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Chen EWC, Chong J, Valluru MK, Durkie M, Simms RJ, Harris PC, Ong ACM. Combining genotype with height-adjusted kidney length predicts rapid progression of ADPKD. Nephrol Dial Transplant 2024; 39:956-966. [PMID: 38224954 DOI: 10.1093/ndt/gfad270] [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: 06/29/2023] [Indexed: 01/17/2024] Open
Abstract
INTRODUCTION Our main objective was to identify baseline prognostic factors predictive of rapid disease progression in a large unselected clinical autosomal dominant polycystic kidney disease (ADPKD) cohort. METHODS A cross-sectional analysis was performed in 618 consecutive ADPKD patients assessed and followed-up for over a decade. A total of 123 patients (19.9%) had reached kidney failure by the study date. Data were available for the following: baseline eGFR (n = 501), genotype (n = 549), baseline ultrasound mean kidney length (MKL, n = 424) and height-adjusted baseline MKL (HtMKL, n = 377). Rapid disease progression was defined as an annualized eGFR decline (∆eGFR) of >2.5 mL/min/year by linear regression over 5 years (n = 158). Patients were further divided into slow, rapid and very rapid ∆eGFR classes for analysis. Genotyped patients were classified into several categories: PKD1 (T, truncating; or NT, non-truncating), PKD2, other genes (non-PKD1 or -PKD2), no mutation detected or variants of uncertain significance. RESULTS A PKD1-T genotype had the strongest influence on the probability of reduced baseline kidney function by age. A multivariate logistic regression model identified PKD1-T genotype and HtMKL (>9.5 cm/m) as independent predictors for rapid disease progression. The combination of both factors increased the positive predictive value for rapid disease progression over age 40 years and of reaching kidney failure by age 60 years to 100%. Exploratory analysis in a subgroup with available total kidney volumes showed higher positive predictive value (100% vs 80%) and negative predictive value (42% vs 33%) in predicting rapid disease progression compared with the Mayo Imaging Classification (1C-E). CONCLUSION Real-world longitudinal data confirm the importance of genotype and kidney length as independent variables determining ∆eGFR. Individuals with the highest risk of rapid disease progression can be positively selected for treatment based on this combination.
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Affiliation(s)
- Eugene W C Chen
- Academic Nephrology Unit, Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Beech Hill Road, Sheffield, UK
- Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Herries Road, Sheffield, UK
| | - Jiehan Chong
- Academic Nephrology Unit, Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Beech Hill Road, Sheffield, UK
- Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Herries Road, Sheffield, UK
| | - Manoj K Valluru
- Academic Nephrology Unit, Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Beech Hill Road, Sheffield, UK
| | - Miranda Durkie
- Sheffield Diagnostics Genetic Service, North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Roslyn J Simms
- Academic Nephrology Unit, Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Beech Hill Road, Sheffield, UK
- Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Herries Road, Sheffield, UK
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic and Foundation, Rochester, MN, USA
| | - Albert C M Ong
- Academic Nephrology Unit, Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Beech Hill Road, Sheffield, UK
- Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Herries Road, Sheffield, UK
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Yeung KC, Fryml E, Lanktree MB. How Does ADPKD Severity Differ Between Family Members? Kidney Int Rep 2024; 9:1198-1209. [PMID: 38707833 PMCID: PMC11068977 DOI: 10.1016/j.ekir.2024.01.053] [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: 09/26/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/07/2024] Open
Abstract
Thousands of pathogenic variants in more than 100 genes can cause kidney cysts with substantial variability in phenotype and risk of subsequent kidney failure. Despite an established genotype-phenotype correlation in cystic kidney diseases, incomplete penetrance and variable disease expressivity are present as is the case in all monogenic diseases. In family members with autosomal dominant polycystic kidney disease (ADPKD), the same causal variant is responsible in all affected family members; however, there can still be striking discordance in phenotype severity. This narrative review explores contributors to within-family discordance in ADPKD severity. Cases of biallelic and digenic inheritance, where 2 rare pathogenic variants in cystogenic genes are coexistent in one family, account for a small proportion of within-family discordance. Genetic background, including cis and trans factors and the polygenic propensity for comorbid disease, also plays a role but has not yet been exhaustively quantified. Environmental exposures, including diet; smoking; alcohol, salt, and protein intake, and comorbid diseases, including obesity, diabetes, hypertension, kidney stones, dyslipidemia, and additional coexistent kidney diseases all contribute to ADPKD phenotypic variability among family members. Given that many of the factors contributing to phenotype variability are preventable, modifiable, or treatable, health care providers and patients need to be aware of these factors and address them in the treatment of ADPKD.
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Affiliation(s)
- Klement C. Yeung
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Elise Fryml
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew B. Lanktree
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Division of Nephrology, St. Joseph’s Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Health Research Methodology, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
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Mahboobipour AA, Ala M, Safdari Lord J, Yaghoobi A. Clinical manifestation, epidemiology, genetic basis, potential molecular targets, and current treatment of polycystic liver disease. Orphanet J Rare Dis 2024; 19:175. [PMID: 38671465 PMCID: PMC11055360 DOI: 10.1186/s13023-024-03187-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Polycystic liver disease (PLD) is a rare condition observed in three genetic diseases, including autosomal dominant polycystic liver disease (ADPLD), autosomal dominant polycystic kidney disease (ADPKD), and autosomal recessive polycystic kidney disease (ARPKD). PLD usually does not impair liver function, and advanced PLD becomes symptomatic when the enlarged liver compresses adjacent organs or increases intra-abdominal pressure. Currently, the diagnosis of PLD is mainly based on imaging, and genetic testing is not required except for complex cases. Besides, genetic testing may help predict patients' prognosis, classify patients for genetic intervention, and conduct early treatment. Although the underlying genetic causes and mechanisms are not fully understood, previous studies refer to primary ciliopathy or impaired ciliogenesis as the main culprit. Primarily, PLD occurs due to defective ciliogenesis and ineffective endoplasmic reticulum quality control. Specifically, loss of function mutations of genes that are directly involved in ciliogenesis, such as Pkd1, Pkd2, Pkhd1, and Dzip1l, can lead to both hepatic and renal cystogenesis in ADPKD and ARPKD. In addition, loss of function mutations of genes that are involved in endoplasmic reticulum quality control and protein folding, trafficking, and maturation, such as PRKCSH, Sec63, ALG8, ALG9, GANAB, and SEC61B, can impair the production and function of polycystin1 (PC1) and polycystin 2 (PC2) or facilitate their degradation and indirectly promote isolated hepatic cystogenesis or concurrent hepatic and renal cystogenesis. Recently, it was shown that mutations of LRP5, which impairs canonical Wnt signaling, can lead to hepatic cystogenesis. PLD is currently treated by somatostatin analogs, percutaneous intervention, surgical fenestration, resection, and liver transplantation. In addition, based on the underlying molecular mechanisms and signaling pathways, several investigational treatments have been used in preclinical studies, some of which have shown promising results. This review discusses the clinical manifestation, complications, prevalence, genetic basis, and treatment of PLD and explains the investigational methods of treatment and future research direction, which can be beneficial for researchers and clinicians interested in PLD.
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Affiliation(s)
- Amir Ali Mahboobipour
- Tracheal Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Moein Ala
- Experimental Medicine Research Center, School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
| | - Javad Safdari Lord
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Yaghoobi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
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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: 4] [Impact Index Per Article: 4.0] [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.
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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
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Aklilu AM, Gulati A, Kolber KJ, Yang H, Harris PC, Dahl NK. The VUS Challenge in Cystic Kidney Disease: A Case-Based Review. KIDNEY360 2024; 5:152-159. [PMID: 37962562 PMCID: PMC10833605 DOI: 10.34067/kid.0000000000000298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
Genetic testing in nephrology is becoming increasingly important to diagnose patients and to provide appropriate care. This is especially true for autosomal dominant polycystic kidney disease (ADPKD) because this is a common cause of kidney failure and genetically complex. In addition to the major genes, PKD1 and PKD2 , there are at least six minor loci, and phenotypic, and in some cases, genetic overlap with other cystic disorders. Targeted next-generation sequencing, a low-cost, high-throughput technique, has made routine genetic testing viable in nephrology clinics. Appropriate pre- and post-testing genetic counseling is essential to the testing process. Carefully assessing variants is also critical, with the genetic report classifying variants in accordance with American College of Medical Genetics and Genomics guidelines. However, variant of uncertain significance (VUSs) may pose a significant challenge for the ordering clinician. In ADPKD, and particularly within PKD1 , there is high allelic heterogeneity; no single variant is present in more than 2% of families. The Mayo/Polycystic Kidney Disease Foundation variant database, a research tool, is the best current database of PKD1 and PKD2 variants containing over 2300 variants identified in individuals with polycystic kidney disease, but novel variants are often identified. In patients with a high pretest probability of ADPKD on the basis of clinical criteria, but no finding of a pathogenic (P) or likely pathogenic (LP) variant in a cystic kidney gene, additional evaluation of cystic gene VUS can be helpful. In this case-based review, we propose an algorithm for the assessment of such variants in a clinical setting and show how some can be reassigned to a diagnostic grouping. When assessing the relevance of a VUS, we consider both patient/family-specific and allele-related factors using population and variant databases and available prediction tools, as well as genetic expertise. This analysis plus further family studies can aid in making a genetic diagnosis.
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Affiliation(s)
- Abinet M. Aklilu
- Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | | | - Kayla J. Kolber
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Hana Yang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Neera K. Dahl
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
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Lanktree MB, Kline T, Pei Y. Assessing the Risk of Progression to Kidney Failure in Patients With Autosomal Dominant Polycystic Kidney Disease. ADVANCES IN KIDNEY DISEASE AND HEALTH 2023; 30:407-416. [PMID: 38097331 DOI: 10.1053/j.akdh.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 12/18/2023]
Abstract
While autosomal dominant polycystic kidney disease (ADPKD) is a dichotomous diagnosis, substantial variability in disease severity exists. Identification of inherited risk through family history, genetic testing, and environmental risk factors through clinical assessment are important components of risk assessment for optimal management of patients with ADPKD. Genetic testing is especially helpful in cases with diagnostic uncertainty, particularly in cases with no apparent family history, in young cases (age less than 25 years) where a definitive diagnosis is sought, or in atypical presentations with early, severe, or discordant findings. Currently, risk assessment in ADPKD may be performed with the use of age-adjusted estimated glomerular filtration rate thresholds, evidence of rapid estimated glomerular filtration rate decline on serial measurements, age- and height-adjusted total kidney volume by Mayo Clinic Imaging Classification, or evidence of early hypertension and urological complications combined with PKD1 or PKD2 mutation class; however, caveats exist with each of these approaches. Fine-tuning of risk stratification with advanced imaging features and biomarkers is the subject of research but is not yet ready for general clinical practice. While conservative treatment strategies will be advised for all patients, those with the greatest rate of disease progression will have the most benefit from aggressive disease-modifying therapy. In this narrative review, we will summarize the evidence behind the clinical assessment and risk stratification of patients with ADPKD.
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Affiliation(s)
- Matthew B Lanktree
- Division of Nephrology, Department of Medicine, St Joseph's Healthcare Hamilton, McMaster University, Hamilton, Ontario, Canada; Population Health Research Institute, Hamilton, Ontario, Canada
| | - Timothy Kline
- Mayo Clinic, Department of Radiology and Division of Nephrology and Hypertension, Rochester, MN
| | - York Pei
- Division of Nephrology, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada.
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7
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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: 8] [Impact Index Per Article: 8.0] [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.
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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
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Which patients with CKD will benefit from genomic sequencing? Synthesizing progress to illuminate the future. Curr Opin Nephrol Hypertens 2022; 31:541-547. [PMID: 36093902 PMCID: PMC9594128 DOI: 10.1097/mnh.0000000000000836] [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] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW This review will summarize and synthesize recent findings in regard to monogenic kidney disorders, including how that evidence is being translated into practice. It will add to existing key knowledge to provide context for clinicians in consolidating existing practice and approaches. RECENT FINDINGS Whilst there are long established factors, which indicate increased likelihood of identifying a monogenic cause for kidney disease, these can now be framed in terms of the identification of new genes, new indications for genomic testing and new evidence for clinical utility of genomic testing in nephrology. Further, inherent in the use of genomics in nephrology are key concepts including robust informed consent, variant interpretation and return of results. Recent findings of variants in genes related to complex or broader kidney phenotypes are emerging in addition to understanding of de novo variants. Phenocopy phenomena are indicating a more pragmatic use of broader gene panels whilst evidence is emerging of a role in unexplained kidney disease. Clinical utility is evolving but is being successfully demonstrated across multiple domains of outcome and practice. SUMMARY We provide an updated framework of evidence to guide application of genomic testing in chronic kidney disease (CKD), building upon existing principles and knowledge to indicate how the practice and implementation of this can be applied today. There are clearly established roles for genomic testing for some patients with CKD, largely those with suspected heritable forms, with these continuing to expand as new evidence emerges.
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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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10
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Lakhia R, Ramalingam H, Chang CM, Cobo-Stark P, Biggers L, Flaten A, Alvarez J, Valencia T, Wallace DP, Lee EC, Patel V. PKD1 and PKD2 mRNA cis-inhibition drives polycystic kidney disease progression. Nat Commun 2022; 13:4765. [PMID: 35965273 PMCID: PMC9376183 DOI: 10.1038/s41467-022-32543-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/04/2022] [Indexed: 12/22/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), among the most common human genetic conditions and a frequent etiology of kidney failure, is primarily caused by heterozygous PKD1 mutations. Kidney cyst formation occurs when PKD1 dosage falls below a critical threshold. However, no framework exists to harness the remaining allele or reverse PKD1 decline. Here, we show that mRNAs produced by the noninactivated PKD1 allele are repressed via their 3'-UTR miR-17 binding element. Eliminating this motif (Pkd1∆17) improves mRNA stability, raises Polycystin-1 levels, and alleviates cyst growth in cellular, ex vivo, and mouse PKD models. Remarkably, Pkd2 is also inhibited via its 3'-UTR miR-17 motif, and Pkd2∆17-induced Polycystin-2 derepression retards cyst growth in Pkd1-mutant models. Moreover, acutely blocking Pkd1/2 cis-inhibition, including after cyst onset, attenuates murine PKD. Finally, modeling PKD1∆17 or PKD2∆17 alleles in patient-derived primary ADPKD cultures leads to smaller cysts, reduced proliferation, lower pCreb1 expression, and improved mitochondrial membrane potential. Thus, evading 3'-UTR cis-interference and enhancing PKD1/2 mRNA translation is a potentially mutation-agnostic ADPKD-arresting approach.
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Affiliation(s)
- Ronak Lakhia
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Harini Ramalingam
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chun-Mien Chang
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Patricia Cobo-Stark
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Laurence Biggers
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Andrea Flaten
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jesus Alvarez
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Darren P Wallace
- Department of Internal Medicine and the Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, USA
| | - Edmund C Lee
- Regulus Therapeutics Inc., San Diego, CA, 92121, USA
| | - Vishal Patel
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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Wang JY, Wang J, Lu XG, Song W, Luo S, Zou DF, Hua LD, Peng Q, Tian Y, Gao LD, Liao WP, He N. Recessive PKD1 Mutations Are Associated With Febrile Seizures and Epilepsy With Antecedent Febrile Seizures and the Genotype-Phenotype Correlation. Front Mol Neurosci 2022; 15:861159. [PMID: 35620448 PMCID: PMC9128595 DOI: 10.3389/fnmol.2022.861159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveThe PKD1 encodes polycystin-1, a large transmembrane protein that plays important roles in cell proliferation, apoptosis, and cation transport. Previous studies have identified PKD1 mutations in autosomal dominant polycystic kidney disease (ADPKD). However, the expression of PKD1 in the brain is much higher than that in the kidney. This study aimed to explore the association between PKD1 and epilepsy.MethodsTrios-based whole-exome sequencing was performed in a cohort of 314 patients with febrile seizures or epilepsy with antecedent febrile seizures. The damaging effects of variants was predicted by protein modeling and multiple in silico tools. The genotype-phenotype association of PKD1 mutations was systematically reviewed and analyzed.ResultsEight pairs of compound heterozygous missense variants in PKD1 were identified in eight unrelated patients. All patients suffered from febrile seizures or epilepsy with antecedent febrile seizures with favorable prognosis. All of the 16 heterozygous variants presented no or low allele frequencies in the gnomAD database, and presented statistically higher frequency in the case-cohort than that in controls. These missense variants were predicted to be damaging and/or affect hydrogen bonding or free energy stability of amino acids. Five patients showed generalized tonic-clonic seizures (GTCS), who all had one of the paired missense mutations located in the PKD repeat domain, suggesting that mutations in the PKD domains were possibly associated with GTCS. Further analysis demonstrated that monoallelic mutations with haploinsufficiency of PKD1 potentially caused kidney disease, compound heterozygotes with superimposed effects of two missense mutations were associated with epilepsy, whereas the homozygotes with complete loss of PKD1 would be embryonically lethal.ConclusionPKD1 gene was potentially a novel causative gene of epilepsy. The genotype-phenotype relationship of PKD1 mutations suggested a quantitative correlation between genetic impairment and phenotypic variation, which will facilitate the genetic diagnosis and management in patients with PKD1 mutations.
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Affiliation(s)
- Jing-Yang Wang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Xin-Guo Lu
- Epilepsy Center, Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Wang Song
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Dong-Fang Zou
- Epilepsy Center, Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Li-Dong Hua
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Qian Peng
- Department of Pediatrics, Dongguan City Maternal and Child Health Hospital, Southern Medical University, Dongguan, China
| | - Yang Tian
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liang-Di Gao
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
- *Correspondence: Na He,
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12
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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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13
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de Fallois J, Schönauer R, Münch J, Nagel M, Popp B, Halbritter J. Challenging Disease Ontology by Instances of Atypical PKHD1 and PKD1 Genetics. Front Genet 2021; 12:682565. [PMID: 34249099 PMCID: PMC8267867 DOI: 10.3389/fgene.2021.682565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/05/2021] [Indexed: 12/03/2022] Open
Abstract
Background Autosomal polycystic kidney disease is distinguished into dominant (ADPKD) and recessive (ARPKD) inheritance usually caused by either monoallelic (PKD1/PKD2) or biallelic (PKHD1) germline variation. Clinical presentations are genotype-dependent ranging from fetal demise to mild chronic kidney disease (CKD) in adults. Additionally, exemptions from dominant and recessive inheritance have been reported in both disorders resulting in respective phenocopies. Here, we comparatively report three young adults with microcystic-hyperechogenic kidney morphology based on unexpected genetic alterations beyond typical inheritance. Methods Next-generation sequencing (NGS)-based gene panel analysis and multiplex ligation-dependent probe amplification (MLPA) of PKD-associated genes, familial segregation analysis, and reverse phenotyping. Results Three unrelated individuals presented in late adolescence for differential diagnosis of incidental microcystic-hyperechogenic kidneys with preserved kidney and liver function. Upon genetic analysis, we identified a homozygous hypomorphic PKHD1 missense variant causing pseudodominant inheritance in a family, a large monoallelic PKDH1-deletion with atypical transmission, and biallelic PKD1 missense hypomorphs with recessive inheritance. Conclusion By this report, we illustrate clinical presentations associated with atypical PKD-gene alterations beyond traditional modes of inheritance. Large monoallelic PKHD1-alterations as well as biallelic hypomorphs of both PKD1 and PKHD1 may lead to mild CKD in the absence of prominent macrocyst formation and functional liver impairment. The long-term renal prognosis throughout life, however, remains undetermined. Increased detection of atypical inheritance challenges our current thinking of disease ontology not only in PKD but also in Mendelian disorders in general.
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Affiliation(s)
- Jonathan de Fallois
- Department of Endocrinology, Nephrology and Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Ria Schönauer
- Department of Endocrinology, Nephrology and Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Johannes Münch
- Department of Endocrinology, Nephrology and Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Mato Nagel
- Center for Nephrology and Metabolic Disorders, Weißwasser, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan Halbritter
- Department of Endocrinology, Nephrology and Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
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14
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Magistroni R, Biagini G. Response letter to the Editorial: "Ketogenic diet in ADPKD patients". PHARMANUTRITION 2021. [DOI: 10.1016/j.phanu.2021.100268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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