1
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Kim T, Rhee EP. Aptamer-Based Proteomics in CKD. Am J Kidney Dis 2024; 83:825-828. [PMID: 38281681 DOI: 10.1053/j.ajkd.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/30/2024]
Affiliation(s)
- Taesoo Kim
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Eugene P Rhee
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
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2
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Chen Z, Satake E, Pezzolesi MG, Md Dom ZI, Stucki D, Kobayashi H, Syreeni A, Johnson AT, Wu X, Dahlström EH, King JB, Groop PH, Rich SS, Sandholm N, Krolewski AS, Natarajan R. Integrated analysis of blood DNA methylation, genetic variants, circulating proteins, microRNAs, and kidney failure in type 1 diabetes. Sci Transl Med 2024; 16:eadj3385. [PMID: 38776390 DOI: 10.1126/scitranslmed.adj3385] [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: 06/28/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Variation in DNA methylation (DNAmet) in white blood cells and other cells/tissues has been implicated in the etiology of progressive diabetic kidney disease (DKD). However, the specific mechanisms linking DNAmet variation in blood cells with risk of kidney failure (KF) and utility of measuring blood cell DNAmet in personalized medicine are not clear. We measured blood cell DNAmet in 277 individuals with type 1 diabetes and DKD using Illumina EPIC arrays; 51% of the cohort developed KF during 7 to 20 years of follow-up. Our epigenome-wide analysis identified DNAmet at 17 CpGs (5'-cytosine-phosphate-guanine-3' loci) associated with risk of KF independent of major clinical risk factors. DNAmet at these KF-associated CpGs remained stable over a median period of 4.7 years. Furthermore, DNAmet variations at seven KF-associated CpGs were strongly associated with multiple genetic variants at seven genomic regions, suggesting a strong genetic influence on DNAmet. The effects of DNAmet variations at the KF-associated CpGs on risk of KF were partially mediated by multiple KF-associated circulating proteins and KF-associated circulating miRNAs. A prediction model for risk of KF was developed by adding blood cell DNAmet at eight selected KF-associated CpGs to the clinical model. This updated model significantly improved prediction performance (c-statistic = 0.93) versus the clinical model (c-statistic = 0.85) at P = 6.62 × 10-14. In conclusion, our multiomics study provides insights into mechanisms through which variation of DNAmet may affect KF development and shows that blood cell DNAmet at certain CpGs can improve risk prediction for KF in T1D.
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Affiliation(s)
- Zhuo Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Eiichiro Satake
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Marcus G Pezzolesi
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Zaipul I Md Dom
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Devorah Stucki
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Hiroki Kobayashi
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
- Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, Tokyo, Japan
| | - Anna Syreeni
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Adam T Johnson
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Xiwei Wu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Emma H Dahlström
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Jaxon B King
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Per-Henrik Groop
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Stephen S Rich
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Niina Sandholm
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Andrzej S Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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3
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Schlosser P, Surapaneni AL, Borisov O, Schmidt IM, Zhou L, Anderson A, Deo R, Dubin R, Ganz P, He J, Kimmel PL, Li H, Nelson RG, Porter AC, Rahman M, Rincon-Choles H, Shah V, Unruh ML, Vasan RS, Zheng Z, Feldman HI, Waikar SS, Köttgen A, Rhee EP, Coresh J, Grams ME. Association of Integrated Proteomic and Metabolomic Modules with Risk of Kidney Disease Progression. J Am Soc Nephrol 2024:00001751-990000000-00281. [PMID: 38640019 DOI: 10.1681/asn.0000000000000343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/01/2024] [Indexed: 04/21/2024] Open
Abstract
Key Points
Integrated analysis of proteome and metabolome identifies modules associated with CKD progression and kidney failure.Ephrin transmembrane proteins and podocyte-expressed CRIM1 and NPNT emerged as central components and warrant experimental and clinical investigation.
Background
Proteins and metabolites play crucial roles in various biological functions and are frequently interconnected through enzymatic or transport processes.
Methods
We present an integrated analysis of 4091 proteins and 630 metabolites in the Chronic Renal Insufficiency Cohort study (N=1708; average follow-up for kidney failure, 9.5 years, with 537 events). Proteins and metabolites were integrated using an unsupervised clustering method, and we assessed associations between clusters and CKD progression and kidney failure using Cox proportional hazards models. Analyses were adjusted for demographics and risk factors, including the eGFR and urine protein–creatinine ratio. Associations were identified in a discovery sample (random two thirds, n=1139) and then evaluated in a replication sample (one third, n=569).
Results
We identified 139 modules of correlated proteins and metabolites, which were represented by their principal components. Modules and principal component loadings were projected onto the replication sample, which demonstrated a consistent network structure. Two modules, representing a total of 236 proteins and 82 metabolites, were robustly associated with both CKD progression and kidney failure in both discovery and validation samples. Using gene set enrichment, several transmembrane-related terms were identified as overrepresented in these modules. Transmembrane–ephrin receptor activity displayed the largest odds (odds ratio=13.2, P value = 5.5×10−5). A module containing CRIM1 and NPNT expressed in podocytes demonstrated particularly strong associations with kidney failure (P value = 2.6×10−5).
Conclusions
This study demonstrates that integration of the proteome and metabolome can identify functions of pathophysiologic importance in kidney disease.
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Affiliation(s)
- Pascal Schlosser
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Institute of Genetic Epidemiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Aditya L Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, New York
| | - Oleg Borisov
- Institute of Genetic Epidemiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Insa M Schmidt
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Amanda Anderson
- Department of Epidemiology, Tulane University, New Orleans, Louisiana
| | - Rajat Deo
- Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ruth Dubin
- Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peter Ganz
- Division of Cardiology, University of California, San Francisco, San Francisco, California
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, Louisiana
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert G Nelson
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
| | - Anna C Porter
- Renal Service, Wellington Regional Hospital, Wellington, New Zealand
| | - Mahboob Rahman
- Department of Kidney Medicine, Cleveland Clinic Foundation, Cleveland, Ohio
| | | | - Vallabh Shah
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Mark L Unruh
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Ramachandran S Vasan
- University of Texas Health Sciences Center, San Antonio, Texas
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harold I Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Institute of Genetic Epidemiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Optimal Aging Institute, Departments of Population Health and Medicine, NYU Grossman School of Medicine, 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, NYU Langone Health, New York, New York
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4
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Murakoshi M, Kamei N, Suzuki Y, Kubota M, Sanuki M, Tashiro H, Iwasawa T, Kato K, Tanaka M, Furuhashi M, Gohda T. Circulating tumor necrosis factor-related biomarkers predict kidney function decline in Japanese patients with diabetes: An observational cohort study. Diabetes Res Clin Pract 2023; 206:111017. [PMID: 37972856 DOI: 10.1016/j.diabres.2023.111017] [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: 09/15/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
AIMS Tumor necrosis factor (TNF) receptors (TNFRs: TNFR1 and, TNFR2) are reportedly associated with chronic kidney disease (CKD) progression chiefly in Caucasian patients with diabetes. We assessed the prognostic value of TNF-related biomarkers for CKD progression in Japanese patients with diabetes. METHODS We estimated TNF-related biomarkers using an enzyme-linked immunosorbent assay in 640 patients with diabetes. Cox proportional hazards analysis was performed to estimate hazard ratios (HRs) per one standard deviation (SD) increase in a log-transformed biomarker. The kidney and the composite outcome were defined as a 30% reduction in estimated glomerular filtration rate (eGFR) from baseline, and kidney outcome plus death before kidney outcome, respectively. RESULTS During the median follow-up of 5.4 years, 75 (11.7%) patients reached the kidney outcome and 37 (5.8%) died before reaching the kidney outcome. Each SD increase in baseline circulating TNFR1, TNFR2, and ephrin type-A receptor 2 (EphA2) was associated with a higher risk of the kidney outcome independently from baseline eGFR and urine albumin-to-creatinine ratio. However, circulating osteoprotegerin was associated with the composite outcome only. CONCLUSIONS Elevated TNFR1, TNFR2, and EphA2 were associated with both kidney and composite outcomes in Japanese patients with diabetes.
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Affiliation(s)
- Maki Murakoshi
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Nozomu Kamei
- Department of Endocrinology and Metabolism, Hiroshima Red Cross Hospital & Atomic-bomb Survivors Hospital, Hiroshima, Japan; Institute for Clinical Research, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Yusuke Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Mitsunobu Kubota
- Department of Endocrinology and Diabetology, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Michiyoshi Sanuki
- Institute for Clinical Research, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Hirotaka Tashiro
- Department of Surgery, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Takumi Iwasawa
- Institute of Life Innovation Studies, Toyo University, Tokyo, Japan
| | - Kazunori Kato
- Institute of Life Innovation Studies, Toyo University, Tokyo, Japan
| | - Marenao Tanaka
- Department of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masato Furuhashi
- Department of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tomohito Gohda
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan.
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5
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van Zonneveld AJ, Zhao Q, Rotmans JI, Bijkerk R. Circulating non-coding RNAs in chronic kidney disease and its complications. Nat Rev Nephrol 2023; 19:573-586. [PMID: 37286733 DOI: 10.1038/s41581-023-00725-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/09/2023]
Abstract
Post-transcriptional regulation by non-coding RNAs (ncRNAs) can modulate the expression of genes involved in kidney physiology and disease. A large variety of ncRNA species exist, including microRNAs, long non-coding RNAs, piwi-interacting RNAs, small nucleolar RNAs, circular RNAs and yRNAs. Despite early assumptions that some of these species may exist as by-products of cell or tissue injury, a growing body of literature suggests that these ncRNAs are functional and participate in a variety of processes. Although they function intracellularly, ncRNAs are also present in the circulation, where they are carried by extracellular vesicles, ribonucleoprotein complexes or lipoprotein complexes such as HDL. These systemic, circulating ncRNAs are derived from specific cell types and can be directly transferred to a variety of cells, including endothelial cells of the vasculature and virtually any cell type in the kidney, thereby affecting the function of the host cell and/or its response to injury. Moreover, chronic kidney disease itself, as well as injury states associated with transplantation and allograft dysfunction, is associated with a shift in the distribution of circulating ncRNAs. These findings may provide opportunities for the identification of biomarkers with which to monitor disease progression and/or the development of therapeutic interventions.
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Affiliation(s)
- Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Qiao Zhao
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Joris I Rotmans
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands.
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands.
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6
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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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7
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Kiernan E, Surapaneni A, Zhou L, Schlosser P, Walker KA, Rhee EP, Ballantyne CM, Deo R, Dubin RF, Ganz P, Coresh J, Grams ME. Alterations in the Circulating Proteome Associated with Albuminuria. J Am Soc Nephrol 2023; 34:1078-1089. [PMID: 36890639 PMCID: PMC10278823 DOI: 10.1681/asn.0000000000000108] [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: 09/08/2022] [Accepted: 02/05/2023] [Indexed: 03/10/2023] Open
Abstract
SIGNIFICANCE STATEMENT We describe circulating proteins associated with albuminuria in a population of African American Study of Kidney Disease and Hypertension with CKD (AASK) using the largest proteomic platform to date: nearly 7000 circulating proteins, representing approximately 2000 new targets. Findings were replicated in a subset of a general population cohort with kidney disease (ARIC) and a population with CKD Chronic Renal Insufficiency Cohort (CRIC). In cross-sectional analysis, 104 proteins were significantly associated with albuminuria in the Black group, of which 67 of 77 available proteins were replicated in ARIC and 68 of 71 available proteins in CRIC. LMAN2, TNFSFR1B, and members of the ephrin superfamily had the strongest associations. Pathway analysis also demonstrated enrichment of ephrin family proteins. BACKGROUND Proteomic techniques have facilitated understanding of pathways that mediate decline in GFR. Albuminuria is a key component of CKD diagnosis, staging, and prognosis but has been less studied than GFR. We sought to investigate circulating proteins associated with higher albuminuria. METHODS We evaluated the cross-sectional associations of the blood proteome with albuminuria and longitudinally with doubling of albuminuria in the African American Study of Kidney Disease and Hypertension (AASK; 38% female; mean GFR 46; median urine protein-to-creatinine ratio 81 mg/g; n =703) and replicated in two external cohorts: a subset of the Atherosclerosis Risk in Communities (ARIC) study with CKD and the Chronic Renal Insufficiency Cohort (CRIC). RESULTS In cross-sectional analysis, 104 proteins were significantly associated with albuminuria in AASK, of which 67 of 77 available proteins were replicated in ARIC and 68 of 71 available proteins in CRIC. Proteins with the strongest associations included LMAN2, TNFSFR1B, and members of the ephrin superfamily. Pathway analysis also demonstrated enrichment of ephrin family proteins. Five proteins were significantly associated with worsening albuminuria in AASK, including LMAN2 and EFNA4, which were replicated in ARIC and CRIC. CONCLUSIONS Among individuals with CKD, large-scale proteomic analysis identified known and novel proteins associated with albuminuria and suggested a role for ephrin signaling in albuminuria progression.
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Affiliation(s)
- Elizabeth Kiernan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, New York
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Pascal Schlosser
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Keenan A. Walker
- Laboratory of Behavioral Neuroscience, Intramural Research Program, National Institute on Aging, Baltimore, Maryland
| | - Eugene P. Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Rajat Deo
- Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ruth F. Dubin
- Division of Nephrology, University of Texas—Southwestern, Dallas, Texas
| | - Peter Ganz
- Division of Cardiology, Zuckerberg San Francisco General Hospital and Department of Medicine, University of California San Francisco, San Francisco, California
| | - Josef Coresh
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- 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
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, New York
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8
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Looker HC, Chang DC, Baier LJ, Hanson RL, Nelson RG. Diagnostic criteria and etiopathogenesis of type 2 diabetes and its complications: Lessons from the Pima Indians. Presse Med 2023; 52:104176. [PMID: 37783422 PMCID: PMC10805453 DOI: 10.1016/j.lpm.2023.104176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/28/2023] [Accepted: 07/19/2023] [Indexed: 10/04/2023] Open
Abstract
The Phoenix Epidemiology and Clinical Research Branch of the National Institute of Diabetes and Digestive and Kidney Diseases has conducted prospective studies of diabetes and its complications in the Pima Indians living in Arizona, USA for over 50 years. In this review we highlight areas in which these studies provided vital insights into the criteria used to diagnose type 2 diabetes, the pathophysiologic changes that accompany the development of type 2 diabetes, and the course and determinants of diabetes complications-focusing specifically on diabetic kidney disease. We include data from our longitudinal population-based study of diabetes and its complications, studies on the role of insulin resistance and insulin secretion in the pathophysiology of type 2 diabetes, and in-depth studies of diabetic kidney disease that include measures of glomerular function and research kidney biopsies. We also focus on the emerging health threat posed by youth-onset type 2 diabetes, which was first seen in the Pima Indians in the 1960s and is becoming an increasing issue worldwide.
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Affiliation(s)
- Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Douglas C Chang
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Leslie J Baier
- Diabetes Molecular Genetics Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert L Hanson
- Diabetes Genetic Epidemiology Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA.
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9
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Zhu Y, Liu L, Chu L, Lan J, Wei J, Li W, Xue C. Microscopic polyangiitis plasma-derived exosomal miR-1287-5p induces endothelial inflammatory injury and neutrophil adhesion by targeting CBL. PeerJ 2023; 11:e14579. [PMID: 36726727 PMCID: PMC9885867 DOI: 10.7717/peerj.14579] [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: 03/17/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023] Open
Abstract
Background An inflammatory environment around the vessel wall caused by leukocyte infiltration is one of the characteristic histopathological features of microscopic polyangiitis (MPA); however, the pathogenic mechanisms are not fully understood. Studies have found that circulating microRNA (miRNA) can be used as potential biomarkers for the diagnosis and classification of anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitides (AAV), and the E3 ubiquitin ligase casitas B-lineage lymphoma (CBL) seems to be associated with inflammation. In addition, evidence indicates that miRNA can be tracked into exosomes and transferred into recipient cells to mediate the process of vascular endothelial injury. Herein, we aimed to identify the profiles of exosomal miRNA, and determine the effect of exosomal miR-1287-5p and its target gene CBL on vascular endothelial cells in MPA. Method We isolated plasma exosomes from patients with MPA (MPA-exo) and healthy controls (HC-exo) by ultracentrifugation and conducted exosome small-RNA sequencing to screen differential miRNA expression in MPA-exo (n = 3) compared to HC-exo (n = 3). We measured the expression levels of miR-1303, miR-1287-5p, and miR-129-1-3p using quantitative reverse transcription-polymerase chain reaction (qRT-PCR, n = 6) and performed dual luciferase reporter gene assays to confirm the downstream target gene of miR-1287-5p. In addition, we treated human umbilical vein endothelial cell (HUVEC) with MPA-exo, or transfected them with miR-1287-5p mimic/inhibitor or with CBL-siRNA/CBL-siRNA+ miR-1287-5p inhibitor. After cell culture, we evaluated the effects on vascular endothelial cells by examining the mRNA levels of IL-6, IL-8, MCP-1, ICAM-1 and E-selectin using qRT-PCR and performed neutrophil adhesion assay with haematoxylin staining. Result Transmission electron microscopy, Western blot and nanoparticle tracking analysis showed that we successfully purified exosomes and MPA-exo could be absorbed into HUVEC. We screened a total of 1,077 miRNA by sequencing and observed a high abundance of miR-1287-5p in the exosomes obtained from MPA plasma. The dual luciferase reporter assay identified CBL as a downstream target gene of miR-1287-5p, and the results revealed that MPA-exo decreased CBL protein expression in HUVEC. In addition, treatment with MPA-exo, up-regulating miR-1287-5p or silencing of CBL in HUVEC significantly increased the mRNA expression of inflammatory factors (including IL-6, IL-8, and MCP-1) and adhesion molecules (including ICAM-1 and E-selection) and promoted the adhesion of neutrophils to HUVEC. However, down-regulating miR-1287-5p had the opposite effect. Conclusion Our study revealed that MPA-exo was involved in the intercellular transfer of miR-1287-5p and subsequently promote the development of acute endothelial injury in MPA. MiR-1287-5p and CBL agonists may be promising therapeutic approach for MPA-induced vascular inflammatory injury.
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Affiliation(s)
- Yan Zhu
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China,The First Affiliated Hospital, Department of Nephrology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Liu Liu
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Liepeng Chu
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jingjing Lan
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jingsi Wei
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Li
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Chao Xue
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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10
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Murakoshi M, Iwasawa T, Koshida T, Suzuki Y, Gohda T, Kato K. Development of an In-House EphA2 ELISA for Human Serum and Measurement of Circulating Levels of EphA2 in Hypertensive Patients with Renal Dysfunction. Diagnostics (Basel) 2022; 12:diagnostics12123023. [PMID: 36553030 PMCID: PMC9776842 DOI: 10.3390/diagnostics12123023] [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: 11/03/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022] Open
Abstract
Identifying novel biomarkers of kidney function in patients with chronic kidney disease (CKD) has strong clinical value as current measures have limitations. This study aims to develop and validate a sensitive and specific ephrin type-A receptor 2 (EphA2) enzyme-linked immunosorbent assay (ELISA) for human serum, and determine whether its results correlate with traditional renal measures in patients with hypertension. The novel ELISA of the current study was validated and used to measure circulating EphA2 levels in 80 hypertensive patients with and without kidney function decline (eGFR less than 60 mL/min/1.73 m2). Validation of the EphA2 ELISA showed good recovery (87%) and linearity (103%) and no cross-reactivity with other Eph receptors. Patients with kidney function decline had lower diastolic blood pressure, and higher UPCR and EphA2 than those without kidney function decline. The association of age and eGFR with EphA2 was maintained in the stepwise multiple regression analysis. In a multivariate logistic model, EphA2 was associated with a lower eGFR (<60 mL/min/1.73 m2) after adjustment for age, sex, and UPCR. High circulating EphA2 levels have potential application as a clinical biomarker for the presence of CKD in patients with hypertension.
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Affiliation(s)
- Maki Murakoshi
- Department of Nephrology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Takumi Iwasawa
- Graduate School of Science and Engineering, Toyo University, Saitama 350-8585, Japan
| | - Takeo Koshida
- Department of Nephrology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Yusuke Suzuki
- Department of Nephrology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Tomohito Gohda
- Department of Nephrology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Correspondence: (T.G.); (K.K.)
| | - Kazunori Kato
- Graduate School of Science and Engineering, Toyo University, Saitama 350-8585, Japan
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Correspondence: (T.G.); (K.K.)
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11
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Braden GL, Landry DL. The Next Frontier: Biomarkers and Artificial Intelligence Predicting Cardiorenal Outcomes in Diabetic Kidney Disease. KIDNEY360 2022; 3:1480-1483. [PMID: 36245646 PMCID: PMC9528371 DOI: 10.34067/kid.0003322022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 11/27/2022]
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12
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Kobayashi H, Looker HC, Satake E, D’Addio F, Wilson JM, Saulnier PJ, Md Dom ZI, O’Neil K, Ihara K, Krolewski B, Badger HS, Petrazzuolo A, Corradi D, Galecki A, Wilson P, Najafian B, Mauer M, Niewczas MA, Doria A, Humphreys B, Duffin KL, Fiorina P, Nelson RG, Krolewski AS. Neuroblastoma suppressor of tumorigenicity 1 is a circulating protein associated with progression to end-stage kidney disease in diabetes. Sci Transl Med 2022; 14:eabj2109. [PMID: 35947673 PMCID: PMC9531292 DOI: 10.1126/scitranslmed.abj2109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Circulating proteins associated with transforming growth factor-β (TGF-β) signaling are implicated in the development of diabetic kidney disease (DKD). It remains to be comprehensively examined which of these proteins are involved in the pathogenesis of DKD and its progression to end-stage kidney disease (ESKD) in humans. Using the SOMAscan proteomic platform, we measured concentrations of 25 TGF-β signaling family proteins in four different cohorts composed in total of 754 Caucasian or Pima Indian individuals with type 1 or type 2 diabetes. Of these 25 circulating proteins, we identified neuroblastoma suppressor of tumorigenicity 1 (NBL1, aliases DAN and DAND1), a small secreted protein known to inhibit members of the bone morphogenic protein family, to be most strongly and independently associated with progression to ESKD during 10-year follow-up in all cohorts. The extent of damage to podocytes and other glomerular structures measured morphometrically in 105 research kidney biopsies correlated strongly with circulating NBL1 concentrations. Also, in vitro exposure to NBL1 induced apoptosis in podocytes. In conclusion, circulating NBL1 may be involved in the disease process underlying progression to ESKD, and its concentration in circulation may identify subjects with diabetes at increased risk of progression to ESKD.
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Affiliation(s)
- Hiroki Kobayashi
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, Tokyo, Japan
| | - Helen C. Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Eiichiro Satake
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Francesca D’Addio
- Pediatric Clinical Research Center Romeo ed Enrica Invernizzi, DIBIC L. Sacco, Università di Milano and Endocrinology Division ASST Sacco-FBF, Milan, Italy
| | - Jonathan M. Wilson
- Diabetes and Complications Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Pierre Jean. Saulnier
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
- CHU Poitiers, University of Poitiers, Inserm, Clinical Investigation Center CIC1402, Poitiers, France
| | - Zaipul I. Md Dom
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kristina O’Neil
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
| | - Katsuhito Ihara
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bozena Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hannah S. Badger
- Diabetes and Complications Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Adriana Petrazzuolo
- Pediatric Clinical Research Center Romeo ed Enrica Invernizzi, DIBIC L. Sacco, Università di Milano and Endocrinology Division ASST Sacco-FBF, Milan, Italy
| | - Domenico Corradi
- Department of Medicine and Surgery, Unit of Pathology, University of Parma, Parma, Italy
| | - Andrzej Galecki
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Parker Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, St. Louis, USA
| | - Behzad Najafian
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Michael Mauer
- Department of Pediatrics and Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Monika A. Niewczas
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alessandro Doria
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Benjamin Humphreys
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Kevin L. Duffin
- Diabetes and Complications Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Paolo Fiorina
- Pediatric Clinical Research Center Romeo ed Enrica Invernizzi, DIBIC L. Sacco, Università di Milano and Endocrinology Division ASST Sacco-FBF, Milan, Italy
- Nephrology Division, Boston Children’s Hospital, Boston, MA, USA
| | - Robert G. Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Andrzej S. Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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13
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Rhee EP. Proteomic discovery in diabetic kidney disease-to what end? Kidney Int 2022; 102:236-238. [PMID: 35870813 DOI: 10.1016/j.kint.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 11/25/2022]
Abstract
Emerging approaches that enable high-throughput analysis of the plasma proteome have been increasingly deployed in nephrology research. Kobayashi et al. provide a valuable addition to this literature, describing an untargeted proteomic analysis of diabetic kidney disease progression to end-stage kidney disease. This commentary places the study's findings in the context of the broader literature and outlines potential avenues toward biological insight and clinical utility.
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Affiliation(s)
- Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.
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14
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Lin Y, Zhu G, Li X, Yu H, Luo Y, Lin J, Li R, Huang Z. Icariin and Competing Endogenous RNA Network: A Potential Protective Strategy Against Contrast-Induced Acute Kidney Injury. Drug Des Devel Ther 2022; 16:2343-2363. [PMID: 35910780 PMCID: PMC9329895 DOI: 10.2147/dddt.s369100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Icariin presents protective effect in several kidney diseases. However, the role of icariin in contrast-induced acute kidney injury (CIAKI) is still unclear. This study aimed to investigate the effect of icariin in CIAKI, as well as exploring the underlying mechanism from the aspect of interaction between protein-coding genes and non-coding RNAs. Methods The effect of icariin was evaluated in both in vivo and in vitro CIAKI models. Rat kidneys were collected for genome-wide sequencing. The differentially expressed genes (DEGs) were screened and visualized by R software. The function annotation of DEGs was analyzed by Metascape. By Cytoscape software, the competing endogenous RNA (ceRNA) network was constructed, and hub genes were selected. Expressions of hub genes were validated by PCR. Association of hub genes in the ceRNA network and renal function was also examined. Results Icariin protected against CIAKI in both in vivo and in vitro models. Based on DEGs in icariin pretreated CIAKI rats, lncRNA- and circRNA-associated ceRNA networks were constructed, respectively. Function annotation showed the ceRNA networks were enriched in ERK1 and ERK2 cascade, MAPK signaling and NF-κB signaling. Further, two circRNAs, six lncRNAs, four miRNAs and nine mRNAs were selected as hub genes of the ceRNA network. Among them, eight mRNAs (Acot1, Cbwd1, Ly6i, Map3k14, Mettl2b, Nyap1, Set and Utp20) were negatively correlated with renal function, while one mRNA (Tmem44) was positively correlated with renal function. Conclusion Icariin presented a protective effect against CIAKI. The ceRNA network, involving Acot1, Cbwd1, Ly6i, Map3k14, Mettl2, Nyap1, Set, Tmem44 and Utp20, might partially contribute to the underlying mechanism of icariin protection by regulation of ERK1 and ERK2 cascade, MAPK signaling and NF-κB signaling.
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Affiliation(s)
- Yan Lin
- Department of Nephrology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Yunkang School of Medicine and Health, Nanfang College, Guangzhou, People’s Republic of China
| | - Gaofeng Zhu
- Department of General Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, People’s Republic of China
| | - Xiaoyong Li
- Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Huaxiao Yu
- The Third Clinical School, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yuhang Luo
- The Third Clinical School, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jiaqiong Lin
- Affiliated Dongguan Maternal and Child Healthcare Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Renyuan Li
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Renyuan Li, Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China, Tel +86-18926146852, Email
| | - Zena Huang
- Yunkang School of Medicine and Health, Nanfang College, Guangzhou, People’s Republic of China
- Correspondence: Zena Huang, Yunkang School of Medicine and Health, Nanfang College, Guangzhou, People’s Republic of China, Tel +86-13570466614, Email
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15
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Kobayashi H, Looker HC, Satake E, Saulnier PJ, Md Dom ZI, O'Neil K, Ihara K, Krolewski B, Galecki AT, Niewczas MA, Wilson JM, Doria A, Duffin KL, Nelson RG, Krolewski AS. Results of untargeted analysis using the SOMAscan proteomics platform indicates novel associations of circulating proteins with risk of progression to kidney failure in diabetes. Kidney Int 2022; 102:370-381. [PMID: 35618095 PMCID: PMC9333266 DOI: 10.1016/j.kint.2022.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 04/04/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
Abstract
This study applies a large proteomics panel to search for new circulating biomarkers associated with progression to kidney failure in individuals with diabetic kidney disease. Four independent cohorts encompassing 754 individuals with type 1 and type 2 diabetes and early and late diabetic kidney disease were followed to ascertain progression to kidney failure. During ten years of follow-up, 227 of 754 individuals progressed to kidney failure. Using the SOMAscan proteomics platform, we measured baseline concentration of 1129 circulating proteins. In our previous publications, we analyzed 334 of these proteins that were members of specific candidate pathways involved in diabetic kidney disease and found 35 proteins strongly associated with risk of progression to kidney failure. Here, we examined the remaining 795 proteins using an untargeted approach. Of these remaining proteins, 11 were significantly associated with progression to kidney failure. Biological processes previously reported for these proteins were related to neuron development (DLL1, MATN2, NRX1B, KLK8, RTN4R and ROR1) and were implicated in the development of kidney fibrosis (LAYN, DLL1, MAPK11, MATN2, endostatin, and ROR1) in cellular and animal studies. Specific mechanisms that underlie involvement of these proteins in progression of diabetic kidney disease must be further investigated to assess their value as targets for kidney-protective therapies. Using multivariable LASSO regression analysis, five proteins (LAYN, ESAM, DLL1, MAPK11 and endostatin) were found independently associated with risk of progression to kidney failure. Thus, our study identified proteins that may be considered as new candidate prognostic biomarkers to predict risk of progression to kidney failure in diabetic kidney disease. Furthermore, three of these proteins (DLL1, ESAM, and MAPK11) were selected as candidate biomarkers when all SOMAscan results were evaluated.
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Affiliation(s)
- Hiroki Kobayashi
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Devision of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, Tokyo, Japan
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Eiichiro Satake
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pierre Jean Saulnier
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA; CHU Poitiers, University of Poitiers, Inserm, Clinical Investigation Center CIC1402, Poitiers, France
| | - Zaipul I Md Dom
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kristina O'Neil
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
| | - Katsuhito Ihara
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bozena Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrzej T Galecki
- Cognitive Health Services Research Program, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Monika A Niewczas
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jonathan M Wilson
- Diabetes and Complication Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Alessandro Doria
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kevin L Duffin
- Diabetes and Complication Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA.
| | - Andrzej S Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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16
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Pinzon Cortes JA, El-Osta A, Fontemaggi G, Delihas N, Miyazaki K, Goel A, Brazane M, Carré C, Dama P, Bayraktar S, Castellano L, Enguita FJ, Mitic T, Caporali A, Gerber AP, Amodio N. The Non-Coding RNA Journal Club: Highlights on Recent Papers-10. Noncoding RNA 2022; 8:3. [PMID: 35076559 PMCID: PMC8788465 DOI: 10.3390/ncrna8010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 12/05/2022] Open
Abstract
We are delighted to share with you our seventh Journal Club and highlight some of the most interesting papers published recently [...].
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Affiliation(s)
- Jairo A. Pinzon Cortes
- Epigenetics in Human Health and Disease, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia;
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia;
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, NY 11794, USA
| | - Katsuki Miyazaki
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA;
- Department of Surgery, Tokushima University, Tokushima 7708503, Japan
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA;
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Mira Brazane
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France
| | - Paola Dama
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Salih Bayraktar
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Leandro Castellano
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM), Imperial College London, London W12 0NN, UK
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Tijana Mitic
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
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17
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Abstract
PURPOSE OF REVIEW Chronic kidney disease (CKD) is a silent disease, causing significant health and economic burden worldwide. It is of strong clinical value to identify novel prognostic, predictive, and pharmacodynamic biomarkers of kidney function, as current available measures have limitations. We reviewed the advances in biomarkers in CKD over the preceding year. RECENT FINDINGS The most frequently studied prognostic plasma biomarkers during recent year were plasma TNFR1, TNFR2, KIM1 and urinary MCP-1 and EGF. New biomarkers such as plasma WFDC2, MMP-7, EFNA4, EPHA2 may also have potential to serve as prognostic biomarkers. There is a shortage of data on biomarkers that are predictive of response to treatments. Data on novel biomarkers to serve as pharmacodynamic biomarkers are limited, but there are emerging data that plasmaTNFR1, TNFR2, KIM-1 are not only prognostic at baseline, but can also contribute to time-updated response signals in response to therapy. SUMMARY Data continue to emerge on applicable biomarkers for prognostic clinical risk stratification, prediction of therapeutic response and assessment of early efficacy of interventions. Although more studies are needed for refinement and specific clinical utility, there seems to be sufficient data to support clinical implementation for some biomarkers.
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Affiliation(s)
- Azadeh Zabetian
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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18
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Sugita E, Hayashi K, Hishikawa A, Itoh H. Epigenetic Alterations in Podocytes in Diabetic Nephropathy. Front Pharmacol 2021; 12:759299. [PMID: 34630127 PMCID: PMC8497789 DOI: 10.3389/fphar.2021.759299] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023] Open
Abstract
Recently, epigenetic alterations have been shown to be involved in the pathogenesis of diabetes and its complications. Kidney podocytes, which are glomerular epithelial cells, are important cells that form a slit membrane—a barrier for proteinuria. Podocytes are terminally differentiated cells without cell division or replenishment abilities. Therefore, podocyte damage is suggested to be one of the key factors determining renal prognosis. Recent studies, including ours, suggest that epigenetic changes in podocytes are associated with chronic kidney disease, including diabetic nephropathy. Furthermore, the association between DNA damage repair and epigenetic changes in diabetic podocytes has been demonstrated. Detection of podocyte DNA damage and epigenetic changes using human samples, such as kidney biopsy and urine-derived cells, may be a promising strategy for estimating kidney damage and renal prognoses in patients with diabetes. Targeting epigenetic podocyte changes and associated DNA damage may become a novel therapeutic strategy for preventing progression to end-stage renal disease (ESRD) and provide a possible prognostic marker in diabetic nephropathy. This review summarizes recent advances regarding epigenetic changes, especially DNA methylation, in podocytes in diabetic nephropathy and addresses detection of these alterations in human samples. Additionally, we focused on DNA damage, which is increased under high-glucose conditions and associated with the generation of epigenetic changes in podocytes. Furthermore, epigenetic memory in diabetes is discussed. Understanding the role of epigenetic changes in podocytes in diabetic nephropathy may be of great importance considering the increasing diabetic nephropathy patient population in an aging society.
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Affiliation(s)
- Erina Sugita
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Kaori Hayashi
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Akihito Hishikawa
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hiroshi Itoh
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
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Vasquez-Rios G, Coca SG. Predictors of Kidney Disease Progression in Diabetes and Precision Medicine: Something Old, Something New, and Something Borrowed. J Am Soc Nephrol 2021; 32:2108-2111. [PMID: 34465605 PMCID: PMC8729853 DOI: 10.1681/asn.2021070945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- George Vasquez-Rios
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York
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