1
|
Dordoni C, Zeni L, Toso D, Mazza C, Mescia F, Cortinovis R, Econimo L, Savoldi G, Alberici F, Scolari F, Izzi C. Monoallelic pathogenic IFT140 variants are a common cause of autosomal dominant polycystic kidney disease-spectrum phenotype. Clin Kidney J 2024; 17:sfae026. [PMID: 38404363 PMCID: PMC10894029 DOI: 10.1093/ckj/sfae026] [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: 11/08/2023] [Indexed: 02/27/2024] Open
Abstract
Background Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder, characterized by development and enlargement of kidney cysts, eventually leading to end-stage kidney disease (ESKD). Pathogenic variants in the PKD1 and PKD2 genes are the major cause of ADPKD; additional rare variants in the GANAB, DNAJB11, ALG5 and ALG9 genes have been found in a minority of ADPKD patients. More recently, a significant number of ADPKD families have been linked to monoallelic variants in the IFT140 gene. Methods In this retrospective study, we tested the prevalence of the known causative genes of ADPKD-spectrum phenotype, including the PKD1, PKD2, GANAB, DNAJB11, ALG5, ALG and IFT140 genes, in a cohort of 129 ADPKD patients who consecutively underwent genetic testing in a single centre in Italy. Genetic testing utilized a combination of targeted next-generation sequencing, long-range polymerase chain reaction, Sanger sequencing and multiplex ligation-dependent probe amplification. Clinical evaluation was conducted through renal function testing and imaging features, including ultrasonography, computer tomography and magnetic resonance imaging. Results Of the 129 enrolled patients, 86 (66.7%) had pathogenic variants in PKD1 and 28 (21.7%) in PKD2, loss of function pathogenic variants in the IFT140 gene were found in 3 unrelated patients (2.3%), no pathogenic variants were found in other ADPKD genes and 12 patients (9.3%) remained genetically unresolved (ADPKD-GUR). Familial clinical and genetic screening of the index patients with ADPKD due to an IFT140 pathogenic variant (ADPKD-IFT140) allowed identification of eight additional affected relatives. In the 11 ADPKD-IFT140 patients, the renal phenotype was characterized by mild and late-onset PKD, with large renal cysts and limited kidney insufficiency. Extrarenal manifestations, including liver cysts, were rarely seen. Conclusion Our data suggest the monoallelic pathogenic IFT140 variants are the third most common cause of the ADPKD-spectrum phenotype in Italy, usually associated with a mild and atypical renal cystic disease.
Collapse
Affiliation(s)
- Chiara Dordoni
- Clinical Genetics Unit, Maternal-Infantile Department, ASST Spedali Civili, Brescia, Italy
| | - Letizia Zeni
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Diego Toso
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Cinzia Mazza
- Medical Genetics Laboratory, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Federica Mescia
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Roberta Cortinovis
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Laura Econimo
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Gianfranco Savoldi
- Medical Genetics Laboratory, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Federico Alberici
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Francesco Scolari
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Claudia Izzi
- Clinical Genetics Unit, Maternal-Infantile Department, ASST Spedali Civili, Brescia, Italy
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| |
Collapse
|
2
|
Ali H, Alahmad B, Senum SR, Warsame S, Bahbahani Y, Abu-Farha M, Abubaker J, Alqaddoumi M, Al-Mulla F, Harris PC. PKD1 Truncating Mutations Accelerate eGFR Decline in Autosomal Dominant Polycystic Kidney Disease Patients. Am J Nephrol 2024; 55:380-388. [PMID: 38194940 PMCID: PMC11151966 DOI: 10.1159/000536165] [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: 10/12/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
INTRODUCTION Autosomal dominant polycystic kidney disease (ADPKD) is a monogenic disease characterized by the accumulation of fluid-filled cysts in the kidneys, leading to renal volume enlargement and progressive kidney function impairment. Disease severity, though, may vary due to allelic and genetic heterogeneity. This study aimed to determine genotype-phenotype correlations between PKD1 truncating and non-truncating mutations and kidney function decline in ADPKD patients. METHODS We established a single-center retrospective cohort study in Kuwait where we followed every patient with a confirmed PKD1-ADPKD diagnosis clinically and genetically. Renal function tests were performed annually. We fitted generalized additive mixed effects models with random intercepts for each individual to analyze repeated measures of kidney function across mutation type. We then calculated survival time to kidney failure in a cox proportional hazards model. Models were adjusted for sex, age at visit, and birth year. RESULTS The study included 22 truncating and 20 non-truncating (42 total) patients followed for an average of 6.6 years (range: 1-12 years). Those with PKD1 truncating mutations had a more rapid rate of eGFR decline (-4.7 mL/min/1.73 m2 per year; 95% CI: -5.0, -4.4) compared to patients with PKD1 non-truncating mutations (-3.5 mL/min/1.73 m2 per year; 95% CI: -4.0, -3.1) (p for interaction <0.001). Kaplan-Meier survival analysis of time to kidney failure showed that patients with PKD1 truncating mutations had a shorter renal survival time (median 51 years) compared to those with non-truncating mutations (median 56 years) (P for log-rank = 0.008). CONCLUSION In longitudinal and survival analyses, patients with PKD1 truncating mutations showed a faster decline in kidney function compared to patients PKD1 non-truncating mutations. Early identification of patients with PKD1 truncating mutations can, at best, inform early clinical interventions or, at least, help suggest aggressive monitoring.
Collapse
Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Jabriya, Kuwait
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Barrak Alahmad
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sarah R. Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Samia Warsame
- Medical Division, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Yousif Bahbahani
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
- Medical Division, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Malak Alqaddoumi
- Department of Pathology, Faculty of Medicine, Health Sciences Center (HSC), Kuwait University, Jabriya, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
3
|
Ghasemi A, Sadr Z, Babanejad M, Rohani M, Alavi A. Copy Number Variations in Hereditary Spastic Paraplegia-Related Genes: Evaluation of an Iranian Hereditary Spastic Paraplegia Cohort and Literature Review. Mol Syndromol 2023; 14:477-484. [PMID: 38058755 PMCID: PMC10697729 DOI: 10.1159/000531507] [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: 05/11/2023] [Accepted: 06/07/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction In human genetic disorders, copy number variations (CNVs) are considered a considerable underlying cause. CNVs are generally detected by array-based methods but can also be discovered by read-depth analysis of whole-exome sequencing (WES) data. We performed WES-based CNV identification in a cohort of 35 Iranian families with hereditary spastic paraplegia (HSP) patients. Methods Thirty-five patients whose routine single-nucleotide variants (SNVs) and insertion/deletion analyses from exome data were unrevealing underwent a pipeline of CNV analysis using the read-depth detection method. Subsequently, a comprehensive search about the existence of CNVs in all 84 known HSP-causing genes was carried out in all reported HSP cases, so far. Results and Discussion CNV analysis of exome data indicated that 1 patient harbored a heterozygous deletion in exon 17 of the SPAST gene. Multiplex ligation-dependent probe amplification analysis confirmed this deletion in the proband and his affected father. Literature review demonstrated that, to date, pathogenic CNVs have been identified in 30 out of 84 HSP-causing genes (∼36%). However, CNVs in only 17 of these genes were specifically associated with the HSP phenotype. Among them, CNVs were more common in L1CAM, PLP1, SPAST, SPG7, SPG11, and REEP1 genes. The identification of the CNV in 1 of our patients suggests that WES allows the detection of both SNVs and CNVs from a single method without additional costs and execution time. However, because of intrinsic issues of WES in the detection of large rearrangements, it may not yet be exploited to replace the CNV detection methods in standard clinical practice.
Collapse
Affiliation(s)
- Aida Ghasemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zahra Sadr
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, Iran University of Medical Sciences, Hazrat Rasool Hospital, Tehran, Iran
| | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
4
|
Ali H, Naim M, Senum SR, AlSahow A, Bahbahani Y, Abu-Farha M, Abubaker J, Mohammad A, Al-Hunayan A, Asbeutah AM, Zayed M, Devarajan S, Hussain N, John SE, Channanath A, Thanaraj TA, Al-Ali M, AlMousawi M, Al-Mulla F, Harris PC. The genetic landscape of autosomal dominant polycystic kidney disease in Kuwait. Clin Kidney J 2023; 16:355-366. [PMID: 36755831 PMCID: PMC9900584 DOI: 10.1093/ckj/sfac236] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Indexed: 11/13/2022] Open
Abstract
Background Autosomal dominant polycystic kidney disease (ADPKD) is the most common renal monogenic disease, characterized by bilateral accumulation of renal fluid-filled cysts leading to progressive renal volume enlargement and gradual impairment of kidney function, often resulting in end-stage renal disease. Kuwait could provide valuable genetic insights about ADPKD, including intrafamilial phenotypic variation, given its large household size. This study aims to provide a comprehensive description of the pathogenic variants linked to ADPKD in the Kuwaiti population using multiple genetic analysis modalities and to describe and analyse the ADPKD phenotypic spectrum in terms of kidney function, kidney volume and renal survival. Methods A total of 126 ADPKD patients from 11 multiplex families and 25 singletons were recruited into the study. A combination of targeted next-generation sequencing (tNGS), long-range polymerase chain reaction, Sanger sequencing and multiplex ligation-dependent probe amplification were utilized for genetic diagnosis. Clinical evaluation was conducted through renal function testing and ultrasonographic kidney volume analysis. Results We identified 29 ADPKD pathogenic mutations from 36 families achieving an overall molecular genetic diagnostic rate of 112/126 (88.9%), including 29/36 (80.6%) in families. A total of 28/36 (77.8%) families had pathogenic mutations in PKD1, of which 17/28 (60.7%) were truncating, and 1/36 (2.8%) had a pathogenic variant in the IFT140 gene. A total of 20/29 (69%) of the identified ADPKD mutations were novel and described for the first time, including a TSC2-PKD1 contiguous syndrome. Clinical analysis indicated that genetically unresolved ADPKD cases had no apparent association between kidney volume and age. Conclusion We describe for the first time the genetic landscape of ADPKD in Kuwait. The observed genetic heterogeneity underlining ADPKD along with the wide phenotypic spectrum reveal the level of complexity in disease pathophysiology. ADPKD genetic testing could improve the care of patients through improved disease prognostication, guided treatment and genetic counselling. However, to fulfil the potential of genetic testing, it is important to overcome the hurdle of genetically unresolved ADPKD cases.
Collapse
Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Medhat Naim
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Ali AlSahow
- Division of Nephrology, Al-Jahra Hospital, Ministry of Health, Al-Jahra, Kuwait
| | - Yousif Bahbahani
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
- Medical Division, Dasman Diabetes Institute, Dasman, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Adel Al-Hunayan
- Department of Surgery, Faculty of Medicine, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Akram M Asbeutah
- Department of Radiological Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Mohamed Zayed
- Department of Radiology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Sriraman Devarajan
- National Dasman Diabetes Biobank, Dasman Diabetes Institute, Dasman, Kuwait
| | - Naser Hussain
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | | | - Mohammad Al-Ali
- Next Generation Sequencing Laboratory, Kuwait Medical Genetics Center, Ministry of Health, Sulaibikhat, Kuwait
| | - Mustafa AlMousawi
- Department of Transplantation, Hamed Al Essa Organ Transplant Centre, Ministry of Health, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
5
|
Li S, Lin J, Li C, Chen Y, Cao B, Yang T, Wei Q, Zhao B, Chen X, Shang H. Clinical and genetic study of a Chinese family affected by both amyotrophic lateral sclerosis and autosomal dominant polycystic kidney disease. Front Neurol 2022; 13:1004909. [PMID: 36341123 PMCID: PMC9630937 DOI: 10.3389/fneur.2022.1004909] [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: 07/27/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterized by loss of the upper and lower motor neurons from the motor cortex, brainstem, and spinal cord. Most ALS cases are sporadic, with 5–10% having a positive family history. Autosomal dominant polycystic kidney disease (ADPKD) is a heritable renal disease that eventually results in end-stage kidney disease. PKD1 is the most prevalent causative gene for ADPKD, accounting for ~85% of cases. Both diseases are currently considered untreatable. In this study, we report a large family that includes 10 patients with ALS phenotype, 3 asymptomatic SOD1-H47R carriers, and 6 with the ADPKD phenotype. Using whole exome sequencing, we found a novel likely pathogenic variant (p.R2787P) in PKD1 among patients with ADPKD, and a pathogenic variant (p.H47R) in SOD1 among patients with ALS. This study highlights the possibility that two different autosomal dominantly inherited diseases can co-exist independently within the same family. Phenotype—genotype correlations among these patients are also described. This research contributes novel phenotype and genotype characteristics of ALS with SOD1 mutations and ADPKD with PKD1 mutations.
Collapse
Affiliation(s)
- Shirong Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yongping Chen
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Bei Cao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Tianmi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Bi Zhao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xueping Chen
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Huifang Shang
| |
Collapse
|
6
|
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.
Collapse
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
| | | |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Senum SR, Li Y(SM, Benson KA, Joli G, Olinger E, Lavu S, Madsen CD, Gregory AV, Neatu R, Kline TL, Audrézet MP, Outeda P, Nau CB, Meijer E, Ali H, Steinman TI, Mrug M, Phelan PJ, Watnick TJ, Peters DJ, Ong AC, Conlon PJ, Perrone RD, Cornec-Le Gall E, Hogan MC, Torres VE, Sayer JA, Harris PC, Harris PC. Monoallelic IFT140 pathogenic variants are an important cause of the autosomal dominant polycystic kidney-spectrum phenotype. Am J Hum Genet 2022; 109:136-156. [PMID: 34890546 DOI: 10.1016/j.ajhg.2021.11.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/15/2021] [Indexed: 12/18/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), characterized by progressive cyst formation/expansion, results in enlarged kidneys and often end stage kidney disease. ADPKD is genetically heterogeneous; PKD1 and PKD2 are the common loci (∼78% and ∼15% of families) and GANAB, DNAJB11, and ALG9 are minor genes. PKD is a ciliary-associated disease, a ciliopathy, and many syndromic ciliopathies have a PKD phenotype. In a multi-cohort/-site collaboration, we screened ADPKD-diagnosed families that were naive to genetic testing (n = 834) or for whom no PKD1 and PKD2 pathogenic variants had been identified (n = 381) with a PKD targeted next-generation sequencing panel (tNGS; n = 1,186) or whole-exome sequencing (WES; n = 29). We identified monoallelic IFT140 loss-of-function (LoF) variants in 12 multiplex families and 26 singletons (1.9% of naive families). IFT140 is a core component of the intraflagellar transport-complex A, responsible for retrograde ciliary trafficking and ciliary entry of membrane proteins; bi-allelic IFT140 variants cause the syndromic ciliopathy, short-rib thoracic dysplasia (SRTD9). The distinctive monoallelic phenotype is mild PKD with large cysts, limited kidney insufficiency, and few liver cysts. Analyses of the cystic kidney disease probands of Genomics England 100K showed that 2.1% had IFT140 LoF variants. Analysis of the UK Biobank cystic kidney disease group showed probands with IFT140 LoF variants as the third most common group, after PKD1 and PKD2. The proximity of IFT140 to PKD1 (∼0.5 Mb) in 16p13.3 can cause diagnostic confusion, and PKD1 variants could modify the IFT140 phenotype. Importantly, our studies link a ciliary structural protein to the ADPKD spectrum.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA.
| |
Collapse
|
9
|
Perrone RD, Abebe KZ, Watnick TJ, Althouse AD, Hallows KR, Lalama CM, Miskulin DC, Seliger SL, Tao C, Harris PC, Bae KT. Primary results of the randomized trial of metformin administration in polycystic kidney disease (TAME PKD). Kidney Int 2021; 100:684-696. [PMID: 34186056 DOI: 10.1016/j.kint.2021.06.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/26/2021] [Accepted: 06/05/2021] [Indexed: 12/16/2022]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is characterized by growth of kidney cysts and glomerular filtration rate (GFR) decline. Metformin was found to impact cystogenesis in preclinical models of polycystic disease, is generally considered safe and may be a promising candidate for clinical investigation in ADPKD. In this phase 2 two-year trial, we randomly assigned 97 patients, 18-60 years of age, with ADPKD and estimated GFR over 50 ml/min/1.73 m2, in a 1:1 ratio to receive metformin or placebo twice daily. Primary outcomes were medication safety and tolerability. Secondary outcomes included estimated GFR decline, and total kidney volume growth. Thirty-eight metformin and 39 placebo participants still received study product at 24-months. Twenty-one participants in the metformin arm reduced drug dose due to inability to tolerate, compared with 14 in the placebo arm (not significant). Proportions of participants experiencing serious adverse events was similar between the groups. The Gastrointestinal Symptoms Rating Scale score was low at baseline and did not significantly change over time. The annual change for estimated GFR was -1.71 with metformin and -3.07 ml/min/1.73m2 per year with placebo (mean difference 1.37 {-0.70, 3.44} ml/min/1.73m2), while mean annual percent change in height-adjusted total kidney volume was 3.87% in metformin and 2.16% per year in placebo, (mean difference 1.68% {-2.11, 5.62}). Thus, metformin in adults with ADPKD was found to be safe and tolerable while slightly reducing estimated GFR decline but not to a significant degree. Hence, evaluation of efficacy requires a larger trial, with sufficient power to detect differences in endpoints.
Collapse
Affiliation(s)
- Ronald D Perrone
- Division of Nephrology, Department of Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA.
| | - Kaleab Z Abebe
- Division of General Internal Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Terry J Watnick
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrew D Althouse
- Division of General Internal Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kenneth R Hallows
- USC/UKRO Kidney Research Center and Division of Nephrology and Hypertension, Department of Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - Christina M Lalama
- Division of General Internal Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dana C Miskulin
- Division of Nephrology, Department of Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Stephen L Seliger
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cheng Tao
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Kyongtae Ty Bae
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|