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Yu Z, Coorens THH, Uddin MM, Ardlie KG, Lennon N, Natarajan P. Genetic variation across and within individuals. Nat Rev Genet 2024; 25:548-562. [PMID: 38548833 DOI: 10.1038/s41576-024-00709-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2024] [Indexed: 04/12/2024]
Abstract
Germline variation and somatic mutation are intricately connected and together shape human traits and disease risks. Germline variants are present from conception, but they vary between individuals and accumulate over generations. By contrast, somatic mutations accumulate throughout life in a mosaic manner within an individual due to intrinsic and extrinsic sources of mutations and selection pressures acting on cells. Recent advancements, such as improved detection methods and increased resources for association studies, have drastically expanded our ability to investigate germline and somatic genetic variation and compare underlying mutational processes. A better understanding of the similarities and differences in the types, rates and patterns of germline and somatic variants, as well as their interplay, will help elucidate the mechanisms underlying their distinct yet interlinked roles in human health and biology.
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Affiliation(s)
- Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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2
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Jones AC, Patki A, Srinivasasainagendra V, Tiwari HK, Armstrong ND, Chaudhary NS, Limdi NA, Hidalgo BA, Davis B, Cimino JJ, Khan A, Kiryluk K, Lange LA, Lange EM, Arnett DK, Young BA, Diamantidis CJ, Franceschini N, Wassertheil-Smoller S, Rich SS, Rotter JI, Mychaleckyj JC, Kramer HJ, Chen YDI, Psaty BM, Brody JA, de Boer IH, Bansal N, Bis JC, Irvin MR. Single-Ancestry versus Multi-Ancestry Polygenic Risk Scores for CKD in Black American Populations. J Am Soc Nephrol 2024:00001751-990000000-00377. [PMID: 39073889 DOI: 10.1681/asn.0000000000000437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
Key Points
The predictive performance of an African ancestry–specific polygenic risk score (PRS) was comparable to a European ancestry–derived PRS for kidney traits.However, multi-ancestry PRSs outperform single-ancestry PRSs in Black American populations.Predictive accuracy of PRSs for CKD was improved with the use of race-free eGFR.
Background
CKD is a risk factor of cardiovascular disease and early death. Recently, polygenic risk scores (PRSs) have been developed to quantify risk for CKD. However, African ancestry populations are underrepresented in both CKD genetic studies and PRS development overall. Moreover, European ancestry–derived PRSs demonstrate diminished predictive performance in African ancestry populations.
Methods
This study aimed to develop a PRS for CKD in Black American populations. We obtained score weights from a meta-analysis of genome-wide association studies for eGFR in the Million Veteran Program and Reasons for Geographic and Racial Differences in Stroke Study to develop an eGFR PRS. We optimized the PRS risk model in a cohort of participants from the Hypertension Genetic Epidemiology Network. Validation was performed in subsets of Black participants of the Trans-Omics in Precision Medicine Consortium and Genetics of Hypertension Associated Treatment Study.
Results
The prevalence of CKD—defined as stage 3 or higher—was associated with the PRS as a continuous predictor (odds ratio [95% confidence interval]: 1.35 [1.08 to 1.68]) and in a threshold-dependent manner. Furthermore, including APOL1 risk status—a putative variant for CKD with higher prevalence among those of sub-Saharan African descent—improved the score's accuracy. PRS associations were robust to sensitivity analyses accounting for traditional CKD risk factors, as well as CKD classification based on prior eGFR equations. Compared with previously published PRS, the predictive performance of our PRS was comparable with a European ancestry–derived PRS for kidney traits. However, single-ancestry PRSs were less predictive than multi-ancestry–derived PRSs.
Conclusions
In this study, we developed a PRS that was significantly associated with CKD with improved predictive accuracy when including APOL1 risk status. However, PRS generated from multi-ancestry populations outperformed single-ancestry PRS in our study.
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Affiliation(s)
- Alana C Jones
- Medical Scientist Training Program, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nicole D Armstrong
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ninad S Chaudhary
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Bertha A Hidalgo
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brittney Davis
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - James J Cimino
- Department of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado-Anschutz, Aurora, Colorado
| | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado-Anschutz, Aurora, Colorado
| | - Donna K Arnett
- Office of the Provost, University of South Carolina, Columbia, South Carolina
| | - Bessie A Young
- Division of Nephrology, University of Washington, Seattle, Washington
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, New York
| | - Stephen S Rich
- Department of Genome Sciences, University of Virginia, Charlottesville, Virginia
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomic and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbort-UCLA Medical Center, Torrance, California
| | - Josyf C Mychaleckyj
- Department of Genome Sciences, University of Virginia, Charlottesville, Virginia
| | - Holly J Kramer
- Departments of Public Health Sciences and Medicine, Loyola University Medical Center, Taywood, Illinois
| | - Yii-Der I Chen
- Department of Pediatrics, The Institute for Translational Genomic and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbort-UCLA Medical Center, Torrance, California
| | - Bruce M Psaty
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Ian H de Boer
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Nisha Bansal
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
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3
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Abdulmelik A, Tila M, Tekilu T, Debalkie A, Habtu E, Sintayehu A, Dendir G, Gordie N, Daniel A, Suleiman Obsa M. Magnitude and associated factors of intraoperative cardiac complications among geriatric patients who undergo non-cardiac surgery at public hospitals in the southern region of Ethiopia: a multi-center cross-sectional study in 2022/2023. Front Med (Lausanne) 2024; 11:1325358. [PMID: 38695033 PMCID: PMC11061426 DOI: 10.3389/fmed.2024.1325358] [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: 10/21/2023] [Accepted: 03/04/2024] [Indexed: 05/04/2024] Open
Abstract
Background Intraoperative cardiac complications are a common cause of morbidity and mortality in non-cardiac surgery. The risk of these complications increased with the average age increasing from 65. In a resource-limited setting, including our study area, the magnitude and associated factors of intraoperative cardiac complications have not been adequately investigated. The aim of this study was to assess the magnitude and associated factors of intraoperative cardiac complications among geriatric patients undergoing non-cardiac surgery. Methods An institutional-based multi-center cross-sectional study was conducted on 304 geriatric patients at governmental hospitals in the southern region of Ethiopia, from 20 March 2022 to 25 August 2022. Data were collected by chart review and patient interviews. Epi Data version 4.6 and SPSS version 25 were used for analysis. The variables that had association (p < 0.25) were considered for multivariable logistic regression. A p value < 0.05 was considered significant for association. Result The overall prevalence of intraoperative cardiac complications was 24.3%. Preoperative ST-segment elevation adjusted odds ratio (AOR = 2.43, CI =2.06-3.67), history of hypertension (AOR = 3.42, CI =2.02-6.08), intraoperative hypoxia (AOR = 3.5, CI = 2.07-6.23), intraoperative hypotension (AOR = 6.2 9, CI =3.51-10.94), age > 85 years (AOR = 6.01, CI = 5.12-12.21), and anesthesia time > 3 h (AOR =2.27, CI = 2.0.2-18.25) were factors significantly associated with intraoperative cardiac complications. Conclusion The magnitude of intraoperative cardiac complications was high among geriatric patients who had undergone non-cardiac surgery. The independent risk factors of intraoperative cardiac complications for this population included age > 85, ST-segment elevation, perioperative hypertension (stage 3 with regular treatment), duration of anesthesia >3 h, intraoperative hypoxia, and intraoperative hypotension. Holistic preoperative evaluation, optimization optimal and perioperative care for preventing perioperative risk factors listed above, and knowing all possible risk factors are suggested to reduce the occurrence of complications.
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Affiliation(s)
- Amina Abdulmelik
- School of Anesthesia, College of Health Science and Medicine, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Mebratu Tila
- School of Anesthesia, College of Health Science and Medicine, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Takele Tekilu
- School of Medical Laboratory, College of Medicine and Health Science, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Ashebir Debalkie
- School of Anesthesia, College of Health Science and Medicine, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Elias Habtu
- School of Anesthesia, College of Health Science and Medicine, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Ashagrie Sintayehu
- School of Anesthesia, College of Health Science and Medicine, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Getahun Dendir
- School of Anesthesia, College of Health Science and Medicine, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Naol Gordie
- School of Anesthesia, College of Health Science and Medicine, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Abel Daniel
- School of Medicine, College of Medicine and Health Science, Wolaita Soddo University, Wolaita Soddo, Ethiopia
| | - Mohammed Suleiman Obsa
- Department of Anesthesia, College of Medicine and Health Science, Arsi University, Assela, Ethiopia
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4
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Weon B, Jang Y, Jo J, Jin W, Ha S, Ko A, Oh YK, Lim CS, Lee JP, Won S, Lee J. Association between dyslipidemia and the risk of incident chronic kidney disease affected by genetic susceptibility: Polygenic risk score analysis. PLoS One 2024; 19:e0299605. [PMID: 38626061 PMCID: PMC11020804 DOI: 10.1371/journal.pone.0299605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/13/2024] [Indexed: 04/18/2024] Open
Abstract
BACKGROUND The effect of dyslipidemia on kidney disease outcomes has been inconclusive, and it requires further clarification. Therefore, we aimed to investigate the effects of genetic factors on the association between dyslipidemia and the risk of chronic kidney disease (CKD) using polygenic risk score (PRS). METHODS We analyzed data from 373,523 participants from the UK Biobank aged 40-69 years with no history of CKD. Baseline data included plasma levels of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglyceride, as well as genome-wide genotype data for PRS. Our primary outcome, incident CKD, was defined as a composite of estimated glomerular filtration rate < 60 ml/min/1.73 m2 and CKD diagnosis according to International Classification of Disease-10 codes. The effects of the association between lipid levels and PRS on incident CKD were assessed using the Cox proportional hazards model. To investigate the effect of this association, we introduced multiplicative interaction terms into a multivariate analysis model and performed subgroup analysis stratified by PRS tertiles. RESULTS In total, 4,424 participants developed CKD. In the multivariable analysis, PRS was significantly predictive of the risk of incident CKD as both a continuous variable and a categorized variable. In addition, lower total cholesterol, LDL-C, HDL-C, and higher triglyceride levels were significantly associated with the risk of incident CKD. There were interactions between triglycerides and intermediate and high PRS, and the interactions were inversely associated with the risk of incident CKD. CONCLUSIONS This study showed that PRS presented significant predictive power for incident CKD and individuals in the low-PRS group had a higher risk of triglyceride-related incident CKD.
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Affiliation(s)
- Boram Weon
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | | | - Jinyeon Jo
- Department of Public Health Sciences, Institute of Health & Environment, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Wencheng Jin
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seounguk Ha
- Korea Medical Institute, Seoul, Republic of Korea
| | - Ara Ko
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yun Kyu Oh
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chun Soo Lim
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung Pyo Lee
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungho Won
- Rexsoft Corporation, Seoul, Republic of Korea
- Department of Public Health Sciences, Institute of Health & Environment, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Jeonghwan Lee
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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5
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Jin J, Zhan J, Zhang J, Zhao R, O'Connell J, Jiang Y, Buyske S, Gignoux C, Haiman C, Kenny EE, Kooperberg C, North K, Koelsch BL, Wojcik G, Zhang H, Chatterjee N. MUSSEL: Enhanced Bayesian polygenic risk prediction leveraging information across multiple ancestry groups. CELL GENOMICS 2024; 4:100539. [PMID: 38604127 PMCID: PMC11019365 DOI: 10.1016/j.xgen.2024.100539] [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: 03/23/2023] [Revised: 09/07/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
Polygenic risk scores (PRSs) are now showing promising predictive performance on a wide variety of complex traits and diseases, but there exists a substantial performance gap across populations. We propose MUSSEL, a method for ancestry-specific polygenic prediction that borrows information in summary statistics from genome-wide association studies (GWASs) across multiple ancestry groups via Bayesian hierarchical modeling and ensemble learning. In our simulation studies and data analyses across four distinct studies, totaling 5.7 million participants with a substantial ancestral diversity, MUSSEL shows promising performance compared to alternatives. For example, MUSSEL has an average gain in prediction R2 across 11 continuous traits of 40.2% and 49.3% compared to PRS-CSx and CT-SLEB, respectively, in the African ancestry population. The best-performing method, however, varies by GWAS sample size, target ancestry, trait architecture, and linkage disequilibrium reference samples; thus, ultimately a combination of methods may be needed to generate the most robust PRSs across diverse populations.
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Affiliation(s)
- Jin Jin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19103, USA.
| | | | - Jingning Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ruzhang Zhao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | | | - Steven Buyske
- Department of Statistics, Rutgers University, New Brunswick, NJ 08854, USA
| | - Christopher Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Eimear E Kenny
- Icahn Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kari North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | | | - Genevieve Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Haoyu Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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6
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Sun C, Cheng X, Xu J, Chen H, Tao J, Dong Y, Wei S, Chen R, Meng X, Ma Y, Tian H, Guo X, Bi S, Zhang C, Kang J, Zhang M, Lv H, Shang Z, Lv W, Zhang R, Jiang Y. A review of disease risk prediction methods and applications in the omics era. Proteomics 2024:e2300359. [PMID: 38522029 DOI: 10.1002/pmic.202300359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
Risk prediction and disease prevention are the innovative care challenges of the 21st century. Apart from freeing the individual from the pain of disease, it will lead to low medical costs for society. Until very recently, risk assessments have ushered in a new era with the emergence of omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and so on, which potentially advance the ability of biomarkers to aid prediction models. While risk prediction has achieved great success, there are still some challenges and limitations. We reviewed the general process of omics-based disease risk model construction and the applications in four typical diseases. Meanwhile, we highlighted the problems in current studies and explored the potential opportunities and challenges for future clinical practice.
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Affiliation(s)
- Chen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Xiangshu Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Jing Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Haiyan Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junxian Tao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Yu Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Rui Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yingnan Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Hongsheng Tian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xuying Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuo Bi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chen Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jingxuan Kang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mingming Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
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7
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Osborne AJ, Bierzynska A, Colby E, Andag U, Kalra PA, Radresa O, Skroblin P, Taal MW, Welsh GI, Saleem MA, Campbell C. Multivariate canonical correlation analysis identifies additional genetic variants for chronic kidney disease. NPJ Syst Biol Appl 2024; 10:28. [PMID: 38459044 PMCID: PMC10924093 DOI: 10.1038/s41540-024-00350-8] [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: 09/04/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
Chronic kidney diseases (CKD) have genetic associations with kidney function. Univariate genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN), two complementary kidney function markers. However, it is unknown whether additional SNPs for kidney function can be identified by multivariate statistical analysis. To address this, we applied canonical correlation analysis (CCA), a multivariate method, to two individual-level CKD genotype datasets, and metaCCA to two published GWAS summary statistics datasets. We identified SNPs previously associated with kidney function by published univariate GWASs with high replication rates, validating the metaCCA method. We then extended discovery and identified previously unreported lead SNPs for both kidney function markers, jointly. These showed expression quantitative trait loci (eQTL) colocalisation with genes having significant differential expression between CKD and healthy individuals. Several of these identified lead missense SNPs were predicted to have a functional impact, including in SLC14A2. We also identified previously unreported lead SNPs that showed significant correlation with both kidney function markers, jointly, in the European ancestry CKDGen, National Unified Renal Translational Research Enterprise (NURTuRE)-CKD and Salford Kidney Study (SKS) datasets. Of these, rs3094060 colocalised with FLOT1 gene expression and was significantly more common in CKD cases in both NURTURE-CKD and SKS, than in the general population. Overall, by using multivariate analysis by CCA, we identified additional SNPs and genes for both kidney function and CKD, that can be prioritised for further CKD analyses.
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Affiliation(s)
- Amy J Osborne
- Intelligent Systems Laboratory, University of Bristol, Bristol, BS8 1TW, UK.
| | - Agnieszka Bierzynska
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, BS1 3NY, UK
| | - Elizabeth Colby
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, BS1 3NY, UK
| | - Uwe Andag
- Department of Metabolic and Renal Diseases, Evotec International GmbH, Marie-Curie-Strasse 7, 37079, Göttingen, Germany
| | - Philip A Kalra
- Department of Renal Medicine, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Stott Lane, Salford, M6 8HD, UK
| | - Olivier Radresa
- Department of Metabolic and Renal Diseases, Evotec International GmbH, Marie-Curie-Strasse 7, 37079, Göttingen, Germany
| | - Philipp Skroblin
- Department of Metabolic and Renal Diseases, Evotec International GmbH, Marie-Curie-Strasse 7, 37079, Göttingen, Germany
| | - Maarten W Taal
- Centre for Kidney Research and Innovation, University of Nottingham, Derby, UK
| | - Gavin I Welsh
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, BS1 3NY, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol, BS1 3NY, UK
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, BS8 1TW, UK.
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8
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Jefferis J, Mallett AJ. Exploring the impact and utility of genomic sequencing in established CKD. Clin Kidney J 2024; 17:sfae043. [PMID: 38464959 PMCID: PMC10921391 DOI: 10.1093/ckj/sfae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Indexed: 03/12/2024] Open
Abstract
Clinical genetics is increasingly recognized as an important area within nephrology care. Clinicians require awareness of genetic kidney disease to recognize clinical phenotypes, consider use of genomics to aid diagnosis, and inform treatment decisions. Understanding the broad spectrum of clinical phenotypes and principles of genomic sequencing is becoming increasingly required in clinical nephrology, with nephrologists requiring education and support to achieve meaningful patient outcomes. Establishment of effective clinical resources, multi-disciplinary teams and education is important to increase application of genomics in clinical care, for the benefit of patients and their families. Novel applications of genomics in chronic kidney disease include pharmacogenomics and clinical translation of polygenic risk scores. This review explores established and emerging impacts and utility of genomics in kidney disease.
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Affiliation(s)
- Julia Jefferis
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Andrew J Mallett
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Department of Renal Medicine, Townsville University Hospital, Douglas, Australia
- College of Medicine and Dentistry, James Cook University, Douglas, Australia
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9
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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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10
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Ba R, Durand A, Mauduit V, Chauveau C, Le Bas-Bernardet S, Salle S, Guérif P, Morin M, Petit C, Douillard V, Rousseau O, Blancho G, Kerleau C, Vince N, Giral M, Gourraud PA, Limou S. KiT-GENIE, the French genetic biobank of kidney transplantation. Eur J Hum Genet 2023; 31:1291-1299. [PMID: 36737541 PMCID: PMC10620190 DOI: 10.1038/s41431-023-01294-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/16/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
KiT-GENIE is a monocentric DNA biobank set up to consolidate the very rich and homogeneous DIVAT French cohort of kidney donors and recipients (D/R) in order to explore the molecular factors involved in kidney transplantation outcomes. We collected DNA samples for kidney transplantations performed in Nantes, and we leveraged GWAS genotyping data for securing high-quality genetic data with deep SNP and HLA annotations through imputations and for inferring D/R genetic ancestry. Overall, the biobank included 4217 individuals (n = 1945 D + 2,272 R, including 1969 D/R pairs), 7.4 M SNPs and over 200 clinical variables. KiT-GENIE represents an accurate snapshot of kidney transplantation clinical practice in Nantes between 2002 and 2018, with an enrichment in living kidney donors (17%) and recipients with focal segmental glomerulosclerosis (4%). Recipients were predominantly male (63%), of European ancestry (93%), with a mean age of 51yo and 86% experienced their first graft over the study period. D/R pairs were 93% from European ancestry, and 95% pairs exhibited at least one HLA allelic mismatch. The mean follow-up time was 6.7 years with a hindsight up to 25 years. Recipients experienced biopsy-proven rejection and graft loss for 16.6% and 21.3%, respectively. KiT-GENIE constitutes one of the largest kidney transplantation genetic cohorts worldwide to date. It includes homogeneous high-quality clinical and genetic data for donors and recipients, hence offering a unique opportunity to investigate immunogenetic and genetic factors, as well as donor-recipient interactions and mismatches involved in rejection, graft survival, primary disease recurrence and other comorbidities.
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Affiliation(s)
- Rokhaya Ba
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Axelle Durand
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Vincent Mauduit
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Christine Chauveau
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Stéphanie Le Bas-Bernardet
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Sonia Salle
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Pierrick Guérif
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Martin Morin
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Clémence Petit
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Venceslas Douillard
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Olivia Rousseau
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Gilles Blancho
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Clarisse Kerleau
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Nicolas Vince
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Magali Giral
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Sophie Limou
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.
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11
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Hirohama D, Abedini A, Moon S, Surapaneni A, Dillon ST, Vassalotti A, Liu H, Doke T, Martinez V, Md Dom Z, Karihaloo A, Palmer MB, Coresh J, Grams ME, Niewczas MA, Susztak K. Unbiased Human Kidney Tissue Proteomics Identifies Matrix Metalloproteinase 7 as a Kidney Disease Biomarker. J Am Soc Nephrol 2023; 34:1279-1291. [PMID: 37022120 PMCID: PMC10356165 DOI: 10.1681/asn.0000000000000141] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
SIGNIFICANCE STATEMENT Although gene expression changes have been characterized in human diabetic kidney disease (DKD), unbiased tissue proteomics information for this condition is lacking. The authors conducted an unbiased aptamer-based proteomic analysis of samples from patients with DKD and healthy controls, identifying proteins with levels that associate with kidney function (eGFR) or fibrosis, after adjusting for key covariates. Overall, tissue gene expression only modestly correlated with tissue protein levels. Kidney protein and RNA levels of matrix metalloproteinase 7 (MMP7) strongly correlated with fibrosis and with eGFR. Single-cell RNA sequencing indicated that kidney tubule cells are an important source of MMP7. Furthermore, plasma MMP7 levels predicted future kidney function decline. These findings identify kidney tissue MMP7 as a biomarker of fibrosis and blood MMP7 as a biomarker for future kidney function decline. BACKGROUND Diabetic kidney disease (DKD) is responsible for close to half of all ESKD cases. Although unbiased gene expression changes have been extensively characterized in human kidney tissue samples, unbiased protein-level information is not available. METHODS We collected human kidney samples from 23 individuals with DKD and ten healthy controls, gathered associated clinical and demographics information, and implemented histologic analysis. We performed unbiased proteomics using the SomaScan platform and quantified the level of 1305 proteins and analyzed gene expression levels by bulk RNA and single-cell RNA sequencing (scRNA-seq). We validated protein levels in a separate cohort of kidney tissue samples as well as in 11,030 blood samples. RESULTS Globally, human kidney transcript and protein levels showed only modest correlation. Our analysis identified 14 proteins with kidney tissue levels that correlated with eGFR and found that the levels of 152 proteins correlated with interstitial fibrosis. Of the identified proteins, matrix metalloprotease 7 (MMP7) showed the strongest association with both fibrosis and eGFR. The correlation between tissue MMP7 protein expression and kidney function was validated in external datasets. The levels of MMP7 RNA correlated with fibrosis in the primary and validation datasets. Findings from scRNA-seq pointed to proximal tubules, connecting tubules, and principal cells as likely cellular sources of increased tissue MMP7 expression. Furthermore, plasma MMP7 levels correlated not only with kidney function but also associated with prospective kidney function decline. CONCLUSIONS Our findings, which underscore the value of human kidney tissue proteomics analysis, identify kidney tissue MMP7 as a diagnostic marker of kidney fibrosis and blood MMP7 as a biomarker for future kidney function decline.
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Affiliation(s)
- Daigoro Hirohama
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amin Abedini
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Salina Moon
- Research Division, Joslin Diabetes Center, One Joslin Place, Boston, Massachusetts
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Simon T. Dillon
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Allison Vassalotti
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- School of Medicine, Tulane University, New Orleans, Louisiana
| | - Hongbo Liu
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tomohito Doke
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Victor Martinez
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zaipul Md Dom
- Research Division, Joslin Diabetes Center, One Joslin Place, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Anil Karihaloo
- Novo Nordisk Research Center Seattle Inc., Seattle, Washington
| | - Matthew B. Palmer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, New York University, New York, New York
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, New York University, New York, New York
| | - Monika A. Niewczas
- Research Division, Joslin Diabetes Center, One Joslin Place, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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12
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Schlosser P, Grams ME, Rhee EP. Proteomics: Progress and Promise of High-Throughput Proteomics in Chronic Kidney Disease. Mol Cell Proteomics 2023; 22:100550. [PMID: 37076045 PMCID: PMC10326701 DOI: 10.1016/j.mcpro.2023.100550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/20/2023] [Accepted: 03/28/2023] [Indexed: 04/21/2023] Open
Abstract
Current proteomic tools permit the high-throughput analysis of the blood proteome in large cohorts, including those enriched for chronic kidney disease (CKD) or its risk factors. To date, these studies have identified numerous proteins associated with cross-sectional measures of kidney function, as well as with the longitudinal risk of CKD progression. Representative signals that have emerged from the literature include an association between levels of testican-2 and favorable kidney prognosis and an association between levels of TNFRSF1A and TNFRSF1B and worse kidney prognosis. For these and other associations, however, understanding whether the proteins play a causal role in kidney disease pathogenesis remains a fundamental challenge, especially given the strong impact that kidney function can have on blood protein levels. Prior to investing in dedicated animal models or randomized trials, methods that leverage the availability of genotyping in epidemiologic cohorts-including Mendelian randomization, colocalization analyses, and proteome-wide association studies-can add evidence for causal inference in CKD proteomics research. In addition, integration of large-scale blood proteome analyses with urine and tissue proteomics, as well as improved assessment of posttranslational protein modifications (e.g., carbamylation), represent important future directions. Taken together, these approaches seek to translate progress in large-scale proteomic profiling into the promise of improved diagnostic tools and therapeutic target identification in kidney disease.
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Affiliation(s)
- Pascal Schlosser
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
| | - Morgan E Grams
- Division of Precision Medicine, Department of Medicine, New York University, New York, New York, USA
| | - Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
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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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Sandholm N, Dahlström EH, Groop PH. Genetic and epigenetic background of diabetic kidney disease. Front Endocrinol (Lausanne) 2023; 14:1163001. [PMID: 37324271 PMCID: PMC10262849 DOI: 10.3389/fendo.2023.1163001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Diabetic kidney disease (DKD) is a severe diabetic complication that affects up to half of the individuals with diabetes. Elevated blood glucose levels are a key underlying cause of DKD, but DKD is a complex multifactorial disease, which takes years to develop. Family studies have shown that inherited factors also contribute to the risk of the disease. During the last decade, genome-wide association studies (GWASs) have emerged as a powerful tool to identify genetic risk factors for DKD. In recent years, the GWASs have acquired larger number of participants, leading to increased statistical power to detect more genetic risk factors. In addition, whole-exome and whole-genome sequencing studies are emerging, aiming to identify rare genetic risk factors for DKD, as well as epigenome-wide association studies, investigating DNA methylation in relation to DKD. This article aims to review the identified genetic and epigenetic risk factors for DKD.
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Affiliation(s)
- Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emma H. Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
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15
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Han M, Moon S, Lee S, Kim K, An WJ, Ryu H, Kang E, Ahn JH, Sung HY, Park YS, Lee SE, Lee SH, Jeong KH, Ahn C, Kelly TN, Hsu JY, Feldman HI, Park SK, Oh KH. Novel Genetic Variants Associated with Chronic Kidney Disease Progression. J Am Soc Nephrol 2023; 34:857-875. [PMID: 36720675 PMCID: PMC10125649 DOI: 10.1681/asn.0000000000000066] [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: 03/16/2022] [Accepted: 12/11/2022] [Indexed: 02/02/2023] Open
Abstract
SIGNIFICANCE STATEMENT eGFR slope has been used as a surrogate outcome for progression of CKD. However, genetic markers associated with eGFR slope among patients with CKD were unknown. We aimed to identify genetic susceptibility loci associated with eGFR slope. A two-phase genome-wide association study identified single nucleotide polymorphisms (SNPs) in TPPP and FAT1-LINC02374 , and 22 of them were used to derive polygenic risk scores that mark the decline of eGFR by disrupting binding of nearby transcription factors. This work is the first to identify the impact of TPPP and FAT1-LINC02374 on CKD progression, providing predictive markers for the decline of eGFR in patients with CKD. BACKGROUND The incidence of CKD is associated with genetic factors. However, genetic markers associated with the progression of CKD have not been fully elucidated. METHODS We conducted a genome-wide association study among 1738 patients with CKD, mainly from the KoreaN cohort study for Outcomes in patients With CKD. The outcome was eGFR slope. We performed a replication study for discovered single nucleotide polymorphisms (SNPs) with P <10 -6 in 2498 patients with CKD from the Chronic Renal Insufficiency Cohort study. Several expression quantitative trait loci (eQTL) studies, pathway enrichment analyses, exploration of epigenetic architecture, and predicting disruption of transcription factor (TF) binding sites explored potential biological implications of the loci. We developed and evaluated the effect of polygenic risk scores (PRS) on incident CKD outcomes. RESULTS SNPs in two novel loci, TPPP and FAT1-LINC02374 , were replicated (rs59402340 in TPPP , Pdiscovery =7.11×10 -7 , PCRIC =8.13×10 -4 , Pmeta =7.23×10 -8 ; rs28629773 in FAT1-LINC02374 , Pdiscovery =6.08×10 -7 , PCRIC =4.33×10 -2 , Pmeta =1.87×10 -7 ). The eQTL studies revealed that the replicated SNPs regulated the expression level of nearby genes associated with kidney function. Furthermore, these SNPs were near gene enhancer regions and predicted to disrupt the binding of TFs. PRS based on the independently significant top 22 SNPs were significantly associated with CKD outcomes. CONCLUSIONS This study demonstrates that SNP markers in the TPPP and FAT1-LINC02374 loci could be predictive markers for the decline of eGFR in patients with CKD.
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Affiliation(s)
- Miyeun Han
- Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Sungji Moon
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sangjun Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Department of Biomedical Science, Seoul National University Graduate School, Seoul, Korea
| | - Kyungsik Kim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Department of Biomedical Science, Seoul National University Graduate School, Seoul, Korea
| | - Woo Ju An
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunjin Ryu
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eunjeong Kang
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, Korea
| | - Jung-Hyuck Ahn
- Department of Biochemistry, Ewha Womans University College of Medicine, Seoul, Korea
| | - Hye Youn Sung
- Department of Biochemistry, Ewha Womans University College of Medicine, Seoul, Korea
| | - Yong Seek Park
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Seung Eun Lee
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Sang-Ho Lee
- Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Kyung Hwan Jeong
- Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Curie Ahn
- Department of Internal Medicine, National Medical Center, Seoul, Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Tanika N. Kelly
- Department of Epidemiology, Tulane University, New Orleans, Louisiana
| | - Jesse Y. Hsu
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sue K. Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
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Douville NJ, Larach DB, Lewis A, Bastarache L, Pandit A, He J, Heung M, Mathis M, Wanderer JP, Kheterpal S, Surakka I, Kertai MD. Genetic predisposition may not improve prediction of cardiac surgery-associated acute kidney injury. Front Genet 2023; 14:1094908. [PMID: 37124606 PMCID: PMC10133500 DOI: 10.3389/fgene.2023.1094908] [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: 11/10/2022] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
Background: The recent integration of genomic data with electronic health records has enabled large scale genomic studies on a variety of perioperative complications, yet genome-wide association studies on acute kidney injury have been limited in size or confounded by composite outcomes. Genome-wide association studies can be leveraged to create a polygenic risk score which can then be integrated with traditional clinical risk factors to better predict postoperative complications, like acute kidney injury. Methods: Using integrated genetic data from two academic biorepositories, we conduct a genome-wide association study on cardiac surgery-associated acute kidney injury. Next, we develop a polygenic risk score and test the predictive utility within regressions controlling for age, gender, principal components, preoperative serum creatinine, and a range of patient, clinical, and procedural risk factors. Finally, we estimate additive variant heritability using genetic mixed models. Results: Among 1,014 qualifying procedures at Vanderbilt University Medical Center and 478 at Michigan Medicine, 348 (34.3%) and 121 (25.3%) developed AKI, respectively. No variants exceeded genome-wide significance (p < 5 × 10-8) threshold, however, six previously unreported variants exceeded the suggestive threshold (p < 1 × 10-6). Notable variants detected include: 1) rs74637005, located in the exonic region of NFU1 and 2) rs17438465, located between EVX1 and HIBADH. We failed to replicate variants from prior unbiased studies of post-surgical acute kidney injury. Polygenic risk was not significantly associated with post-surgical acute kidney injury in any of the models, however, case duration (aOR = 1.002, 95% CI 1.000-1.003, p = 0.013), diabetes mellitus (aOR = 2.025, 95% CI 1.320-3.103, p = 0.001), and valvular disease (aOR = 0.558, 95% CI 0.372-0.835, p = 0.005) were significant in the full model. Conclusion: Polygenic risk score was not significantly associated with cardiac surgery-associated acute kidney injury and acute kidney injury may have a low heritability in this population. These results suggest that susceptibility is only minimally influenced by baseline genetic predisposition and that clinical risk factors, some of which are modifiable, may play a more influential role in predicting this complication. The overall impact of genetics in overall risk for cardiac surgery-associated acute kidney injury may be small compared to clinical risk factors.
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Affiliation(s)
- Nicholas J. Douville
- Department of Anesthesiology, University of Michigan Health System, Ann Arbor, MI, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan Health System, Ann Arbor, MI, United States
- Michigan Integrated Center for Health Analytics and Medical Prediction, Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, United States
| | - Daniel B. Larach
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Adam Lewis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anita Pandit
- Center for Statistical Genetics and Precision Health Initiative, University of Michigan, Ann Arbor, MI, United States
| | - Jing He
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Michael Heung
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Michael Mathis
- Department of Anesthesiology, University of Michigan Health System, Ann Arbor, MI, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan Health System, Ann Arbor, MI, United States
- Michigan Integrated Center for Health Analytics and Medical Prediction, Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, United States
| | - Jonathan P. Wanderer
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Sachin Kheterpal
- Department of Anesthesiology, University of Michigan Health System, Ann Arbor, MI, United States
| | - Ida Surakka
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Miklos D. Kertai
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN, United States
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17
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Michalek DA, Onengut-Gumuscu S, Repaske DR, Rich SS. Precision Medicine in Type 1 Diabetes. J Indian Inst Sci 2023; 103:335-351. [PMID: 37538198 PMCID: PMC10393845 DOI: 10.1007/s41745-023-00356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/04/2023] [Indexed: 03/09/2023]
Abstract
Type 1 diabetes is a complex, chronic disease in which the insulin-producing beta cells in the pancreas are sufficiently altered or impaired to result in requirement of exogenous insulin for survival. The development of type 1 diabetes is thought to be an autoimmune process, in which an environmental (unknown) trigger initiates a T cell-mediated immune response in genetically susceptible individuals. The presence of islet autoantibodies in the blood are signs of type 1 diabetes development, and risk of progressing to clinical type 1 diabetes is correlated with the presence of multiple islet autoantibodies. Currently, a "staging" model of type 1 diabetes proposes discrete components consisting of normal blood glucose but at least two islet autoantibodies (Stage 1), abnormal blood glucose with at least two islet autoantibodies (Stage 2), and clinical diagnosis (Stage 3). While these stages may, in fact, not be discrete and vary by individual, the format suggests important applications of precision medicine to diagnosis, prevention, prognosis, treatment and monitoring. In this paper, applications of precision medicine in type 1 diabetes are discussed, with both opportunities and barriers to global implementation highlighted. Several groups have implemented components of precision medicine, yet the integration of the necessary steps to achieve both short- and long-term solutions will need to involve researchers, patients, families, and healthcare providers to fully impact and reduce the burden of type 1 diabetes.
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Affiliation(s)
- Dominika A. Michalek
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA USA
| | - David R. Repaske
- Division of Endocrinology, Department of Pediatrics, University of Virginia, Charlottesville, VA USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA USA
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18
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Liao LN, Li TC, Yeh CC, Li CI, Liu CS, Yang CW, Yang YF, Lin CH, Tsai FJ, Lin CC. Risk prediction of nephropathy by integrating clinical and genetic information among adult patients with type 2 diabetes. Acta Diabetol 2023; 60:413-424. [PMID: 36576562 DOI: 10.1007/s00592-022-02017-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 12/10/2022] [Indexed: 12/29/2022]
Abstract
AIMS Diabetic nephropathy (DN) is a major healthcare challenge. We developed and internally and externally validated a risk prediction model of DN by integrating clinical factors and SNPs from genes of multiple CKD-related pathways in the Han Chinese population. MATERIALS AND METHODS A total of 1526 patients with type 2 diabetes were randomly allocated into derivation (n = 1019) or validation (n = 507) sets. External validation was performed with 3899 participants from the Taiwan Biobank. We selected 66 SNPs identified from literature review for building our weighted genetic risk score (wGRS). The steps for prediction model development integrating clinical and genetic information were based on the Framingham Heart Study. RESULTS The AUROC (95% CI) for this DN prediction model with combined clinical factors and wGRS was 0.81 (0.78, 0.84) in the derivation set. Furthermore, by directly using the information of these 66 SNPs, our final prediction model had AUROC values of 0.85 (0.82, 0.87), 0.89 (0.86, 0.91), and 0.77 (0.74, 0.80) in the derivation, internal validation, and external validation sets, respectively. Under the combined model, the results with a cutoff point of 30% showed 70.91% sensitivity, 67.84% specificity, 51.54% positive predictive value, and 82.86% negative predictive value. CONCLUSIONS We developed and internally and externally validated a model with clinical factors and SNPs from genes of multiple CKD-related pathways to predict DN in Taiwan. This model can be used in clinical risk management practice as a screening tool to identify persons who are genetically predisposed to DN for early intervention and prevention.
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Affiliation(s)
- Li-Na Liao
- Department of Public Health, College of Public Health, China Medical University, Taichung, Taiwan, R.O.C
| | - Tsai-Chung Li
- Department of Public Health, College of Public Health, China Medical University, Taichung, Taiwan, R.O.C
- Department of Healthcare Administration, College of Medical and Health Science, Asia University, Taichung, Taiwan, R.O.C
| | - Chih-Ching Yeh
- Department of Public Health, College of Public Health, China Medical University, Taichung, Taiwan, R.O.C
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan, R.O.C
- Master Program in Applied Epidemiology, College of Public Health, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Chia-Ing Li
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
- School of Medicine, College of Medicine, China Medical University, No. 100, Sec. 1, Jingmao Rd., Beitun Dist., Taichung, 406040, Taiwan, R.O.C
| | - Chiu-Shong Liu
- School of Medicine, College of Medicine, China Medical University, No. 100, Sec. 1, Jingmao Rd., Beitun Dist., Taichung, 406040, Taiwan, R.O.C
- Department of Family Medicine, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Chuan-Wei Yang
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Ya-Fei Yang
- Department of Nephrology, Everan Hospital, Taichung, Taiwan, R.O.C
| | - Chih-Hsueh Lin
- School of Medicine, College of Medicine, China Medical University, No. 100, Sec. 1, Jingmao Rd., Beitun Dist., Taichung, 406040, Taiwan, R.O.C
- Department of Family Medicine, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Fuu-Jen Tsai
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, No. 100, Sec. 1, Jingmao Rd., Beitun Dist., Taichung, 406040, Taiwan, R.O.C..
- Human Genetic Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C..
| | - Cheng-Chieh Lin
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C..
- School of Medicine, College of Medicine, China Medical University, No. 100, Sec. 1, Jingmao Rd., Beitun Dist., Taichung, 406040, Taiwan, R.O.C..
- Department of Family Medicine, China Medical University Hospital, Taichung, Taiwan, R.O.C..
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19
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Steinbrenner I, Yu Z, Jin J, Schultheiss UT, Kotsis F, Grams ME, Coresh J, Wuttke M, Kronenberg F, Eckardt KU, Chatterjee N, Sekula P, Köttgen A. A polygenic score for reduced kidney function and adverse outcomes in a cohort with chronic kidney disease. Kidney Int 2023; 103:421-424. [PMID: 36481179 PMCID: PMC9868068 DOI: 10.1016/j.kint.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Inga Steinbrenner
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jin Jin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Department of Medicine IV-Nephrology and Primary Care, University of Freiburg, Freiburg, Germany
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Department of Medicine IV-Nephrology and Primary Care, University of Freiburg, Freiburg, Germany
| | - Morgan E Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA; Department of Medicine, New York University Grossman School of Medicine, New York, New York, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA; Department of Medicine, New York University Grossman School of Medicine, New York, New York, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Department of Medicine IV-Nephrology and Primary Care, University of Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
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20
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Mohammedi K, Marre M, Hadjadj S, Potier L, Velho G. Redox Genetic Risk Score and the Incidence of End-Stage Kidney Disease in People with Type 1 Diabetes. Cells 2022; 11:cells11244131. [PMID: 36552894 PMCID: PMC9777489 DOI: 10.3390/cells11244131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
End-stage kidney disease (ESKD) is a multifactorial condition influenced by genetic background, but the extent to which a genetic risk score (GRS) improves ESKD prediction is unknown. We built a redox GRS on the base of previous association studies (six polymorphisms from six redox genes) and tested its relationship with ESKD in three cohorts of people with type 1 diabetes. Among 1012 participants, ESKD (hemodialysis requirement, kidney transplantation, eGFR < 15 mL/min/1.73 m2) occurred in 105 (10.4%) during a 14-year follow-up. High redox GRS was associated with increased ESKD risk (adjusted HR for the upper versus the lowest GRS tertile: 2.60 (95% CI, 1.51-4.48), p = 0.001). Each additional risk-allele was associated with a 20% increased risk of ESKD (95% CI, 8-33, p < 0.0001). High GRS yielded a relevant population attributable fraction (30%), but only a marginal enhancement in c-statistics index (0.928 [0.903-0.954]) over clinical factors 0.921 (0.892-0.950), p = 0.04). This is the first report of an independent association between redox GRS and increased risk of ESKD in type 1 diabetes. Our results do not support the use of this GRS in clinical practice but provide new insights into the involvement of oxidative stress genetic factors in ESKD risk in type 1 diabetes.
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Affiliation(s)
- Kamel Mohammedi
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France
- Population Health Research Institute, McMaster University and Hamilton Health Sciences, Hamilton, ON L8S 4L8, Canada
- Correspondence:
| | - Michel Marre
- Institut Necker-Enfants Malades, INSERM, Université de Paris, 75013 Paris, France
- Clinique Ambroise Paré, 92200 Neuilly-sur-Seine, France
| | - Samy Hadjadj
- Institut du Thorax, INSERM, CNRS, UNIV Nantes, CHU Nantes, 44109 Nantes, France
| | - Louis Potier
- Institut Necker-Enfants Malades, INSERM, Université de Paris, 75013 Paris, France
- Clinique Ambroise Paré, 92200 Neuilly-sur-Seine, France
- Service d’Endocrinologie Diabétologie Nutrition, Hôpital Bichat, AP-HP, 75013 Paris, France
| | - Gilberto Velho
- Institut Necker-Enfants Malades, INSERM, Université de Paris, 75013 Paris, France
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21
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Ruilope LM, Ortiz A, Lucia A, Miranda B, Alvarez-Llamas G, Barderas MG, Volpe M, Ruiz-Hurtado G, Pitt B. Prevention of cardiorenal damage: importance of albuminuria. Eur Heart J 2022; 44:1112-1123. [PMID: 36477861 DOI: 10.1093/eurheartj/ehac683] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/20/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
Chronic kidney disease (CKD) is projected to become a leading global cause of death by 2040, and its early detection is critical for effective and timely management. The current definition of CKD identifies only advanced stages, when kidney injury has already destroyed >50% of functioning kidney mass as reflected by an estimated glomerular filtration rate <60 mL/min/1.73 m2 or a urinary albumin/creatinine ratio >six-fold higher than physiological levels (i.e. > 30 mg/g). An elevated urinary albumin-excretion rate is a known early predictor of future cardiovascular events. There is thus a ‘blind spot’ in the detection of CKD, when kidney injury is present but is undetectable by current diagnostic criteria, and no intervention is made before renal and cardiovascular damage occurs. The present review discusses the CKD ‘blind spot’ concept and how it may facilitate a holistic approach to CKD and cardiovascular disease prevention and implement the call for albuminuria screening implicit in current guidelines. Cardiorenal risk associated with albuminuria in the high-normal range, novel genetic and biochemical markers of elevated cardiorenal risk, and the role of heart and kidney protective drugs evaluated in recent clinical trials are also discussed. As albuminuria is a major risk factor for cardiovascular and renal disease, starting from levels not yet considered in the definition of CKD, the implementation of opportunistic or systematic albuminuria screening and therapy, possibly complemented with novel early biomarkers, has the potential to improve cardiorenal outcomes and mitigate the dismal 2040 projections for CKD and related cardiovascular burden.
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Affiliation(s)
- Luis M Ruilope
- Cardiorenal Translational Laboratory, Institute of Research Imas12, Hospital Universitario , 12 de Octubre, Avenida de Córdoba s/n , Spain
- CIBER-CV, Hospital Universitario , Av. de Córdoba s/n, 28041, Madrid , Spain
- Faculty of Sport Sciences, Universidad Europea de Madrid , Tajo, s/n, 28670 Villaviciosa de Odón, Madrid , Spain
| | - Alberto Ortiz
- IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid , Av. de los Reyes Católicos, 2, 28040 Madrid , Spain
- RICORS2040, Hospital Universitario Fundación Jiménez Díaz , Madrid , Spain
| | - Alejandro Lucia
- Faculty of Sport Sciences, Universidad Europea de Madrid , Tajo, s/n, 28670 Villaviciosa de Odón, Madrid , Spain
| | - Blanca Miranda
- Fundación Renal Íñigo Álvarez de Toledo , José Abascal, 42, 28003 Madrid , Spain
| | - Gloria Alvarez-Llamas
- IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid , Av. de los Reyes Católicos, 2, 28040 Madrid , Spain
- RICORS2040, Hospital Universitario Fundación Jiménez Díaz , Madrid , Spain
| | - Maria G Barderas
- Department of Vascular Physiopathology, Hospital Nacional de Parapléjicos (HNP), SESCAM , FINCA DE, Carr. de la Peraleda, S/N, 45004 Toledo , Spain
| | - Massimo Volpe
- Cardiology, Department of Clinical and Molecular Medicine, Sapienza University of Rome and IRCCS San Raffaele Rome , Sant'Andrea Hospital, Rome , Italy
| | - Gema Ruiz-Hurtado
- Cardiorenal Translational Laboratory, Institute of Research Imas12, Hospital Universitario , 12 de Octubre, Avenida de Córdoba s/n , Spain
- CIBER-CV, Hospital Universitario , Av. de Córdoba s/n, 28041, Madrid , Spain
| | - Bertram Pitt
- Division of Cardiology, University of Michigan School of Medicine , Ann Arbor, MI , USA
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22
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Wang J, Li D, Sun Y, Tian Y. Air pollutants, genetic factors, and risk of chronic kidney disease: Findings from the UK Biobank. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114219. [PMID: 36306611 DOI: 10.1016/j.ecoenv.2022.114219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Experiment studies have suggested the emerging role of air pollutants in chronic kidney disease (CKD). However, only a few population studies conducted in Asia and North America have assessed their association, and the conclusions remained controversial. This study aims to investigate the effect of air pollutants exposure on CKD in the European population and first explores the modification effect of genetic risk on this association. METHODS 458,968 participants from the UK Biobank were included in this study. Cox proportional hazards model was used to assess the associations of air pollutants (PM2.5, PM10, NO2, and NOx) with incident CKD. A genetic risk score of 53 single nucleotide polymorphisms was constructed to represent the genetic susceptibility to CKD. To assess the interaction effect between air pollutants and the genetic risk, we added a multiplicative interaction term and did a stratified analysis. RESULTS During a median follow-up of 11.7 years, 16,637 incidents of CKD were identified. We observed positive associations between air pollutants exposure and CKD risk with the HRs for CKD were 1.09 (1.07, 1.11), 1.08 (1.06, 1.10), 1.05 (1.03, 1.07), 1.06 (1.04, 1.08) with per IQR (interquartile range) increment in PM2.5, PM10, NO2, and NOx, respectively. Stratified analysis showed that the associations between air pollutants and CKD were modest and marginal in the high genetic risk population (P > 0.05), while the associations were statistically significant in the low and intermediate genetic risk groups. CONCLUSIONS Our study indicated that exposure to various air pollutants, including PM2.5, PM10, NO2, and NOx, was associated with an elevated risk of CKD. This finding provide evidence that formulating strategies to improve air quality can be helpful to reduce the burden of CKD.
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Affiliation(s)
- Jianing Wang
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dankang Li
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yaohua Tian
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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23
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Yu Z, Wuttke M. Including APOL1 alleles and ancestry adjustments improve a genome-wide polygenic CKD score. Kidney Int 2022; 102:954-955. [PMID: 35985372 PMCID: PMC10018747 DOI: 10.1016/j.kint.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Zhi Yu
- Program of Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Masschusetts, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany.
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24
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Gulamali FF, Sawant AS, Nadkarni GN. Machine learning for risk stratification in kidney disease. Curr Opin Nephrol Hypertens 2022; 31:548-552. [PMID: 36004937 PMCID: PMC9529795 DOI: 10.1097/mnh.0000000000000832] [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] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW Risk stratification for chronic kidney is becoming increasingly important as a clinical tool for both treatment and prevention measures. The goal of this review is to identify how machine learning tools contribute and facilitate risk stratification in the clinical setting. RECENT FINDINGS The two key machine learning paradigms to predictively stratify kidney disease risk are genomics-based and electronic health record based approaches. These methods can provide both quantitative information such as relative risk and qualitative information such as characterizing risk by subphenotype. SUMMARY The four key methods to stratify chronic kidney disease risk are genomics, multiomics, supervised and unsupervised machine learning methods. Polygenic risk scores utilize whole genome sequencing data to generate an individual's relative risk compared with the population. Multiomic methods integrate information from multiple biomarkers to generate trajectories and prognostic different outcomes. Supervised machine learning methods can directly utilize the growing compendia of electronic health records such as laboratory results and notes to generate direct risk predictions, while unsupervised machine learning methods can cluster individuals with chronic kidney disease into subphenotypes with differing approaches to care.
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25
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Polesel M, Kaminska M, Haenni D, Bugarski M, Schuh C, Jankovic N, Kaech A, Mateos JM, Berquez M, Hall AM. Spatiotemporal organisation of protein processing in the kidney. Nat Commun 2022; 13:5732. [PMID: 36175561 PMCID: PMC9522658 DOI: 10.1038/s41467-022-33469-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
The kidney regulates plasma protein levels by eliminating them from the circulation. Proteins filtered by glomeruli are endocytosed and degraded in the proximal tubule and defects in this process result in tubular proteinuria, an important clinical biomarker. However, the spatiotemporal organization of renal protein metabolism in vivo was previously unclear. Here, using functional probes and intravital microscopy, we track the fate of filtered proteins in real time in living mice, and map specialized processing to tubular structures with singular value decomposition analysis and three-dimensional electron microscopy. We reveal that degradation of proteins requires sequential, coordinated activity of distinct tubular sub-segments, each adapted to specific tasks. Moreover, we leverage this approach to pinpoint the nature of endo-lysosomal disorders in disease models, and show that compensatory uptake in later regions of the proximal tubule limits urinary protein loss. This means that measurement of proteinuria likely underestimates severity of endocytotic defects in patients. Polesel et al. visualize plasma protein filtration, uptake and metabolism in the kidneys of living mice in real-time. They reveal coordinated activity of different specialized tubular segments, with major compensatory adaptations occurring in disease states.
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Affiliation(s)
| | - Monika Kaminska
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Dominik Haenni
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Milica Bugarski
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Claus Schuh
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Nevena Jankovic
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Jose M Mateos
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Marine Berquez
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Andrew M Hall
- Institute of Anatomy, University of Zurich, Zurich, Switzerland. .,Department of Nephrology, University Hospital Zurich, Zurich, Switzerland.
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26
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A polygenic score predicts CKD across ancestries. Nat Rev Nephrol 2022; 18:681-682. [PMID: 35953653 DOI: 10.1038/s41581-022-00622-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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UMOD and the architecture of kidney disease. Pflugers Arch 2022; 474:771-781. [PMID: 35881244 PMCID: PMC9338900 DOI: 10.1007/s00424-022-02733-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 12/17/2022]
Abstract
The identification of genetic factors associated with the risk, onset, and progression of kidney disease has the potential to provide mechanistic insights and therapeutic perspectives. In less than two decades, technological advances yielded a trove of information on the genetic architecture of chronic kidney disease. The spectrum of genetic influence ranges from (ultra)rare variants with large effect size, involved in Mendelian diseases, to common variants, often non-coding and with small effect size, which contribute to polygenic diseases. Here, we review the paradigm of UMOD, the gene coding for uromodulin, to illustrate how a kidney-specific protein of major physiological importance is involved in a spectrum of kidney disorders. This new field of investigation illustrates the importance of genetic variation in the pathogenesis and prognosis of disease, with therapeutic implications.
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28
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Khan A, Turchin MC, Patki A, Srinivasasainagendra V, Shang N, Nadukuru R, Jones AC, Malolepsza E, Dikilitas O, Kullo IJ, Schaid DJ, Karlson E, Ge T, Meigs JB, Smoller JW, Lange C, Crosslin DR, Jarvik GP, Bhatraju PK, Hellwege JN, Chandler P, Torvik LR, Fedotov A, Liu C, Kachulis C, Lennon N, Abul-Husn NS, Cho JH, Ionita-Laza I, Gharavi AG, Chung WK, Hripcsak G, Weng C, Nadkarni G, Irvin MR, Tiwari HK, Kenny EE, Limdi NA, Kiryluk K. Genome-wide polygenic score to predict chronic kidney disease across ancestries. Nat Med 2022; 28:1412-1420. [PMID: 35710995 PMCID: PMC9329233 DOI: 10.1038/s41591-022-01869-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/11/2022] [Indexed: 01/03/2023]
Abstract
Chronic kidney disease (CKD) is a common complex condition associated with high morbidity and mortality. Polygenic prediction could enhance CKD screening and prevention; however, this approach has not been optimized for ancestrally diverse populations. By combining APOL1 risk genotypes with genome-wide association studies (GWAS) of kidney function, we designed, optimized and validated a genome-wide polygenic score (GPS) for CKD. The new GPS was tested in 15 independent cohorts, including 3 cohorts of European ancestry (n = 97,050), 6 cohorts of African ancestry (n = 14,544), 4 cohorts of Asian ancestry (n = 8,625) and 2 admixed Latinx cohorts (n = 3,625). We demonstrated score transferability with reproducible performance across all tested cohorts. The top 2% of the GPS was associated with nearly threefold increased risk of CKD across ancestries. In African ancestry cohorts, the APOL1 risk genotype and polygenic component of the GPS had additive effects on the risk of CKD.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Michael C Turchin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Rajiv Nadukuru
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alana C Jones
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tian Ge
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jordan W Smoller
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jacklyn N Hellwege
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paulette Chandler
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura Rasmussen Torvik
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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29
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Affiliation(s)
- Daigoro Hirohama
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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