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Siew ED, Hellwege JN, Hung AM, Birkelo BC, Vincz AJ, Parr SK, Denton J, Greevy RA, Robinson-Cohen C, Liu H, Susztak K, Matheny ME, Velez Edwards DR. Genome-wide association study of hospitalized patients and acute kidney injury. Kidney Int 2024; 106:291-301. [PMID: 38797326 PMCID: PMC11260539 DOI: 10.1016/j.kint.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 03/15/2024] [Accepted: 04/05/2024] [Indexed: 05/29/2024]
Abstract
Acute kidney injury (AKI) is a common and devastating complication of hospitalization. Here, we identified genetic loci associated with AKI in patients hospitalized between 2002-2019 in the Million Veteran Program and data from Vanderbilt University Medical Center's BioVU. AKI was defined as meeting a modified KDIGO Stage 1 or more for two or more consecutive days or kidney replacement therapy. Control individuals were required to have one or more qualifying hospitalizations without AKI and no evidence of AKI during any other observed hospitalizations. Genome-wide association studies (GWAS), stratified by race, adjusting for sex, age, baseline estimated glomerular filtration rate (eGFR), and the top ten principal components of ancestry were conducted. Results were meta-analyzed using fixed effects models. In total, there were 54,488 patients with AKI and 138,051 non-AKI individuals included in the study. Two novel loci reached genome-wide significance in the meta-analysis: rs11642015 near the FTO locus on chromosome 16 (obesity traits) (odds ratio 1.07 (95% confidence interval, 1.05-1.09)) and rs4859682 near the SHROOM3 locus on chromosome 4 (glomerular filtration barrier integrity) (odds ratio 0.95 (95% confidence interval, 0.93-0.96)). These loci colocalized with previous studies of kidney function, and genetic correlation indicated significant shared genetic architecture between AKI and eGFR. Notably, the association at the FTO locus was attenuated after adjustment for BMI and diabetes, suggesting that this association may be partially driven by obesity. Both FTO and the SHROOM3 loci showed nominal evidence of replication from diagnostic-code-based summary statistics from UK Biobank, FinnGen, and Biobank Japan. Thus, our large GWA meta-analysis found two loci significantly associated with AKI suggesting genetics may explain some risk for AKI.
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Affiliation(s)
- Edward D Siew
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease (VCKD) and Integrated Program for AKI Research (VIP-AKI), Nashville, Tennessee, USA.
| | - Jacklyn N Hellwege
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Adriana M Hung
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease (VCKD) and Integrated Program for AKI Research (VIP-AKI), Nashville, Tennessee, USA
| | - Bethany C Birkelo
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease (VCKD) and Integrated Program for AKI Research (VIP-AKI), Nashville, Tennessee, USA
| | - Andrew J Vincz
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease (VCKD) and Integrated Program for AKI Research (VIP-AKI), Nashville, Tennessee, USA
| | - Sharidan K Parr
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease (VCKD) and Integrated Program for AKI Research (VIP-AKI), Nashville, Tennessee, USA
| | - Jason Denton
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA
| | - Robert A Greevy
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cassianne Robinson-Cohen
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Center for Kidney Disease (VCKD) and Integrated Program for AKI Research (VIP-AKI), Nashville, Tennessee, USA
| | - Hongbo Liu
- Division of Renal Electrolyte and Hypertension, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA; Philadelphia Veterans Affairs Medical Center, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Division of Renal Electrolyte and Hypertension, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA; Philadelphia Veterans Affairs Medical Center, Philadelphia, Pennsylvania, USA
| | - Michael E Matheny
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Digna R Velez Edwards
- Tennessee Valley Health Systems, Nashville Veterans Affairs, Nashville, Tennessee, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Si S, Liu H, Xu L, Zhan S. Identification of novel therapeutic targets for chronic kidney disease and kidney function by integrating multi-omics proteome with transcriptome. Genome Med 2024; 16:84. [PMID: 38898508 PMCID: PMC11186236 DOI: 10.1186/s13073-024-01356-x] [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: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a progressive disease for which there is no effective cure. We aimed to identify potential drug targets for CKD and kidney function by integrating plasma proteome and transcriptome. METHODS We designed a comprehensive analysis pipeline involving two-sample Mendelian randomization (MR) (for proteins), summary-based MR (SMR) (for mRNA), and colocalization (for coding genes) to identify potential multi-omics biomarkers for CKD and combined the protein-protein interaction, Gene Ontology (GO), and single-cell annotation to explore the potential biological roles. The outcomes included CKD, extensive kidney function phenotypes, and different CKD clinical types (IgA nephropathy, chronic glomerulonephritis, chronic tubulointerstitial nephritis, membranous nephropathy, nephrotic syndrome, and diabetic nephropathy). RESULTS Leveraging pQTLs of 3032 proteins from 3 large-scale GWASs and corresponding blood- and tissue-specific eQTLs, we identified 32 proteins associated with CKD, which were validated across diverse CKD datasets, kidney function indicators, and clinical types. Notably, 12 proteins with prior MR support, including fibroblast growth factor 5 (FGF5), isopentenyl-diphosphate delta-isomerase 2 (IDI2), inhibin beta C chain (INHBC), butyrophilin subfamily 3 member A2 (BTN3A2), BTN3A3, uromodulin (UMOD), complement component 4A (C4a), C4b, centrosomal protein of 170 kDa (CEP170), serologically defined colon cancer antigen 8 (SDCCAG8), MHC class I polypeptide-related sequence B (MICB), and liver-expressed antimicrobial peptide 2 (LEAP2), were confirmed. To our knowledge, 20 novel causal proteins have not been previously reported. Five novel proteins, namely, GCKR (OR 1.17, 95% CI 1.10-1.24), IGFBP-5 (OR 0.43, 95% CI 0.29-0.62), sRAGE (OR 1.14, 95% CI 1.07-1.22), GNPTG (OR 0.90, 95% CI 0.86-0.95), and YOD1 (OR 1.39, 95% CI 1.18-1.64,) passed the MR, SMR, and colocalization analysis. The other 15 proteins were also candidate targets (GATM, AIF1L, DQA2, PFKFB2, NFATC1, activin AC, Apo A-IV, MFAP4, DJC10, C2CD2L, TCEA2, HLA-E, PLD3, AIF1, and GMPR1). These proteins interact with each other, and their coding genes were mainly enrichment in immunity-related pathways or presented specificity across tissues, kidney-related tissue cells, and kidney single cells. CONCLUSIONS Our integrated analysis of plasma proteome and transcriptome data identifies 32 potential therapeutic targets for CKD, kidney function, and specific CKD clinical types, offering potential targets for the development of novel immunotherapies, combination therapies, or targeted interventions.
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Affiliation(s)
- Shucheng Si
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Hongyan Liu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Lu Xu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Siyan Zhan
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China.
- Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
- Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
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Lanktree MB, Collister D, Pigyere M, Mazzetti A, Paré G, Walsh M. Proteome-Wide Changes in Blood Biomarkers During Hemodialysis. Kidney Int Rep 2024; 9:177-181. [PMID: 38312796 PMCID: PMC10831367 DOI: 10.1016/j.ekir.2023.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 02/06/2024] Open
Affiliation(s)
- Matthew B. Lanktree
- Population Health Research Institute, Hamilton, Ontario, Canada
- Division of Nephrology, Department of Medicine, McMaster University and St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - David Collister
- Division of Nephrology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marie Pigyere
- Population Health Research Institute, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Andrea Mazzetti
- Population Health Research Institute, Hamilton, Ontario, Canada
- Division of Nephrology, Department of Medicine, McMaster University and St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Guillaume Paré
- Population Health Research Institute, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael Walsh
- Population Health Research Institute, Hamilton, Ontario, Canada
- Division of Nephrology, Department of Medicine, McMaster University and St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
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Schlosser P. Advancing proteomics in nephrology: unraveling causal pathways and therapeutic targets. Kidney Int 2023; 104:1059-1061. [PMID: 37981427 DOI: 10.1016/j.kint.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/03/2023] [Indexed: 11/21/2023]
Abstract
Proteomics has illuminated disease pathophysiology, unearthed novel biomarkers, and bolstered risk assessment strategies. In nephrology, observational analyses unveil biomarkers associated with adverse outcomes, whereas genetics offer insights into causal pathways. Mendelian randomization offers the potential to link the two, uncovering causal relationships between biomarkers and kidney function. Lanktree et al. demonstrate Mendelian randomization's utility in identifying additional proteins affecting kidney function and kidney disease progression.
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Affiliation(s)
- Pascal Schlosser
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.
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