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Payne NG, Boddu SP, Wymer KM, Heidenberg D, Van Der Walt C, Mi L, Keddis M, Stern K. The Use of Genetic Testing in Nephrolithiasis Evaluation: A Retrospective Review from a Multidisciplinary Kidney Stone Clinic. Urology 2024:S0090-4295(24)00595-8. [PMID: 39047952 DOI: 10.1016/j.urology.2024.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
OBJECTIVES To describe genetic and clinical characteristics for patients undergoing genetic testing at our multidisciplinary kidney stone clinic. METHODS A retrospective review was performed on patients evaluated in our stone clinic and referred to genetics between 2018 and 2022. Patient demographic, clinical, stone, and genetic data were included. We assessed the specific variants identified in our cohort, both those with a pathogenic association and variants of unknown significance (VUS). RESULTS Of 825 patients seen in our stone clinic from 2018-2022, 50 patients were referred to genetics. Among these patients, 33/50 (66%) underwent genetic testing and were included in the analysis. Of those who underwent genetic testing, a variant was identified in 19/33 (58%) patients, and 9/33 (27%) of these were a known pathogenic variant. Among patients with a pathogenic variant identified, the majority had a family history of stones (55.6%), calcium-based stones (77.8%), had their first stone prior to age 18 (66.7), were recurrent stone formers (100%), and had been managed medically (88.9%) or surgically (88.9%) prior to testing. When comparing patients with a pathogenic variant, VUS, and no variant, there were no significant differences in demographic or clinical parameters. CONCLUSION In our stone practice, more than half of patients who underwent genetic testing were found to have a variant. However, the majority of these variants were of unknown significance. Further evaluation regarding how genetic testing can impact nephrolithiasis management is needed.
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Affiliation(s)
| | | | | | | | | | - Lanyu Mi
- Mayo Clinic, Department of Quantitative Health Sciences
| | - Mira Keddis
- Mayo Clinic Arizona, Department of Nephrology
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Cellini B. A molecular journey on the pathogenesis of primary hyperoxaluria. Curr Opin Nephrol Hypertens 2024; 33:398-404. [PMID: 38602143 PMCID: PMC11139248 DOI: 10.1097/mnh.0000000000000987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
PURPOSE OF REVIEW Primary hyperoxalurias (PHs) are rare disorders caused by the deficit of liver enzymes involved in glyoxylate metabolism. Their main hallmark is the increased excretion of oxalate leading to the deposition of calcium oxalate stones in the urinary tract. This review describes the molecular aspects of PHs and their relevance for the clinical management of patients. RECENT FINDINGS Recently, the study of PHs pathogenesis has received great attention. The development of novel in vitro and in vivo models has allowed to elucidate how inherited mutations lead to enzyme deficit, as well as to confirm the pathogenicity of newly-identified mutations. In addition, a better knowledge of the metabolic consequences in disorders of liver glyoxylate detoxification has been crucial to identify the key players in liver oxalate production, thus leading to the identification and validation of new drug targets. SUMMARY The research on PHs at basic, translational and clinical level has improved our knowledge on the critical factors that modulate disease severity and the response to the available treatments, leading to the development of new drugs, either in preclinical stage or, very recently, approved for patient treatment.
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Affiliation(s)
- Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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Wu CHW, Badreddine J, Su E, Tay K, Lin HTC, Rhodes S, Schumacher F, Bodner D. Beyond the kidney: extra-renal manifestations of monogenic nephrolithiasis and their significance. Pediatr Nephrol 2024; 39:1429-1434. [PMID: 38057433 DOI: 10.1007/s00467-023-06242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND The objective of this study was to explore the frequency of occurrence of extra-renal manifestations associated with monogenic nephrolithiasis. METHODS A literature review was conducted to identify genes that are monogenic causes of nephrolithiasis. The Online Mendelian Inheritance in Man (OMIM) database was used to identify associated diseases and their properties. Disease phenotypes were ascertained using OMIM clinical synopses and sorted into 24 different phenotype categories as classified in OMIM. Disease phenotypes caused by the same gene were merged into a phenotypic profile of a gene (PPG) such that one PPG encompasses all related disease phenotypes for a specific gene. The total number of PPGs involving each phenotype category was measured, and the median phenotype category was determined. Phenotype categories were classified as overrepresented or underrepresented if the number of PPGs involving them was higher or lower than the median, respectively. Chi-square test was conducted to determine whether the number of PPGs affecting a given category significantly deviated from the median. RESULTS Fifty-five genes were identified as monogenic causes of nephrolithiasis. A total of six significantly overrepresented and three significantly underrepresented phenotype categories were identified (p < 0.05). Four phenotypic categories (growth, neurological, skeletal, and abdomen/gastrointestinal) are significantly overrepresented after Bonferroni correction for multiple comparisons (p < 0.002). Among all phenotypes, impaired growth is the most common manifestation. CONCLUSION Recognizing the extra-renal manifestations associated with monogenic causes of kidney stones is critical for earlier diagnosis and optimal care in patients.
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Affiliation(s)
- Chen-Han Wilfred Wu
- Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA.
| | - Jad Badreddine
- Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
| | - Ethan Su
- Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
| | - Kimberly Tay
- Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
| | - Hsin-Ti Cindy Lin
- Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
| | - Stephen Rhodes
- Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
| | - Fredrick Schumacher
- Department of Population and Quantitative Health Sciences, School of Medicine, Cleveland, OH, USA
| | - Donald Bodner
- Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, 11100 Euclid Ave., Cleveland, OH, 44106, USA
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Huang Y, Zhu W, Zhou J, Huang Q, Zeng G. Navigating the Evolving Landscape of Primary Hyperoxaluria: Traditional Management Defied by the Rise of Novel Molecular Drugs. Biomolecules 2024; 14:511. [PMID: 38785918 PMCID: PMC11117870 DOI: 10.3390/biom14050511] [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: 03/20/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
Primary hyperoxalurias (PHs) are inherited metabolic disorders marked by enzymatic cascade disruption, leading to excessive oxalate production that is subsequently excreted in the urine. Calcium oxalate deposition in the renal tubules and interstitium triggers renal injury, precipitating systemic oxalate build-up and subsequent secondary organ impairment. Recent explorations of novel therapeutic strategies have challenged and necessitated the reassessment of established management frameworks. The execution of diverse clinical trials across various medication classes has provided new insights and knowledge. With the evolution of PH treatments reaching a new milestone, prompt and accurate diagnosis is increasingly critical. Developing early, effective management and treatment plans is essential to improve the long-term quality of life for PH patients.
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Affiliation(s)
- Yueqi Huang
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China; (Y.H.); (J.Z.)
| | - Wei Zhu
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China;
| | - Jia Zhou
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China; (Y.H.); (J.Z.)
| | - Qiulin Huang
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China; (Y.H.); (J.Z.)
| | - Guohua Zeng
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China; (Y.H.); (J.Z.)
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China;
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Liu Y, Ge Y, Zhan R, Zhao Z, Li J, Wang W. Identification of mutations in 15 nephrolithiasis-related genes leading to a molecular diagnosis in 85 Chinese pediatric patients. Pediatr Nephrol 2023; 38:3645-3661. [PMID: 37306718 DOI: 10.1007/s00467-023-06028-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND The aim of this study was to describe the genotypic and phenotypic characteristics of Chinese pediatric patients with hereditary nephrolithiasis. METHODS Whole-exome sequencing (WES) was performed on 218 Chinese pediatric patients with kidney stones, and genetic and clinical data were collected and analyzed retrospectively. RESULTS The median age at onset in our cohort was 2.5 years (age range, 0.3-13 years). We detected 79 causative mutations in 15 genes, leading to a molecular diagnosis in 38.99% (85/218) of all cases. Monogenic mutations were present in 80 cases, and digenic mutations were present in 5 cases; 34.18% (27/79) of mutations were not included in the databases. Six common mutant genes, i.e., HOGA1, AGXT, GRHPR, SLC3A1, SLC7A9, and SLC4A1, were found in 84.71% of the patients overall. Furthermore, three mutations (A278A, c.834_834 + 1GG > TT, and C257G) in HOGA1, two mutations (K12QfX156 and S275RfX28) in AGXT, and one mutation (C289DfX22) in GRHPR represented hotspot mutations. The patients with HOGA1 mutations had the earliest onset age (0.8 years), followed by those with SLC7A9 (1.8 years), SLC4A1 (2.7 years), AGXT (4.3 years), SLC3A1 (4.8 years), and GRHPR (8 years) mutations (p = 0.002). Nephrocalcinosis was most commonly observed in patients with AGXT gene mutations. CONCLUSIONS Fifteen causative genes were detected in 85 Chinese pediatric patients with kidney stone diseases. The most common mutant genes, novel mutations, hotspot mutations, and genotype-phenotype correlations were also found. This study contributes to the understanding of genetic profiles and clinical courses in pediatric patients with hereditary nephrolithiasis. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Yukun Liu
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, 95 YongAn Road, Xicheng District, Beijing, 100050, China
| | - Yucheng Ge
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, 95 YongAn Road, Xicheng District, Beijing, 100050, China
| | - Ruichao Zhan
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, 95 YongAn Road, Xicheng District, Beijing, 100050, China
| | - Zhenqiang Zhao
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, 95 YongAn Road, Xicheng District, Beijing, 100050, China
| | - Jun Li
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, 95 YongAn Road, Xicheng District, Beijing, 100050, China
| | - Wenying Wang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, 95 YongAn Road, Xicheng District, Beijing, 100050, China.
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Alharbi SA, Alshenqiti AM, Asiri AH, Alqarni MA, Alqahtani SA. The Role of Genetic Testing in Pediatric Renal Diseases: Diagnostic, Prognostic, and Social Implications. Cureus 2023; 15:e44490. [PMID: 37664254 PMCID: PMC10471834 DOI: 10.7759/cureus.44490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 09/05/2023] Open
Abstract
Pediatric renal diseases vary widely and are linked to high morbidity and mortality; hence, early diagnosis is vital. Presently, genetic testing is being incorporated into the standard of care for children and their families with kidney disease, primarily as a diagnostic tool. In the present review, we aim to collect all potential evidence from relevant studies that reported the role of genetic testing in pediatric renal disease diagnostic, prognostic, and social implications. We have conducted both electronic and manual searches within PubMed, the Cochrane Library, Web of Science, and Scopus to find relevant studies. Studies from the years 2013-2023 were included. Case reports with limited sample sizes and no descriptive statistics, along with review papers and meta-analyses, were excluded from this review. Quality assessment for all included studies was performed. The pooled diagnostic yields were calculated using the common effect and random effect models utilizing the R program (R Foundation for Statistical Computing, Vienna, Austria). The pooled result for the diagnostic yield as per the common effect model is a pooled proportion of 0.42 (42%) 95% confidence interval (CI): [0.39,0.44], while with the random effects model the pooled proportion is 0.43 (43%) 95% CI: [0.31,0.57]. The diagnostic yield for the included studies ranged from 78.10% to 16.8%. The spectrum of kidney diseases included nephrolithiasis/nephrocalcinosis, glomerular diseases, cystic kidney disease, ciliopathies, tubulopathies, chronic kidney disease, and congenital anomalies of the kidneys and urinary tracts (CAKUT), while hematuria and proteinuria were reported by two studies and autosomal recessive and autosomal dominant idiopathic kidney disease was reported by only one study. Genetic testing validates clinical diagnosis and aids in tailoring management strategies; hence, a more precise treatment plan is developed and unnecessary investigations are avoided, which is crucial in the case of children during routine nephrology clinic visits. Genetic counselling is of the utmost importance, so all ethical and social concerns related to genetic testing are addressed in addition to patient satisfaction.
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Affiliation(s)
- Sultan A Alharbi
- Department of Pediatrics, Prince Mohammed Bin Abdulaziz Hospital, Madinah, SAU
| | | | - Ali H Asiri
- Department of Pediatrics, Khamis Mushait Maternity and Children Hospital, Khamis Mushait, SAU
| | - Musaed A Alqarni
- Department of Pediatrics, Khamis Mushait Maternity and Children Hospital, Khamis Mushait, SAU
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Vaisitti T, Bracciamà V, Faini AC, Brach Del Prever GM, Callegari M, Kalantari S, Mioli F, Romeo CM, Luca M, Camilla R, Mattozzi F, Gianoglio B, Peruzzi L, Amoroso A, Deaglio S. The role of genetic testing in the diagnostic workflow of pediatric patients with kidney diseases: the experience of a single institution. Hum Genomics 2023; 17:10. [PMID: 36782285 PMCID: PMC9926680 DOI: 10.1186/s40246-023-00456-w] [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: 11/07/2022] [Accepted: 02/03/2023] [Indexed: 02/15/2023] Open
Abstract
PURPOSE Inherited kidney diseases are among the leading causes of kidney failure in children, resulting in increased mortality, high healthcare costs and need for organ transplantation. Next-generation sequencing technologies can help in the diagnosis of rare monogenic conditions, allowing for optimized medical management and therapeutic choices. METHODS Clinical exome sequencing (CES) was performed on a cohort of 191 pediatric patients from a single institution, followed by Sanger sequencing to confirm identified variants and for family segregation studies. RESULTS All patients had a clinical diagnosis of kidney disease: the main disease categories were glomerular diseases (32.5%), ciliopathies (20.4%), CAKUT (17.8%), nephrolithiasis (11.5%) and tubular disease (10.5%). 7.3% of patients presented with other conditions. A conclusive genetic test, based on CES and Sanger validation, was obtained in 37.1% of patients. The highest detection rate was obtained for ciliopathies (74.4%), followed by nephrolithiasis (45.5%), tubular diseases (45%), while most glomerular diseases and CAKUT remained undiagnosed. CONCLUSIONS Results indicate that genetic testing consistently used in the diagnostic workflow of children with chronic kidney disease can (i) confirm clinical diagnosis, (ii) provide early diagnosis in the case of inherited conditions, (iii) find the genetic cause of previously unrecognized diseases and (iv) tailor transplantation programs.
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Affiliation(s)
- Tiziana Vaisitti
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Via Santena 19, 10126, Turin, Italy. .,Department of Medical Sciences, University of Turin, Via Nizza 52, 10126, Turin, Italy.
| | - Valeria Bracciamà
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy
| | - Angelo Corso Faini
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Via Santena 19, 10126, Turin, Italy.
| | - Giulia Margherita Brach Del Prever
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy
| | - Martina Callegari
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy
| | - Silvia Kalantari
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy
| | - Fiorenza Mioli
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy
| | - Carmelo Maria Romeo
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy
| | - Maria Luca
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy
| | - Roberta Camilla
- Pediatric Nephrology Dialysis and Transplantation, University Hospital “Città della Salute e della Scienza di Torino”, Turin, Italy
| | - Francesca Mattozzi
- Pediatric Nephrology Dialysis and Transplantation, University Hospital “Città della Salute e della Scienza di Torino”, Turin, Italy
| | - Bruno Gianoglio
- Pediatric Nephrology Dialysis and Transplantation, University Hospital “Città della Salute e della Scienza di Torino”, Turin, Italy
| | - Licia Peruzzi
- Pediatric Nephrology Dialysis and Transplantation, University Hospital “Città della Salute e della Scienza di Torino”, Turin, Italy
| | - Antonio Amoroso
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy ,grid.7605.40000 0001 2336 6580Department of Medical Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy
| | - Silvia Deaglio
- Immunogenetics and Transplant Biology Service, University Hospital “Città della Salute e della Scienza di Torino”, Via Santena 19, 10126 Turin, Italy ,grid.7605.40000 0001 2336 6580Department of Medical Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy
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