A, Doğan M, İli EG, Doğan T, Özgentürk NÖ. Whole-Exome Sequencing (WES) results of 50 patients with chronic kidney diseases: a perspective of Alport syndrome. Rev Assoc Med Bras (1992) 2022; 68:1282-1287. [PMID: 36134775 PMCID: PMC9575037 DOI: 10.1590/1806-9282.20220405] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/12/2022] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE: Chronic kidney disease (CKD) remains one of the major common health problems, and the number of people affected by the disease is progressively increasing in Turkey and worldwide. This study aimed to investigate molecular defects in Alport syndrome (AS) and other genes in patients with clinically suspected CKD using whole-exome sequencing (WES). METHODS: Patients with clinical suspicion of CKD were included in the study. Molecular genetic analyses were performed on genomic DNA by using WES. RESULTS: A total of 15 with 5 different pathogenic or likely pathogenic variants were identified in CKD patients, with a diagnostic rate of 30%. Eight variants of uncertain significance were also detected. In this study, 10 variants were described for the first time. As a result, we detected variants associated with CKD in our study population and found AS as the most common CKD after other related kidney diseases. CONCLUSIONS: Our results suggest that in heterogeneous diseases such as CKD, WES analysis enables accurate identification of underlying molecular defects promptly. Although CKD accounts for 10–14% of all renal dysfunction, molecular genetic diagnosis is necessary for optimal long-term treatment, prognosis, and effective genetic counseling.
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Affiliation(s)
- Cüneyd Yavaş
- Yildiz Technical University, Turkey; Başaksehir Çam and Sakura City Hospital, Turkey
| | | | | | | | | | | | - Tunay Doğan
- Başaksehir Çam and Sakura City Hospital, Turkey
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35
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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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36
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Zhao JL, Qiao XH, Mao JH, Liu F, Fu HD. The interaction between cellular senescence and chronic kidney disease as a therapeutic opportunity. Front Pharmacol 2022; 13:974361. [PMID: 36091755 PMCID: PMC9459105 DOI: 10.3389/fphar.2022.974361] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/03/2022] [Indexed: 01/10/2023] Open
Abstract
Chronic kidney disease (CKD) is an increasingly serious public health problem in the world, but the effective therapeutic approach is quite limited at present. Cellular senescence is characterized by the irreversible cell cycle arrest, senescence-associated secretory phenotype (SASP) and senescent cell anti-apoptotic pathways (SCAPs). Renal senescence shares many similarities with CKD, including etiology, mechanism, pathological change, phenotype and outcome, however, it is difficult to judge whether renal senescence is a trigger or a consequence of CKD, since there is a complex correlation between them. A variety of cellular signaling mechanisms are involved in their interactive association, which provides new potential targets for the intervention of CKD, and then extends the researches on senotherapy. Our review summarizes the common features of renal senescence and CKD, the interaction between them, the strategies of senotherapy, and the open questions for future research.
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Affiliation(s)
- Jing-Li Zhao
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiao-Hui Qiao
- Department of Pediatric Internal Medicine, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Jian-Hua Mao
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- *Correspondence: Jian-Hua Mao,
| | - Fei Liu
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Hai-Dong Fu
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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37
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Khan A, Turchin MC, Patki A, Srinivasasainagendra V, Shang N, Nadukuru R, Jones AC, Malolepsza E, Dikilitas O, Kullo IJ, Schaid DJ, Karlson E, Ge T, Meigs JB, Smoller JW, Lange C, Crosslin DR, Jarvik GP, Bhatraju PK, Hellwege JN, Chandler P, Torvik LR, Fedotov A, Liu C, Kachulis C, Lennon N, Abul-Husn NS, Cho JH, Ionita-Laza I, Gharavi AG, Chung WK, Hripcsak G, Weng C, Nadkarni G, Irvin MR, Tiwari HK, Kenny EE, Limdi NA, Kiryluk K. Genome-wide polygenic score to predict chronic kidney disease across ancestries. Nat Med 2022; 28:1412-1420. [PMID: 35710995 PMCID: PMC9329233 DOI: 10.1038/s41591-022-01869-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/11/2022] [Indexed: 01/03/2023]
Abstract
Chronic kidney disease (CKD) is a common complex condition associated with high morbidity and mortality. Polygenic prediction could enhance CKD screening and prevention; however, this approach has not been optimized for ancestrally diverse populations. By combining APOL1 risk genotypes with genome-wide association studies (GWAS) of kidney function, we designed, optimized and validated a genome-wide polygenic score (GPS) for CKD. The new GPS was tested in 15 independent cohorts, including 3 cohorts of European ancestry (n = 97,050), 6 cohorts of African ancestry (n = 14,544), 4 cohorts of Asian ancestry (n = 8,625) and 2 admixed Latinx cohorts (n = 3,625). We demonstrated score transferability with reproducible performance across all tested cohorts. The top 2% of the GPS was associated with nearly threefold increased risk of CKD across ancestries. In African ancestry cohorts, the APOL1 risk genotype and polygenic component of the GPS had additive effects on the risk of CKD.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Michael C Turchin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Rajiv Nadukuru
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alana C Jones
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tian Ge
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jordan W Smoller
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jacklyn N Hellwege
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paulette Chandler
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura Rasmussen Torvik
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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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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39
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Guérin C, Crestani B, Dupin C, Kawano-Dourado L, Ba I, Kannengiesser C, Borie R. [Telomeres and lung]. Rev Mal Respir 2022; 39:595-606. [PMID: 35715316 DOI: 10.1016/j.rmr.2022.03.011] [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: 03/12/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
Genetic studies of familial forms of interstitial lung disease (ILD) have led to the discovery of telomere-related gene (TRG) mutations (TERT, TERC, RTEL1, PARN, DKC1, TINF2, NAF1, NOP10, NHP2, ACD, ZCCH8) in approximately 30% of familial ILD forms. ILD patients with TRG mutation are also subject to extra-pulmonary (immune-hematological, hepatic and/or mucosal-cutaneous) manifestations. TRG mutations may be associated not only with idiopathic pulmonary fibrosis (IPF), but also with non-IPF ILDs, including idiopathic and secondary ILDs, such as hypersensitivity pneumonitis (HP). The presence of TRG mutation may also be associated with an accelerated decline of forced vital capacity (FVC) or poorer prognosis after lung transplantation, notwithstanding which, usual ILD treatments may be proposed. Lastly, patients and their relatives are called upon to reduce their exposure to environmental lung toxicity, and are likely to derive benefit from specific genetic counseling and pre-symptomatic genetic testing.
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Affiliation(s)
- C Guérin
- Service de Pneumologie A, Centre de compétences maladies pulmonaires rares, AP-HP, Hôpital Bichat, Paris, France..
| | - B Crestani
- Service de Pneumologie A, Centre de compétences maladies pulmonaires rares, AP-HP, Hôpital Bichat, Paris, France.; INSERM, Unité 1152; Université Paris Diderot, Paris, France
| | - C Dupin
- Service de Pneumologie A, Centre de compétences maladies pulmonaires rares, AP-HP, Hôpital Bichat, Paris, France.; INSERM, Unité 1152; Université Paris Diderot, Paris, France
| | - L Kawano-Dourado
- INSERM, Unité 1152; Université Paris Diderot, Paris, France.; HCor Research Institute, Hôpital de Caracao, Sao Paulo, Brésil.; Département de Pneumologie, InCor, Université de Sao Paulo, Sao Paulo, Brésil
| | - I Ba
- INSERM, Unité 1152; Université Paris Diderot, Paris, France.; Département de Génétique, AP-HP, Hôpital Bichat, Paris, France
| | - C Kannengiesser
- INSERM, Unité 1152; Université Paris Diderot, Paris, France.; Département de Génétique, AP-HP, Hôpital Bichat, Paris, France
| | - R Borie
- Service de Pneumologie A, Centre de compétences maladies pulmonaires rares, AP-HP, Hôpital Bichat, Paris, France.; INSERM, Unité 1152; Université Paris Diderot, Paris, France
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40
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Savige J. Heterozygous pathogenic COL4A3 or COL4A4 variants (AD Alport syndrome) is common, and not typically associated with end-stage kidney failure, hearing loss or ocular abnormalities. Kidney Int Rep 2022; 7:1933-1938. [PMID: 36090501 PMCID: PMC9458992 DOI: 10.1016/j.ekir.2022.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 12/03/2022] Open
Abstract
The term “autosomal dominant (AD) Alport syndrome” is often used to describe the condition associated with heterozygous pathogenic COL4A3 or COL4A4 variants and has largely replaced “thin basement membrane nephropathy (TBMN).” AD Alport syndrome implies that affected individuals develop end-stage kidney failure (ESKF) as well as the typical Alport hearing loss and ocular abnormalities, but these features have been considered rare with TBMN. Recent studies suggest that ESKF occurs in 14% to 30% of those with heterozygous pathogenic COL4A3 or COL4A4 variants but confirm that the hearing loss and ocular defects occur uncommonly if at all. Uncertainty over the risk of ESKF has persisted. However all the cited studies of heterozygous pathogenic COL4A3 or COL4A4 variants and kidney failure are from hospital-based patients and thus biased toward more severe disease. Multiple unselected cohorts with ESKF have found heterozygous pathogenic variants in COL4A3 and COL4A4 occur about as often as COL4A5 variants, which suggests that AD Alport syndrome causes ESKF as often as X-linked (XL) disease. In the normal population, heterozygous pathogenic COL4A3 and COL4A4 variants are present 20 times more often than COL4A5 variants. Therefore, AD Alport syndrome is complicated by ESKF 20 times less often than XL disease and occurs in fewer than 3% of those with pathogenic COL4A3 or COL4A4 variants by the age of 60. Nevertheless, individuals with heterozygous pathogenic COL4A3 or COL4A4 variants referred to a hospital are still more likely to develop impaired kidney function than those who remain at home undiagnosed.
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Wopperer FJ, Knaup KX, Stanzick KJ, Schneider K, Jobst-Schwan T, Ekici AB, Uebe S, Wenzel A, Schliep S, Schürfeld C, Seitz R, Bernhardt W, Gödel M, Wiesener A, Popp B, Stark KJ, Gröne HJ, Friedrich B, Weiß M, Basic-Jukic N, Schiffer M, Schröppel B, Huettel B, Beck BB, Sayer JA, Ziegler C, Büttner-Herold M, Amann K, Heid IM, Reis A, Pasutto F, Wiesener MS. Diverse molecular causes of unsolved autosomal dominant tubulointerstitial kidney diseases. Kidney Int 2022; 102:405-420. [DOI: 10.1016/j.kint.2022.04.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Accepted: 04/08/2022] [Indexed: 12/11/2022]
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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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Leenen E, Erger F, Altmüller J, Wenzel A, Thiele H, Harth A, Tschernoster N, Lokhande S, Joerres A, Becker JU, Ekici A, Huettel B, Beck B, Weidemann A. Alport syndrome and autosomal dominant tubulointerstitial kidney disease frequently underlie end stage renal disease of unknown origin - a single center analysis. Nephrol Dial Transplant 2022; 37:1895-1905. [PMID: 35485766 DOI: 10.1093/ndt/gfac163] [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: 11/23/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The prevalence of end stage renal disease of unknown etiology in adult patients is globally high and accounts for almost 20% of all dialysis patients. Recent studies have suggested that the percentage of adult patients with a causal genetic variant has been underestimated so far. Despite severe prognostic and therapeutic implications, awareness about prevalence and manifestations of genetic kidney diseases in adult renal patients is still limited. MATERIALS AND METHODS We recruited 58 individuals from 39 families at our transplantation center, fulfilling at least one of the following criteria: 1) unclear etiology of kidney disease 2) clinically suspected genetic kidney disease 3) positive family history for nephropathies. The cohort consisted of patients waitlisted for kidney transplantation and patients in the follow-up after transplantation. Detailed documentation of family history and phenotype was obtained before initiating gene panel sequencing of 479 nephropathy-associated genes. RESULTS With this study design, a molecular genetic diagnosis was established in one third of all patients. Mutations in the collagen COL4A-genes, and mutations in MUC1 and UMOD were the most frequent among all detected causal variants. Overall, rare genetic variants were detected in more than half of all cases. CONCLUSION The combination of detailed phenotyping prior to NGS diagnostics was highly efficient. Elucidating the underlying genetic causes in a cohort of adult renal patients has considerable clinical impact on medical management.
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Affiliation(s)
- Esther Leenen
- Department of Medicine I - Nephrology, Transplantation & Medical Intensive Care, University Witten/Herdecke, Medical Center Cologne-Merheim, Germany
| | - Florian Erger
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare and Hereditary Kidney Disease, Cologne, University Hospital of Cologne, Cologne, Germany
| | - Janine Altmüller
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Andrea Wenzel
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare and Hereditary Kidney Disease, Cologne, University Hospital of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Ana Harth
- Department of Medicine I - Nephrology, Transplantation & Medical Intensive Care, University Witten/Herdecke, Medical Center Cologne-Merheim, Germany
| | - Nikolai Tschernoster
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare and Hereditary Kidney Disease, Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Shanti Lokhande
- Department of Medicine I - Nephrology, Transplantation & Medical Intensive Care, University Witten/Herdecke, Medical Center Cologne-Merheim, Germany
| | - Achim Joerres
- Department of Medicine I - Nephrology, Transplantation & Medical Intensive Care, University Witten/Herdecke, Medical Center Cologne-Merheim, Germany
| | - Jan-Ulrich Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Arif Ekici
- Institute of Human Genetics, University Hospital Erlangen, Germany
| | - Bruno Huettel
- Max-Plank-Genome-Centre Cologne (MP-GC), Cologne, Germany
| | - Bodo Beck
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare and Hereditary Kidney Disease, Cologne, University Hospital of Cologne, Cologne, Germany
| | - Alexander Weidemann
- Department of Medicine I - Nephrology, Transplantation & Medical Intensive Care, University Witten/Herdecke, Medical Center Cologne-Merheim, Germany.,Department of Nephrology, St. Vincenz Hospital, Paderborn, Germany
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Walsh M, West K, Taylor JA, Thompson BA, Hopkins A, Sexton A, Ragunathan A, Verma KP, Panetta J, Matotek E, Fahey MC, Christie M, Winship IM, Trainer AH, James PA. Real world outcomes and implementation pathways of exome sequencing in an adult genetic department. Genet Med 2022; 24:1536-1544. [PMID: 35416776 DOI: 10.1016/j.gim.2022.03.010] [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: 11/17/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE This study aimed to correlate the indications and diagnostic yield of exome sequencing (ES) in adult patients across various clinical settings. The secondary aim was to examine the clinical utility of ES in adult patients. METHODS Data on demographics, clinical indications, results, management changes, and cascade testing were collected for 250 consecutive patients who underwent ES through an adult genetics department between 2016 and 2021. Data were analyzed using descriptive and inferential statistics. Testing in which traditional gene panels were in standard use, such as in heritable cancers, was excluded. RESULTS The average age at testing was 43 years (range = 17-80 years). A molecular diagnosis was identified in 29% of patients. Older age at symptom onset did not pre-exclude a substantial diagnostic yield. Patients with syndromic intellectual disability and multiple system disorders had the highest yield. In >50% of patients with an exome diagnosis, the results changed management. Cascade testing occured in at least one family member for 30% of patients with a diagnosis. Diagnostic results had reproductive implications for 26% of patients and 31% of patients' relatives. CONCLUSION ES has a robust diagnostic yield and clear clinical utility in adult patients across a range of ages and phenotypes.
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Affiliation(s)
- Maie Walsh
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Kirsty West
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jessica A Taylor
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Adelaide Hopkins
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Abiramy Ragunathan
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Kunal P Verma
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Julie Panetta
- Metabolic Diseases Unit (MDU), The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ebony Matotek
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael C Fahey
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael Christie
- Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul A James
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
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de Haan A, Eijgelsheim M, Vogt L, van der Zwaag B, van Eerde AM, Knoers NVAM, de Borst MH. Diagnostic yield of massively parallel sequencing in patients with chronic kidney disease of unknown etiology: rationale and design of a national prospective cohort study. BMJ Open 2022; 12:e057829. [PMID: 35393322 PMCID: PMC8991067 DOI: 10.1136/bmjopen-2021-057829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Chronic kidney disease (CKD) can be caused by a variety of systemic or primary renal diseases. The cause of CKD remains unexplained in approximately 20% of patients. Retrospective studies indicate that massively parallel sequencing (MPS)-based gene panel testing may lead to a genetic diagnosis in 12%-56% of patients with unexplained CKD, depending on patient profile. The diagnostic yield of MPS-based testing in a routine healthcare setting is unclear. Therefore, the primary aim of the VARIETY (Validation of algoRithms and IdEnTification of genes in Young patients with unexplained CKD) study is to prospectively address the diagnostic yield of MPS-based gene panel testing in patients with unexplained CKD and an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2 before the age of 50 years in clinical practice. METHODS AND ANALYSIS The VARIETY study is an ongoing, prospective, nationwide observational cohort study to investigate the diagnostic yield of MPS-based testing in patients with unexplained CKD in a routine healthcare setting in the Netherlands. Patients are recruited from outpatient clinics in hospitals across the Netherlands. At least 282 patients will be included to meet the primary aim. Secondary analyses include subgroup analyses according to age and eGFR at first presentation, family history, and the presence of extrarenal symptoms. ETHICS AND DISSEMINATION Ethical approval for the study has been obtained from the institutional review board of the University Medical Center Groningen. Study findings should inform physicians and policymakers towards optimal implementation of MPS-based diagnostic testing in patients with unexplained CKD.
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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
| | - Liffert Vogt
- Department of Internal Medicine, Section Nephrology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 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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Phillips-Houlbracq M, Mal H, Cottin V, Gauvain C, Beier F, Sicre de Fontbrune F, Sidali S, Mornex JF, Hirschi S, Roux A, Weisenburger G, Roussel A, Wémeau-Stervinou L, Le Pavec J, Pison C, Marchand Adam S, Froidure A, Lazor R, Naccache JM, Jouneau S, Nunes H, Reynaud-Gaubert M, Le Borgne A, Boutboul D, Ba I, Boileau C, Crestani B, Kannengiesser C, Borie R. Determinants of survival after lung transplantation in telomerase-related gene mutation carriers: A retrospective cohort. Am J Transplant 2022; 22:1236-1244. [PMID: 34854205 DOI: 10.1111/ajt.16893] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/01/2021] [Accepted: 10/20/2021] [Indexed: 01/25/2023]
Abstract
Carriers of germline telomerase-related gene (TRG) mutations can show poor prognosis, with an increase in common hematological complications after lung transplantation (LT) for pulmonary fibrosis. The aim of this study was to describe the outcomes after LT in recipients carrying a germline TRG mutation and to identify the predictors of survival. In a multicenter cohort of LT patients, we retrospectively reviewed those carrying pathogenic TRG variations (n = 38; TERT, n = 23, TERC, n = 9, RTEL1, n = 6) between 2009 and 2018. The median age at LT was 54 years (interquartile range [IQR] 46-59); 68% were male and 71% had idiopathic pulmonary fibrosis. During the diagnosis of pulmonary fibrosis, 28 (74%) had a hematological disease, including eight with myelodysplasia. After a median follow-up of 26 months (IQR 15-46), 38 patients received LT. The overall post-LT median survival was 3.75 years (IQR 1.8-NA). The risk of death after LT was increased for patients with myelodysplasia (HR 4.1 [95% CI 1.5-11.5]) or short telomere (HR 2.2 [1.0-5.0]) before LT. After LT, all patients had anemia, 66% had thrombocytopenia, and 39% had neutropenia. Chronic lung allograft dysfunction frequency was 29% at 4 years. The present findings support the use of LT in TRG mutation carriers without myelodysplasia. Hematological evaluation should be systematically performed before LT.
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Affiliation(s)
- Mathilde Phillips-Houlbracq
- Service de Pneumologie A, Centre de référence des maladies pulmonaires rares (site constitutif), APHP, Hôpital Bichat, Paris, France
| | - Hervé Mal
- Université de Paris and INSERM U1152, Paris, France.,Service de Pneumologie B, APHP, Hôpital Bichat, Paris, France
| | - Vincent Cottin
- Service de Pneumologie, Centre coordonnateur national de référence des maladies pulmonaires rares, Hôpital Louis Pradel, Université Claude Bernard Lyon 1, Université de Lyon, INRAE, ERN-LUNG, Lyon, France
| | - Clément Gauvain
- Service d'oncologie, Hôpital Calmette, CHU de Lille, Lille, France
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany.,Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | | | - Sabrina Sidali
- Service d'hépatologie, Hôpital Beaujon, APHP, Clichy, France
| | - Jean François Mornex
- Service de Pneumologie, Centre coordonnateur national de référence des maladies pulmonaires rares, Hôpital Louis Pradel, Université Claude Bernard Lyon 1, Université de Lyon, INRAE, ERN-LUNG, Lyon, France
| | - Sandrine Hirschi
- Service de Pneumologie, Centre de compétence des maladies pulmonaires rares, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Antoine Roux
- Service de Pneumologie, Hôpital Foch, Suresnes, France
| | - Gaelle Weisenburger
- Université de Paris and INSERM U1152, Paris, France.,Service de Pneumologie B, APHP, Hôpital Bichat, Paris, France
| | - Arnaud Roussel
- Service de chirurgie vasculaire et thoracique, Hopital Bichat, Paris, France
| | - Lidwine Wémeau-Stervinou
- Service de Pneumologie, Centre de référence des maladies pulmonaires rares (site constitutif), CHU de Lille, Lille, France
| | - Jérôme Le Pavec
- Service de Chirurgie Thoracique, Vasculaire et Transplantation Cardio-pulmonaire, Groupe Hospitalier Saint Joseph/Marie-Lannelongue, Le Plessis-Robinson, France.,Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France.,UMR_S 999, Université Paris-Sud, INSERM, Hôpital Marie Lannelongue, Le Plessis Robinson, France
| | - Christophe Pison
- Service Hospitalier Universitaire Pneumologie Physiologie, Pôle Thorax et Vaisseaux, CHU Grenoble Alpes, Université Grenoble Alpes, Grenoble, France
| | | | - Antoine Froidure
- Service de pneumologie, Cliniques universitaires Saint-Luc, Bruxelles, Belgique
| | - Romain Lazor
- Service de Pneumologie, Centre hospitalier universitaire vaudois, Lausanne, Suisse
| | - Jean-Marc Naccache
- Service de Pneumologie, Centre de référence des maladies pulmonaires rares (site constitutif), Hôpital Tenon, Paris, France
| | - Stéphane Jouneau
- Service de Pneumologie, Centre de compétences des maladies rares pulmonaires, Hôpital Pontchaillou, IRSET UMR 1085, Université de Rennes 1, Rennes, France
| | - Hilario Nunes
- Service de Pneumologie Centre de référence des maladies pulmonaires rares (site constitutif), Hôpital Avicenne, Bobigny, France
| | - Martine Reynaud-Gaubert
- Service de Pneumologie, Centre de compétences des maladies pulmonaires rares, CHU Nord, AP-HM, Marseille, France.,Aix-Marseille Université, IHU Méditerranée Infection, MEPHI, Marseille, France
| | - Aurélie Le Borgne
- Service de Pneumologie, Centre de compétence des maladies pulmonaires rares Hôpital Larrey CHU Toulouse, Toulouse, France
| | - David Boutboul
- Service d'Immunopathologie Clinique, Hôpital St Louis, APHP, Paris, France
| | - Ibrahima Ba
- Laboratoire de Génétique, APHP, Hôpital Bichat, Paris, France
| | | | - Bruno Crestani
- Service de Pneumologie A, Centre de référence des maladies pulmonaires rares (site constitutif), APHP, Hôpital Bichat, Paris, France
| | | | - Raphaël Borie
- Service de Pneumologie A, Centre de référence des maladies pulmonaires rares (site constitutif), APHP, Hôpital Bichat, Paris, France
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Gutierrez E, Trujillo H, Aubert L, Sandino J, Hernández E, Auñón P, Cavero T, Morales E, Praga M. ¿Por qué se debe incorporar el estudio genético a la práctica clínica habitual en nefrología? La utilidad de consultas monográficas. Una necesidad emergente. Nefrologia 2022. [DOI: 10.1016/j.nefro.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Devarajan P, Chertow GM, Susztak K, Levin A, Agarwal R, Stenvinkel P, Chapman AB, Warady BA. Emerging Role of Clinical Genetics in CKD. Kidney Med 2022; 4:100435. [PMID: 35372818 PMCID: PMC8971313 DOI: 10.1016/j.xkme.2022.100435] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chronic kidney disease (CKD) afflicts 15% of adults in the United States, of whom 25% have a family history. Genetic testing is supportive in identifying and possibly confirming diagnoses of CKD, thereby guiding care. Advances in the clinical genetic evaluation include next-generation sequencing with targeted gene panels, whole exome sequencing, and whole genome sequencing. These platforms provide DNA sequence reads with excellent coverage throughout the genome and have identified novel genetic causes of CKD. New pathologic genetic variants identified in previously unrecognized biological pathways have elucidated disease mechanisms underlying CKD etiologies, potentially establishing prognosis and guiding treatment selection. Molecular diagnoses using genetic sequencing can detect rare, potentially treatable mutations, avoid misdiagnoses, guide selection of optimal therapy, and decrease the risk of unnecessary and potentially harmful interventions. Genetic testing has been widely adopted in pediatric nephrology; however, it is less frequently used to date in adult nephrology. Extension of clinical genetic approaches to adult patients may achieve similar benefits in diagnostic refinement and treatment selection. This review aimed to identify clinical CKD phenotypes that may benefit the most from genetic testing, outline the commonly available platforms, and provide examples of successful deployment of these approaches in CKD.
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Seltzsam S, Wang C, Zheng B, Mann N, Connaughton DM, Wu CHW, Schneider S, Schierbaum L, Kause F, Kolvenbach CM, Nakayama M, Dai R, Ottlewski I, Schneider R, Deutsch K, Buerger F, Klämbt V, Mao Y, Onuchic-Whitford AC, Nicolas-Frank C, Yousef K, Pantel D, Lai EW, Salmanullah D, Majmundar AJ, Bauer SB, Rodig NM, Somers MJG, Traum AZ, Stein DR, Daga A, Baum MA, Daouk GH, Tasic V, Awad HS, Eid LA, El Desoky S, Shalaby M, Kari JA, Fathy HM, Soliman NA, Mane SM, Shril S, Ferguson MA, Hildebrandt F. Reverse phenotyping facilitates disease allele calling in exome sequencing of patients with CAKUT. Genet Med 2022; 24:307-318. [PMID: 34906515 PMCID: PMC8876311 DOI: 10.1016/j.gim.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/08/2021] [Accepted: 09/14/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the leading cause of chronic kidney disease in children. In total, 174 monogenic causes of isolated or syndromic CAKUT are known. However, syndromic features may be overlooked when the initial clinical diagnosis of CAKUT is made. We hypothesized that the yield of a molecular genetic diagnosis by exome sequencing (ES) can be increased by applying reverse phenotyping, by re-examining the case for signs/symptoms of the suspected clinical syndrome that results from the genetic variant detected by ES. METHODS We conducted ES in an international cohort of 731 unrelated families with CAKUT. We evaluated ES data for variants in 174 genes, in which variants are known to cause isolated or syndromic CAKUT. In cases in which ES suggested a previously unreported syndromic phenotype, we conducted reverse phenotyping. RESULTS In 83 of 731 (11.4%) families, we detected a likely CAKUT-causing genetic variant consistent with an isolated or syndromic CAKUT phenotype. In 19 of these 83 families (22.9%), reverse phenotyping yielded syndromic clinical findings, thereby strengthening the genotype-phenotype correlation. CONCLUSION We conclude that employing reverse phenotyping in the evaluation of syndromic CAKUT genes by ES provides an important tool to facilitate molecular genetic diagnostics in CAKUT.
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Affiliation(s)
- Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chunyan Wang
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bixia Zheng
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nina Mann
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dervla M Connaughton
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chen-Han Wilfred Wu
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sophia Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Luca Schierbaum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Franziska Kause
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Caroline M Kolvenbach
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Makiko Nakayama
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Rufeng Dai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Isabel Ottlewski
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ronen Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Konstantin Deutsch
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Florian Buerger
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Verena Klämbt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Youying Mao
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ana C Onuchic-Whitford
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Camille Nicolas-Frank
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Kirollos Yousef
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dalia Pantel
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ethan W Lai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Daanya Salmanullah
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Amar J Majmundar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nancy M Rodig
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael J G Somers
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Avram Z Traum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Deborah R Stein
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ankana Daga
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ghaleb H Daouk
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Sherif El Desoky
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Mohammed Shalaby
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Jameela A Kari
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael A Ferguson
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
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50
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Elhassan EAE, Murray SL, Connaughton DM, Kennedy C, Cormican S, Cowhig C, Stapleton C, Little MA, Kidd K, Bleyer AJ, Živná M, Kmoch S, Fennelly NK, Doyle B, Dorman A, Griffin MD, Casserly L, Harris PC, Hildebrandt F, Cavalleri GL, Benson KA, Conlon PJ. The utility of a genetic kidney disease clinic employing a broad range of genomic testing platforms: experience of the Irish Kidney Gene Project. J Nephrol 2022; 35:1655-1665. [PMID: 35099770 PMCID: PMC9300532 DOI: 10.1007/s40620-021-01236-2] [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: 10/19/2021] [Accepted: 12/16/2021] [Indexed: 10/24/2022]
Abstract
BACKGROUND AND AIMS Genetic testing presents a unique opportunity for diagnosis and management of genetic kidney diseases (GKD). Here, we describe the clinical utility and valuable impact of a specialized GKD clinic, which uses a variety of genomic sequencing strategies. METHODS In this prospective cohort study, we undertook genetic testing in adults with suspected GKD according to prespecified criteria. Over 7 years, patients were referred from tertiary centres across Ireland to an academic medical centre as part of the Irish Kidney Gene Project. RESULTS Among 677 patients, the mean age was of 37.2 ± 13 years, and 73.9% of the patients had family history of chronic kidney disease (CKD). We achieved a molecular diagnostic rate of 50.9%. Four genes accounted for more than 70% of identified pathogenic variants: PKD1 and PKD2 (n = 186, 53.4%), MUC1 (8.9%), and COL4A5 (8.3%). In 162 patients with a genetic diagnosis, excluding PKD1/PKD2, the a priori diagnosis was confirmed in 58% and in 13% the diagnosis was reclassified. A genetic diagnosis was established in 22 (29.7%) patients with CKD of uncertain aetiology. Based on genetic testing, a diagnostic kidney biopsy was unnecessary in 13 (8%) patients. Presence of family history of CKD and the underlying a priori diagnosis were independent predictors (P < 0.001) of a positive genetic diagnosis. CONCLUSIONS A dedicated GKD clinic is a valuable resource, and its implementation of various genomic strategies has resulted in a direct, demonstrable clinical and therapeutic benefits to affected patients.
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Affiliation(s)
- Elhussein A E Elhassan
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland. .,Department of Medicine, Dublin, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Susan L Murray
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland.,Department of Medicine, Dublin, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Dervla M Connaughton
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Division of Nephrology, Department of Medicine, London Health Sciences Centre, London, ON, Canada
| | - Claire Kennedy
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Sarah Cormican
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Cliona Cowhig
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Caragh Stapleton
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | - Mark A Little
- Trinity Health Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, St James' Street, Dublin 8, Ireland
| | - Kendrah Kidd
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Anthony J Bleyer
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Stanislav Kmoch
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Research Unit for Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | - Brendan Doyle
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Anthony Dorman
- Department of Pathology, Beaumont Hospital, Dublin, Ireland.,Department of Pathology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Matthew D Griffin
- Nephrology Department, Galway University Hospitals, Saolta University Healthcare Group, Galway, Ireland.,Regenerative Medicine Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, National University of Ireland, Galway, Ireland
| | - Liam Casserly
- Department of Nephrology and Internal Medicine, University Hospital Limerick, Limerick, Ireland
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Friedhelm Hildebrandt
- Department of Paediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | - Katherine A Benson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | - Peter J Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland.,Department of Medicine, Dublin, Royal College of Surgeons in Ireland, Dublin, Ireland
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