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Sim JJ, Shu YH, Bhandari SK, Chen Q, Harrison TN, Lee MY, Munis MA, Morrissette K, Sundar S, Pareja K, Nourbakhsh A, Willey CJ. Data driven approach to characterize rapid decline in autosomal dominant polycystic kidney disease. PLoS One 2024; 19:e0298484. [PMID: 38837988 DOI: 10.1371/journal.pone.0298484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a genetic kidney disease with high phenotypic variability. Furthering insights into patients' ADPKD progression could lead to earlier detection, management, and alter the course to end stage kidney disease (ESKD). We sought to identify patients with rapid decline (RD) in kidney function and to determine clinical factors associated with RD using a data-driven approach. A retrospective cohort study was performed among patients with incident ADPKD (1/1/2002-12/31/2018). Latent class mixed models were used to identify RD patients using differences in eGFR trajectories over time. Predictors of RD were selected based on agreements among feature selection methods, including logistic, regularized, and random forest modeling. The final model was built on the selected predictors and clinically relevant covariates. Among 1,744 patients with incident ADPKD, 125 (7%) were identified as RD. Feature selection included 42 clinical measurements for adaptation with multiple imputations; mean (SD) eGFR was 85.2 (47.3) and 72.9 (34.4) in the RD and non-RD groups, respectively. Multiple imputed datasets identified variables as important features to distinguish RD and non-RD groups with the final prediction model determined as a balance between area under the curve (AUC) and clinical relevance which included 6 predictors: age, sex, hypertension, cerebrovascular disease, hemoglobin, and proteinuria. Results showed 72%-sensitivity, 70%-specificity, 70%-accuracy, and 0.77-AUC in identifying RD. 5-year ESKD rates were 38% and 7% among RD and non-RD groups, respectively. Using real-world routine clinical data among patients with incident ADPKD, we observed that six variables highly predicted RD in kidney function.
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Affiliation(s)
- John J Sim
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
- Division of Nephrology and Hypertension, Kaiser Permanente Los Angeles Medical Center, Los Angeles, CA, United States of America
- Departments of Health Systems and Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, United States of America
| | - Yu-Hsiang Shu
- Biostatistics and Programming Clinical Affairs, Inari Medical, Irvine, CA, United States of America
| | - Simran K Bhandari
- Department of Internal Medicine, Bellflower Medical Center, Bellflower, CA, United States of America
| | - Qiaoling Chen
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Teresa N Harrison
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Min Young Lee
- Division of Nephrology and Hypertension, Kaiser Permanente Los Angeles Medical Center, Los Angeles, CA, United States of America
| | - Mercedes A Munis
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Kerresa Morrissette
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Shirin Sundar
- Otsuka Pharmaceutical Development & Commercialization, Inc., Princeton, NJ, United States of America
| | - Kristin Pareja
- Otsuka Pharmaceutical Development & Commercialization, Inc., Princeton, NJ, United States of America
| | - Ali Nourbakhsh
- Otsuka Pharmaceutical Development & Commercialization, Inc., Princeton, NJ, United States of America
| | - Cynthia J Willey
- College of Pharmacy, University of Rhode Island, Kingston, RI, United States of America
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2
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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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3
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Vishy CE, Thomas C, Vincent T, Crawford DK, Goddeeris MM, Freedman BS. Genetics of cystogenesis in base-edited human organoids reveal therapeutic strategies for polycystic kidney disease. Cell Stem Cell 2024; 31:537-553.e5. [PMID: 38579684 DOI: 10.1016/j.stem.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/19/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
In polycystic kidney disease (PKD), microscopic tubules expand into macroscopic cysts. Among the world's most common genetic disorders, PKD is inherited via heterozygous loss-of-function mutations but is theorized to require additional loss of function. To test this, we establish human pluripotent stem cells in allelic series representing four common nonsense mutations, using CRISPR base editing. When differentiated into kidney organoids, homozygous mutants spontaneously form cysts, whereas heterozygous mutants (original or base corrected) express no phenotype. Using these, we identify eukaryotic ribosomal selective glycosides (ERSGs) as PKD therapeutics enabling ribosomal readthrough of these same nonsense mutations. Two different ERSGs not only prevent cyst initiation but also limit growth of pre-formed cysts by partially restoring polycystin expression. Furthermore, glycosides accumulate in cyst epithelia in organoids and mice. Our findings define the human polycystin threshold as a surmountable drug target for pharmacological or gene therapy interventions, with relevance for understanding disease mechanisms and future clinical trials.
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Affiliation(s)
- Courtney E Vishy
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Chardai Thomas
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Thomas Vincent
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Daniel K Crawford
- Eloxx Pharmaceuticals, Inc., 950 Winter Street, Waltham, MA 02451, USA
| | | | - Benjamin S Freedman
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA; Plurexa, 1209 6th Ave. N., Seattle, WA 98109, USA.
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4
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Gallini JW, Jasien CL, Mrug M, Cui X. US Veterans Administration Autosomal Dominant Polycystic Kidney Disease Cohort: Demographic, Comorbidity, and Key Laboratory Data Characteristics. KIDNEY360 2024; 5:529-537. [PMID: 38424672 PMCID: PMC11093548 DOI: 10.34067/kid.0000000000000405] [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: 11/10/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Key Points We built a cohort of 12,217 patients diagnosed with autosomal dominant polycystic kidney disease from 1999 to 2020 in the national Veteran Affairs electronic medical record system. We characterized the cohort on demographics, comorbidities, and key laboratory measurements. Background We used the largest integrated US healthcare system, the Veterans Health Administration, to establish a robust resource for demographic, longitudinal outcome, and predictive modeling studies in autosomal dominant polycystic kidney disease (ADPKD). Methods We built the ADPKD cohort by extracting the relevant electronic health record data from nationwide Veterans Health Administration database (years 1999–2020). Results We identified 12,217 patients diagnosed with ADPKD. By the end of the 20-year study period, 5342 patients with ADPKD were deceased, 1583 were alive but reached ESKD, and 4827 remained alive without ESKD. Most demographic characteristics of this ADPKD cohort resemble the total US veteran population. For example, 94% were male patients, 45% age 65 years or older, 85% non-Hispanic, and 66% white; however, 19% were Black/African Americans (versus 12% in the general veteran population; a relevant enrichment after considering age and sex distributions between races). The comorbidities overrepresented in the ADPKD cohort include hypertension (89% versus 50%), diabetes (32% versus 22%), depression (40% versus 10%), chronic obstructive pulmonary disease (30% versus 6%), and congestive heart failure (21% versus 1%). By contrast, obesity was underrepresented in veterans with ADPKD (30% versus 41%). Conclusions We established a large electronic medical record-based cohort of ADPKD veterans. Here, we provide initial analysis of its demographic, comorbidity, and key laboratory data.
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Affiliation(s)
- Julia W. Gallini
- Foundation for Atlanta Veterans Education and Research, Decatur, Georgia
| | - Christine L. Jasien
- Department of Veterans Affairs Medical Center, Atlanta VA Health Care System, Decatur, Georgia
| | - Michal Mrug
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Veterans Affairs Medical Center, Birmingham, Alabama
| | - Xiangqin Cui
- Department of Veterans Affairs Medical Center, Atlanta VA Health Care System, Decatur, Georgia
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia
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Hathaway QA. Evolving Diagnostic Interpretation: How Automated Algorithms for Autosomal Dominant Polycystic Kidney Disease (ADPKD) Address Inter-Reader Variability and Physician Burnout. Acad Radiol 2024; 31:900-901. [PMID: 38368162 DOI: 10.1016/j.acra.2024.01.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/19/2024]
Affiliation(s)
- Quincy A Hathaway
- West Virginia University School of Medicine, Department of Medical Education, 1 Medical Center Drive, Morgantown, West Virginia 26505, USA; Department of Radiology and Radiologic Sciences, Johns Hopkins University, Baltimore, Maryland, USA.
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Ali H, Malik MZ, Abu-Farha M, Abubaker J, Cherian P, Nizam R, Jacob S, Bahbahani Y, Naim M, Ahmad S, Al-Sayegh M, Thanaraj TA, Ong ACM, Harris PC, Al-Mulla F. Global analysis of urinary extracellular vesicle small RNAs in autosomal dominant polycystic kidney disease. J Gene Med 2024; 26:e3674. [PMID: 38404150 DOI: 10.1002/jgm.3674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent monogenic renal disease progressing to end-stage renal disease. There is a pressing need for the identification of early ADPKD biomarkers to enable timely intervention and the development of effective therapeutic approaches. Here, we profiled human urinary extracellular vesicles small RNAs by small RNA sequencing in patients with ADPKD and compared their differential expression considering healthy control individuals to identify dysregulated small RNAs and analyze downstream interaction to gain insight about molecular pathophysiology. METHODS This is a cross-sectional study where urine samples were collected from a total of 23 PKD1-ADPKD patients and 28 healthy individuals. Urinary extracellular vesicles were purified, and small RNA was isolated and sequenced. Differentially expressed Small RNA were identified and functional enrichment analysis of the critical miRNAs was performed to identify driver genes and affected pathways. RESULTS miR-320b, miR-320c, miR-146a-5p, miR-199b-3p, miR-671-5p, miR-1246, miR-8485, miR-3656, has_piR_020497, has_piR_020496 and has_piR_016271 were significantly upregulated in ADPKD patient urine extracellular vesicles and miRNA-29c was significantly downregulated. Five 'driver' target genes (FBRS, EDC3, FMNL3, CTNNBIP1 and KMT2A) were identified. CONCLUSIONS The findings of the present study make significant contributions to the understanding of ADPKD pathogenesis and to the identification of novel biomarkers and potential drug targets aimed at slowing disease progression in ADPKD.
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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
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, 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
| | - Preethi Cherian
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Rasheeba Nizam
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Sindhu Jacob
- Department of Genetics and Bioinformatics, 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
| | - Medhat Naim
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Sajjad Ahmad
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Mohammad Al-Sayegh
- Biology Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Albert C M Ong
- Academic Nephrology Unit, Division of Clinical Medicine, School of Medicine and Population Health, Faculty of Health, University of Sheffield, Sheffield, UK
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Fahd Al-Mulla
- Department of Translational Medicine, Dasman Diabetes Institute (DDI), Dasman, Kuwait
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7
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Yasinoglu SA, Kuipers TB, Suidgeest E, van der Weerd L, Mei H, Baelde HJ, Peters DJM. Transcriptomic profiling of Polycystic Kidney Disease identifies paracrine factors in the early cyst microenvironment. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166987. [PMID: 38070582 DOI: 10.1016/j.bbadis.2023.166987] [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: 08/23/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
Initial cysts that are formed upon Pkd1 loss in mice impose persistent stress on surrounding tissue and trigger a cystic snowball effect, in which local aberrant PKD-related signaling increases the likelihood of new cyst formation, ultimately leading to accelerated disease progression. Although many pathways have been associated with PKD progression, the knowledge of early changes near initial cysts is limited. To perform an unbiased analysis of transcriptomic alterations in the cyst microenvironment, microdomains were collected from kidney sections of iKsp-Pkd1del mice with scattered Pkd1-deletion using Laser Capture Microdissection. These microdomains were defined as F4/80-low cystic, representing early alterations in the cyst microenvironment, F4/80-high cystic, with more advanced alterations, or non-cystic. RNA sequencing and differential gene expression analysis revealed 953 and 8088 dysregulated genes in the F4/80-low and F4/80-high cyst microenvironment, respectively, when compared to non-cystic microdomains. In the early cyst microenvironment, several injury-repair, growth, and tissue remodeling-related pathways were activated, accompanied by mild metabolic changes. In the more advanced F4/80-high microdomains, these pathways were potentiated and the metabolism was highly dysregulated. Upstream regulator analysis revealed a series of paracrine factors with increased activity in the early cyst microenvironment, including TNFSF12 and OSM. In line with the upstream regulator analysis, TWEAK and Oncostatin-M promoted cell proliferation and inflammatory gene expression in renal epithelial cells and fibroblasts in vitro. Collectively, our data provide an overview of molecular alterations that specifically occur in the cyst microenvironment and identify paracrine factors that may mediate early and advanced alterations in the cyst microenvironment.
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Affiliation(s)
- Sevtap A Yasinoglu
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas B Kuipers
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Ernst Suidgeest
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Louise van der Weerd
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans J Baelde
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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Drake AM, Paynter JA, Yim A, Tempo JA, Manning TG, Brennan J, Qin KR. Prevalence of Renal Neoplasia in Autosomal Dominant Polycystic Kidney Disease: Systematic Review and Meta-Analysis. Nephron Clin Pract 2024; 148:457-467. [PMID: 38301614 PMCID: PMC11216357 DOI: 10.1159/000536245] [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: 11/01/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited condition; however, its relationship with renal cell carcinoma (RCC) remains unclear. This paper aims to establish the prevalence of RCC and its subtypes amongst ADPKD patients. METHODS A database search was conducted to retrieve studies reporting RCC occurrence within ADPKD patients until July 2023. Key outcomes included number and subtype of RCC cases, and number of RCCs presenting incidentally. A random-effects meta-analysis was performed. RESULTS Our search yielded 569 articles, 16 met the inclusion criteria. Nephrectomy specimens from 1,147 ADPKD patients were identified. Of studies reporting per-kidney results (n = 13), 73 RCCs were detected amongst 1,493 kidneys, equating to a per-kidney prevalence of 4.3% (95% CI, 3.1-5.7, I2 = 15.7%). 75 ADPKD patients were found to have RCC (75/1,147), resulting in a per-person prevalence of 5.7% (95% CI, 3.7-7.9, I2 = 40.3%) (n = 16). As 7 patients had bilateral disease, 82 RCCs were detected in total. Of these, 39 were clear cell RCC, 35 were papillary and 8 were other. As such, papillary RCCs made up 41.1% (95% CI, 25.9-56.9, I2 = 18.1%) of detected cancers. The majority of RCCs were detected incidentally (72.5% [95% CI, 43.7-95.1, I2 = 66.9%]). CONCLUSION ADPKD appears to be associated with the papillary RCC subtype. The clinical implications of these findings are unclear, however, may become apparent as outcomes and life expectancy amongst APDKD patients improve.
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Affiliation(s)
- Anna M. Drake
- School of Rural Health, Monash University, Bendigo, VIC, Australia
| | - Jessica A. Paynter
- School of Rural Health, Monash University, Bendigo, VIC, Australia
- Department of Urology, Bendigo Health, Bendigo, VICAustralia
| | - Arthur Yim
- Department of Urology, Austin Health, Melbourne, VIC, Australia
| | - Jake A. Tempo
- Department of Urology, Austin Health, Melbourne, VIC, Australia
| | - Todd G. Manning
- School of Rural Health, Monash University, Bendigo, VIC, Australia
| | - Janelle Brennan
- School of Rural Health, Monash University, Bendigo, VIC, Australia
- Department of Urology, Bendigo Health, Bendigo, VICAustralia
| | - Kirby R. Qin
- School of Rural Health, Monash University, Bendigo, VIC, Australia
- Department of Urology, Bendigo Health, Bendigo, VICAustralia
- Department of Paediatrics, Monash University, Melbourne, VIC, Australia
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9
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Salman MA, Elgebaly A, Soliman NA. Epidemiology and outcomes of pediatric autosomal recessive polycystic kidney disease in the Middle East and North Africa. Pediatr Nephrol 2024:10.1007/s00467-024-06281-0. [PMID: 38261064 DOI: 10.1007/s00467-024-06281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
The incidence of rare diseases is expected to be comparatively higher in the Middle East and North Africa (MENA) region than in other parts of the world, attributed to the high prevalence of consanguinity. Most MENA countries share social and economic statuses, cultural relativism, religious beliefs, and healthcare policies. Polycystic kidney diseases (PKDs) are the most common genetic causes of kidney failure, accounting for nearly 8.0% of dialysis cases. The development of PKDs is linked to variants in several genes, including PKD1, PKD2, PKHD1, DZIP1L, and CYS1. Autosomal recessive PKD (ARPKD) is the less common yet aggressive form of PKD. ARPKD has an estimated incidence between 1:10,000 and 1:40,000. Most patients with ARPKD require kidney replacement therapy earlier than patients with autosomal dominant polycystic kidney disease (ADPKD), often in their early years of life. This review gathered data from published research studies and reviews of ARPKD, highlighting the epidemiology, phenotypic presentation, investigations, genetic analysis, outcomes, and management. Although limited data are available, the published literature suggests that the incidence of ARPKD may be higher in the MENA region due to consanguineous marriages. Patients with ARPKD from the MENA region usually present at a later disease stage and have a relatively short time to progress to kidney failure. Limited data are available regarding the management practice in the region, which warrants further investigations.
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Affiliation(s)
| | - Ahmed Elgebaly
- Smart Health Unit, University of East London, London, E16 2, UK
| | - Neveen A Soliman
- Center of Pediatric Nephrology & Transplantation, Kasr Al Ainy Medical School, Cairo University, Cairo, Egypt
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
- Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
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10
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Jefferis J, Hudson R, Lacaze P, Bakshi A, Hawley C, Patel C, Mallett A. Monogenic and polygenic concepts in chronic kidney disease (CKD). J Nephrol 2024; 37:7-21. [PMID: 37989975 PMCID: PMC10920206 DOI: 10.1007/s40620-023-01804-8] [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: 05/08/2023] [Accepted: 10/11/2023] [Indexed: 11/23/2023]
Abstract
Kidney function is strongly influenced by genetic factors with both monogenic and polygenic factors contributing to kidney function. Monogenic disorders with primarily autosomal dominant inheritance patterns account for 10% of adult and 50% of paediatric kidney diseases. However, kidney function is also a complex trait with polygenic architecture, where genetic factors interact with environment and lifestyle factors. Family studies suggest that kidney function has significant heritability at 35-69%, capturing complexities of the genome with shared environmental factors. Genome-wide association studies estimate the single nucleotide polymorphism-based heritability of kidney function between 7.1 and 20.3%. These heritability estimates, measuring the extent to which genetic variation contributes to CKD risk, indicate a strong genetic contribution. Polygenic Risk Scores have recently been developed for chronic kidney disease and kidney function, and validated in large populations. Polygenic Risk Scores show correlation with kidney function but lack the specificity to predict individual-level changes in kidney function. Certain kidney diseases, such as membranous nephropathy and IgA nephropathy that have significant genetic components, may benefit most from polygenic risk scores for improved risk stratification. Genetic studies of kidney function also provide a potential avenue for the development of more targeted therapies and interventions. Understanding the development and validation of genomic scores is required to guide their implementation and identify the most appropriate potential implications in clinical practice. In this review, we provide an overview of the heritability of kidney function traits in population studies, explore both monogenic and polygenic concepts in kidney disease, with a focus on recently developed polygenic risk scores in kidney function and chronic kidney disease, and review specific diseases which are most amenable to incorporation of genomic scores.
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Affiliation(s)
- Julia Jefferis
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, Australia.
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia.
| | - Rebecca Hudson
- Faculty of Medicine, University of Queensland, Brisbane, Australia
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Paul Lacaze
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Andrew Bakshi
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Carmel Hawley
- Department of Nephrology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
- Australasian Kidney Trials Network, The University of Queensland, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Andrew Mallett
- Institutional for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Saint Lucia, Australia.
- Department of Renal Medicine, Townsville University Hospital, Douglas, QLD, Australia.
- College of Medicine and Dentistry, James Cook University, Douglas, QLD, Australia.
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Orr S, Sayer JA. Many lessons still to learn about autosomal dominant polycystic kidney disease. JOURNAL OF RARE DISEASES (BERLIN, GERMANY) 2023; 2:13. [PMID: 37664187 PMCID: PMC10471629 DOI: 10.1007/s44162-023-00017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023]
Abstract
We are still learning the genetic basis for many rare diseases. Here we provide a commentary on the analysis of the genetic landscape of patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD), one of the most common genetic kidney diseases. Approaches including both phenotype first and genotype first allows some interesting and informative observations within this disease population. PKD1 and PKD2 are the most frequent genetic causes of ADPKD accounting for 78% and 15% respectively, whilst around 7-8% of cases have an alternative genetic diagnosis. These rarer forms include IFT140, GANAB, PKHD1, HNF1B, ALG8, and ALG9. Some previously reported likely pathogenic PKD1 and PKD2 alleles may have a reduced penetrance, or indeed may have been misclassified in terms of their pathogenicity. This recent data concerning all forms of ADPKD points to the importance of performing genetics tests in all families with a clinical diagnosis of ADPKD as well as those with more atypical cystic kidney appearances. Following allele identification, performing segregation analysis wherever possible remains vital so that we continue to learn about these important genetic causes of kidney failure.
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Affiliation(s)
- Sarah Orr
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - John A. Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- Renal Services, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, NE7 7DN UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne, NE4 5PL UK
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12
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Camargo JT, González CA, Herrera L, Yomayusa-González N, Ibañez M, Valbuena-García AM, Acuña-Merchán L. Autosomal dominant polycystic kidney disease in Colombia. BMC Nephrol 2023; 24:211. [PMID: 37460967 DOI: 10.1186/s12882-023-03266-3] [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: 01/10/2023] [Accepted: 07/09/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic cause of chronic kidney disease (CKD) that requires dialysis. Knowing geographical clusters can be critical for early diagnosis, progression control, and genetic counseling. The objective was to establish the prevalence, geographic location, and ethnic groups of patients with ADPKD who underwent dialysis or kidney transplant in Colombia between 2015 and 2019. METHODS We did a cross-sectional study with data from the National Registry of Chronic Kidney Disease (NRCKD) managed by the High-Cost Diseases Fund (Cuenta de Alto Costo [CAC] in Spanish) between July 1, 2015, and June 30, 2019. We included Colombian population with CKD with or without renal replacement therapy (RRT) due to ADPKD. Crude and adjusted prevalence rates were estimated by state and city. RESULTS 3,339 patients with ADPKD were included, period prevalence was 9.81 per 100,000 population; there were 4.35 cases of RRT per 100,000 population, mean age of 52.58 years (± 13.21), and 52.78% women. Seventy-six patients were Afro-Colombians, six were indigenous, and one Roma people. A total of 46.07% began scheduled dialysis. The highest adjusted prevalence rate was in Valle del Cauca (6.55 cases per 100,000 population), followed by Risaralda, and La Guajira. Regarding cities, Cali had the highest prevalence rate (9.38 cases per 100,000 population), followed by Pasto, Medellin, and Bucaramanga. CONCLUSIONS ADPKD prevalence is lower compared to Europe and US; some states with higher prevalence could be objective to genetic prevalence study.
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Affiliation(s)
| | - Camilo A González
- Unidad Renal, Clínica Colsanitas, Calle 127 No 20-78 Piso 2, Bogotá, D.C, Colombia.
| | - Lina Herrera
- Cuenta de Alto Costo, Fondo Colombiano de Enfermedades de Alto Costo, Bogotá, D.C, Colombia
| | | | - Milciades Ibañez
- Instituto de Investigación, Fundación Universitaria Sanitas, Bogotá, DC, Colombia
| | - Ana M Valbuena-García
- Cuenta de Alto Costo, Fondo Colombiano de Enfermedades de Alto Costo, Bogotá, D.C, Colombia
| | - Lizbeth Acuña-Merchán
- Cuenta de Alto Costo, Fondo Colombiano de Enfermedades de Alto Costo, Bogotá, D.C, Colombia
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13
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Bakshi A, Jefferis J, Wolfe R, Wetmore JB, McNeil JJ, Murray AM, Polkinghorne KR, Mallett A, Lacaze P. Association of polygenic scores with chronic kidney disease phenotypes in a longitudinal study of older adults. Kidney Int 2023; 103:1156-1166. [PMID: 37001602 PMCID: PMC10200771 DOI: 10.1016/j.kint.2023.03.017] [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: 08/01/2022] [Revised: 02/09/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023]
Abstract
Risk of chronic kidney disease (CKD) is influenced by environmental and genetic factors and increases sharply in individuals 70 years and older. Polygenic scores (PGS) for kidney disease-related traits have shown promise but require validation in well-characterized cohorts. Here, we assessed the performance of recently developed PGSs for CKD-related traits in a longitudinal cohort of healthy older individuals enrolled in the Australian ASPREE randomized controlled trial of daily low-dose aspirin with CKD risk at baseline and longitudinally. Among 11,813 genotyped participants aged 70 years or more with baseline eGFR measures, we tested associations between PGSs and measured eGFR at baseline, clinical phenotype of CKD, and longitudinal rate of eGFR decline spanning up to six years of follow-up per participant. A PGS for eGFR was associated with baseline eGFR, with a significant decrease of 3.9 mL/min/1.73m2 (95% confidence interval -4.17 to -3.68) per standard deviation (SD) increase of the PGS. This PGS, as well as a PGS for CKD stage 3 were both associated with higher risk of baseline CKD stage 3 in cross-sectional analysis (Odds Ratio 1.75 per SD, 95% confidence interval 1.66-1.85, and Odds Ratio 1.51 per SD, 95% confidence interval 1.43-1.59, respectively). Longitudinally, two separate PGSs for eGFR slope were associated with significant kidney function decline during follow-up. Thus, our study demonstrates that kidney function has a considerable genetic component in older adults, and that new PGSs for kidney disease-related phenotypes may have potential utility for CKD risk prediction in advanced age.
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Affiliation(s)
- Andrew Bakshi
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Julia Jefferis
- Department of Nephrology, Princess Alexandra Hospital, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | | | - James B. Wetmore
- Chronic Disease Research Group, Hennepin Healthcare Research Institute, Minneapolis, Minnesota, USA
- Division of Nephrology, Hennepin Healthcare, Minneapolis, Minnesota, USA
| | - John J McNeil
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Anne M. Murray
- Geriatric Division, Department of Medicine, Hennepin Healthcare Minneapolis, Minnesota, USA
- Medical Director, Berman Centre for Clinical Research, Hennepin Healthcare Research Institute, Minneapolis, USA
- Professor of Medicine and Geriatrics, Adjunct Neurology, University of Minnesota
| | - Kevan R. Polkinghorne
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
- Department of Nephrology, Monash Medical Centre, Monash Health, Melbourne, Victoria, Australia
| | - Andrew Mallett
- Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, Douglas, QLD, Australia
- College of Medicine and Dentistry, James Cook University, Douglas, QLD
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
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14
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Chang AR, Moore BS, Luo JZ, Sartori G, Fang B, Jacobs S, Abdalla Y, Taher M, Carey DJ, Triffo WJ, Singh G, Mirshahi T. Exome Sequencing of a Clinical Population for Autosomal Dominant Polycystic Kidney Disease. JAMA 2022; 328:2412-2421. [PMID: 36573973 PMCID: PMC9856880 DOI: 10.1001/jama.2022.22847] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
IMPORTANCE Most studies of autosomal dominant polycystic kidney disease (ADPKD) genetics have used kidney specialty cohorts, focusing on PKD1 and PKD2. These can lead to biased estimates of population prevalence of ADPKD-associated gene variants and their phenotypic expression. OBJECTIVE To determine the prevalence of ADPKD and contributions of PKD1, PKD2, and other genes related to cystic kidney disease in a large, unselected cohort. DESIGN, SETTING, AND PARTICIPANTS This retrospective observational study used an unselected health system-based cohort in central and northeast Pennsylvania with exome sequencing (enrolled from 2004 to 2020) and electronic health record data (up to October 2021). The genotype-first approach included the entire cohort and the phenotype-first approach focused on patients with ADPKD diagnosis codes, confirmed by chart and imaging review. EXPOSURES Loss-of-function (LOF) variants in PKD1, PKD2, and other genes associated with cystic kidney disease (ie, ALG8, ALG9, DNAJB11, GANAB, HNF1B, IFT140, SEC61B, PKHD1, PRKCSH, SEC63); likely pathogenic missense variants in PKD1 and PKD2. MAIN OUTCOMES AND MEASURES Genotype-first analysis: ADPKD diagnosis code (Q61.2, Q61.3, 753.13, 753.12); phenotype-first analysis: presence of a rare variant in PKD1, PKD2, or other genes associated with cystic kidney disease. RESULTS Of 174 172 patients (median age, 60 years; 60.6% female; 93% of European ancestry), 303 patients had ADPKD diagnosis codes, including 235 with sufficient chart review data for confirmation. In addition to PKD1 and PKD2, LOF variants in IFT140, GANAB, and HNF1B were associated with ADPKD diagnosis after correction for multiple comparisons. Among patients with LOF variants in PKD1, 66 of 68 (97%) had ADPKD; 43 of 43 patients (100%) with LOF variants in PKD2 had ADPKD. In contrast, only 24 of 77 patients (31.2%) with a PKD1 missense variant previously classified as "likely pathogenic" had ADPKD, suggesting misclassification or variable penetrance. Among patients with ADPKD diagnosis confirmed by chart review, 180 of 235 (76.6%) had a potential genetic cause, with the majority being rare variants in PKD1 (127 patients) or PKD2 (34 patients); 19 of 235 (8.1%) had variants in other genes associated with cystic kidney disease. Of these 235 patients with confirmed ADPKD, 150 (63.8%) had a family history of ADPKD. The yield for a genetic determinant of ADPKD was higher for those with a family history of ADPKD compared with those without family history (91.3% [137/150] vs 50.6% [43/85]; difference, 40.7% [95% CI, 29.2%-52.3%]; P < .001). Previously unreported PKD1, PKD2, and GANAB variants were identified with pedigree data suggesting pathogenicity, and several PKD1 missense variants previously reported as likely pathogenic appeared to be benign. CONCLUSIONS AND RELEVANCE This study demonstrates substantial genetic and phenotypic variability in ADPKD among patients within a regional health system in the US.
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Affiliation(s)
- Alexander R. Chang
- Center for Kidney Health Research, Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
- Department of Nephrology, Geisinger, Danville, Pennsylvania
| | - Bryn S. Moore
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | - Jonathan Z. Luo
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | - Gino Sartori
- Department of Radiology, Geisinger, Danville, Pennsylvania
| | - Brian Fang
- Center for Kidney Health Research, Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
| | - Steven Jacobs
- Department of Nephrology, Geisinger, Danville, Pennsylvania
| | - Yoosif Abdalla
- Department of Nephrology, Geisinger, Danville, Pennsylvania
| | - Mohammed Taher
- Center for Kidney Health Research, Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
| | - David J. Carey
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | | | - Gurmukteshwar Singh
- Center for Kidney Health Research, Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
- Department of Nephrology, Geisinger, Danville, Pennsylvania
| | - Tooraj Mirshahi
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
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15
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Harrison TN, Chen Q, Lee MY, Munis MA, Morrissette K, Sundar S, Pareja K, Nourbakhsh A, Shu YH, Willey CJ, Sim JJ. Health Disparities in Kidney Failure Among Patients With Autosomal Dominant Polycystic Kidney Disease: A Cross-Sectional Study. Kidney Med 2022; 5:100577. [PMID: 36718187 PMCID: PMC9883284 DOI: 10.1016/j.xkme.2022.100577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rationale & Objective Understanding potential differences in patterns of kidney failure among patients with autosomal dominant polycystic kidney disease (ADPKD) may provide insights into improving disease management. We sought to characterize patients with ADPKD and kidney failure across different race/ethnicities. Study Design Cross-sectional study. Setting & Participants Kaiser Permanente Southern California members diagnosed with ADPKD between January1, 2002, and December 31, 2018. Exposure ADPKD. Outcome Kidney failure, dialysis, or receipt of kidney transplant. Analytical Approach Differences in characteristics by race/ethnicity were assessed using analysis of variance F test and χ2 test. To compare the range and distribution of the average age at onset of kidney failure by race/ethnicity and sex, we used box plots and confidence intervals. Multivariable logistic regression was used to estimate OR for kidney transplant. Results Among 3,677 ADPKD patients, 1,027 (27.3%) had kidney failure. The kidney failure cohort was comprised of Black (n=138; 30.7%), White (n=496; 30.6%), Hispanic (n=306; 24.7%), and Asian (n=87; 23.6%) patients. Hispanic patients had the youngest mean age of kidney failure onset (50 years) compared to Black (56 years) and White (57 years) patients. Black (44.2%; OR, 0.72) and Hispanic (49.7%; OR, 0.65) patients had lower rates of kidney transplantation compared to White (53.8%) patients. Preemptive kidney transplantations occurred in 15.0% of patients. Limitations Retrospective study design and possible misclassification of ADPKD cases. Kidney function calculations were based on equations incorporating race, potentially overestimating kidney function in African Americans. The study was conducted within a single, integrated health care system in 1 geographic region and may not be generalizable to all ADPKD patients. Conclusions Among a large diverse ADPKD population, we observed racial/ethnic differences in rates of kidney failure, age of kidney failure onset, and rates of kidney transplantation. Our real-world ADPKD cohort provides insight into racial/ethnic variation in clinical features of disease and potential disparities in care, which may affect ADPKD outcomes.
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Affiliation(s)
- Teresa N. Harrison
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Qiaoling Chen
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Min Young Lee
- Division of Nephrology and Hypertension, Kaiser Permanente Los Angeles Medical Center, Los Angeles, California
| | - Mercedes A. Munis
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Kerresa Morrissette
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Shirin Sundar
- Otsuka Pharmaceutical Development & Commercialization, Inc, Princeton, New Jersey
| | - Kristin Pareja
- Otsuka Pharmaceutical Development & Commercialization, Inc, Princeton, New Jersey
| | - Ali Nourbakhsh
- Otsuka Pharmaceutical Development & Commercialization, Inc, Princeton, New Jersey
| | - Yu-Hsiang Shu
- Department of Biostatistics and Programming, Inari Medical, Irvine, California
| | - Cynthia J. Willey
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island
| | - John J. Sim
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California,Division of Nephrology and Hypertension, Kaiser Permanente Los Angeles Medical Center, Los Angeles, California,Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California,Address for Correspondence: John J. Sim, MD, Division of Nephrology and Hypertension, Kaiser Permanente Los Angeles Medical Center, 4700 Sunset Bl 2nd Floor, Los Angeles, CA 90027.
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16
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Zhang Z, Blumenfeld J, Ramnauth A, Barash I, Zhou P, Levine D, Parker T, Rennert H. A common intronic single nucleotide variant modifies PKD1 expression level. Clin Genet 2022; 102:483-493. [PMID: 36029107 PMCID: PMC10947153 DOI: 10.1111/cge.14214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/26/2022]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), caused by mutations in PKD1 and PKD2 (PKD1/2), has unexplained phenotypic variability likely affected by environmental and other genetic factors. Approximately 10% of individuals with ADPKD phenotype have no causal mutation detected, possibly due to unrecognized risk variants of PKD1/2. This study was designed to identify risk variants of PKD genes through population genetic analyses. We used Wright's F-statistics (Fst) to evaluate common single nucleotide variants (SNVs) potentially favored by positive natural selection in PKD1 from 1000 Genomes Project (1KG) and genotyped 388 subjects from the Rogosin Institute ADPKD Data Repository. The variants with >90th percentile Fst scores underwent further investigation by in silico analysis and molecular genetics analyses. We identified a deep intronic SNV, rs3874648G> A, located in a conserved binding site of the splicing regulator Tra2-β in PKD1 intron 30. Reverse-transcription PCR (RT-PCR) of peripheral blood leukocytes (PBL) from an ADPKD patient homozygous for rs3874648-A identified an atypical PKD1 splice form. Functional analyses demonstrated that rs3874648-A allele increased Tra2-β binding affinity and activated a cryptic acceptor splice-site, causing a frameshift that introduced a premature stop codon in mRNA, thereby decreasing PKD1 full-length transcript level. PKD1 transcript levels were lower in PBL from rs3874648-G/A carriers than in rs3874648-G/G homozygotes in a small cohort of normal individuals and patients with PKD2 inactivating mutations. Our findings indicate that rs3874648G > A is a PKD1 expression modifier attenuating PKD1 expression through Tra2-β, while the derived G allele advantageously maintains PKD1 expression and is predominant in all subpopulations.
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Affiliation(s)
- Zhengmao Zhang
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Jon Blumenfeld
- Department of Medicine, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Andrew Ramnauth
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Irina Barash
- Department of Medicine, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Pengbo Zhou
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Daniel Levine
- Department of Biochemistry, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Thomas Parker
- Department of Biochemistry, Weill Cornell Medicine, New York, NY
- The Rogosin Institute, New York, NY
| | - Hanna Rennert
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
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17
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Chong J, Harris T, Ong ACM. Regional variation in tolvaptan prescribing across England: national data and retrospective evaluation from an expert centre. Clin Kidney J 2022; 16:61-68. [PMID: 36726434 PMCID: PMC9871855 DOI: 10.1093/ckj/sfac190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
Background Tolvaptan, a vasopressin V2 receptor antagonist, was approved in 2015 by the UK National Institute for Health and Care Excellence for use in patients with autosomal dominant polycystic kidney disease (ADPKD) and rapid disease progression. Simultaneous guidance was issued by the UK Kidney Association (UKKA) to facilitate national implementation. Methods Data on tolvaptan prescribing in England was obtained through the National Health Service (NHS) Digital, a national survey of all 77 adult kidney units, and the implementation of UKKA guidance was evaluated at an expert PKD centre. Results A regional variation of up to 4-fold for tolvaptan prescribing in England was found. Despite most kidney units following UKKA guidance, centre-based estimates of eligible or treated patient numbers were highly variable. Retrospective evaluation at an expert PKD centre revealed that in a cohort demonstrating rapid estimated glomerular filtration rate (eGFR) decline, 14% would not be eligible for tolvaptan by Mayo imaging classification and more than half (57%) would not be eligible by Predicting Renal Outcome in Polycystic Kidney Disease score. The 3-year discontinuation rate was higher than expected (56%), the majority (70%) due to aquaretic symptoms. In patients taking tolvaptan for at least 2 years, 81% showed a reduction in the rate of eGFR decline compared with baseline, with earlier disease associated with positive treatment response. Conclusion Real-world data have revealed a much higher regional variation in tolvaptan prescribing for ADPKD in England than expected. We propose further investigation into the factors responsible for this variation.
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Affiliation(s)
- Jiehan Chong
- Academic Nephrology Unit, Department of Infection, Immunity, and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
- Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, Medical School, University of Leeds, Leeds, UK
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18
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Mohottige D, McElroy LM, Boulware LE. Addressing "Second Hits" in the Pursuit of Greater Equity in Health Outcomes for Individuals with ADPKD. Clin J Am Soc Nephrol 2022; 17:936-938. [PMID: 35725554 PMCID: PMC9269624 DOI: 10.2215/cjn.05970522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Dinushika Mohottige
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Lisa M McElroy
- Division of Abdominal Transplant, Duke Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - L Ebony Boulware
- Division of General Internal Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
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