1
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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; 35:923-935. [PMID: 38640019 DOI: 10.1681/asn.0000000000000343] [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: 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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Steinbrenner I, Schultheiss UT, Bächle H, Cheng Y, Behning C, Schmid M, Yeo WJ, Yu B, Grams ME, Schlosser P, Stockmann H, Gronwald W, Oefner PJ, Schaeffner E, Eckardt KU, Köttgen A, Sekula P. Associations of Urine and Plasma Metabolites with Kidney Failure and Death in a CKD Cohort. Am J Kidney Dis 2024:S0272-6386(24)00787-X. [PMID: 38815646 DOI: 10.1053/j.ajkd.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/09/2024] [Accepted: 03/12/2024] [Indexed: 06/01/2024]
Abstract
RATIONALE & OBJECTIVE Biomarkers that enable better identification of persons with chronic kidney disease (CKD) who are at higher risk for disease progression and adverse events are needed. This study sought to identify urine and plasma metabolites associated with progression of kidney disease. STUDY DESIGN Prospective metabolome-wide association study. SETTING & PARTICIPANTS Persons with CKD enrolled in the German CKD Study (GCKD) with metabolite measurements; with external validation within the Atherosclerosis Risk in Communities Study. EXPOSURES 1,513 urine and 1,416 plasma metabolites (Metabolon, Inc.) measured at study entry using untargeted mass spectrometry. OUTCOMES Main endpoints were kidney failure (KF), and a composite endpoint of KF, eGFR <15 mL/min/1.73m2, or 40% decline in eGFR (CKE). Death from any cause was a secondary endpoint. After a median of 6.5 years follow-up, 500 persons experienced KF, 1,083 experienced CKE and 680 died. ANALYTICAL APPROACH Time-to-event analyses using multivariable proportional hazard regression models in a discovery-replication design, with external validation. RESULTS 5,088 GCKD participants were included in analyses of urine metabolites and 5,144 in analyses of plasma metabolites. Among 182 unique metabolites, 30 were significantly associated with KF, 49 with CKE, and 163 with death. The strongest association with KF was observed for plasma hydroxyasparagine (hazard ratio: 1.95, 95% confidence interval: 1.68-2.25). An unnamed metabolite measured in plasma and urine was significantly associated with KF, CKE, and death. External validation of the identified associations of metabolites with KF or CKE revealed direction-consistency for 88% of observed associations. Selected associations of 18 metabolites with study outcomes have not been previously reported. LIMITATIONS Use of observational data and semi-quantitative metabolite measurements at a single time point. CONCLUSIONS The observed associations between metabolites and KF, CKE or death in persons with CKD confirmed previously reported findings and also revealed several associations not previously described. These findings warrant confirmatory research in other study cohorts.
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Affiliation(s)
- Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany
| | - Helena Bächle
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Neurology and Neurophysiology, Faculty of Medicine and Medical Center - University of Freiburg, Breisacher Str. 64, 79106 Freiburg, Germany
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany
| | - Charlotte Behning
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Matthias Schmid
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Wan-Jin Yeo
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Bing Yu
- Department of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Morgan E Grams
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, NY 10016, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Helena Stockmann
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; Department of Nephrology, University Medical Center Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053 Regensburg
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053 Regensburg
| | - Elke Schaeffner
- Institute of Public Health, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany.
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Schneider MP, Schmid M, Nadal J, Krane V, Saritas T, Busch M, Schultheiss UT, Meiselbach H, Friedrich N, Nauck M, Floege J, Kronenberg F, Wanner C, Eckardt KU. Copeptin, Natriuretic Peptides, and Cardiovascular Outcomes in Patients With CKD: The German Chronic Kidney Disease (GCKD) Study. Kidney Med 2023; 5:100725. [PMID: 37915964 PMCID: PMC10616426 DOI: 10.1016/j.xkme.2023.100725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Rationale & Objective Copeptin and Midrange pro-atrial natriuretic peptide (MR-pro-ANP) are associated with outcomes independently of N-terminal pro-brain natriuretic peptide (NT-pro-BNP) in patients with heart failure (HF). The value of these markers in patients with chronic kidney disease (CKD) has not been studied. Study Design Prospective cohort study. Setting & Participants A total of 4,417 patients enrolled in the German Chronic Kidney Disease (GCKD) study with an estimated glomerular filtration rate of 30-60 mL/min/1.73m2 or overt proteinuria (urinary albumin-creatinine ratio >300mg/g or equivalent). Exposures Copeptin, MR-pro-ANP, and NT-pro-BNP levels were measured in baseline samples. Outcomes Noncardiovascular death, cardiovascular (CV) death, major adverse CV event (MACE), and hospitalization for HF. Analytical Approach HRs for associations of Copeptin, MR-pro-ANP, and NT-pro-BNP with outcomes were estimated using Cox regression analyses adjusted for established risk factors. Results During a maximum follow-up of 6.5 years, 413 non-CV deaths, 179 CV deaths, 519 MACE, and 388 hospitalizations for HF were observed. In Cox regression analyses adjusted for established risk factors, each one of the 3 markers were associated with all the 4 outcomes, albeit the highest HRs were found for NT-pro-BNP. When models were extended to include all the 3 markers, NT-pro-BNP remained associated with all 4 outcomes. Conversely, from the 2 novel markers, associations remained only for Copeptin with non-CV death (HR, 1.62; 95% CI, 1.04-2.54 for highest vs lowest quintile) and with hospitalizations for HF (HR, 1.73; 95% CI, 1.08-2.75). Limitations Single-point measurements of Copeptin, MR-pro-ANP, and NT-pro-BNP. Conclusions In patients with moderately severe CKD, we confirm NT-pro-BNP to be strongly associated with all outcomes examined. As the main finding, the novel marker Copeptin demonstrated independent associations with non-CV death and hospitalizations for HF, and should therefore be evaluated further for risk assessment in CKD. Plain-Language Summary A blood sample-based biomarker that indicates high cardiovascular risk in a patient with kidney disease would help to guide interventions and has the potential to improve outcomes. In 4,417 patients of the German Chronic Kidney Disease study, we assessed the relationship of Copeptin, pro-atrial natriuretic peptide, and N-terminal pro-brain natriuretic peptide (NT-pro-BNP) with important outcomes over a follow-up period of 6.5 years. NT-pro-BNP was strongly associated with all of the 4 outcomes, including death unrelated to cardiovascular disease, death because of cardiovascular disease, a major cardiovascular event, and hospitalization for heart failure. Copeptin was associated with death unrelated to cardiovascular disease and hospitalization for heart failure. NT-pro-BNP and Copeptin are, therefore, promising candidates for a blood sample-based strategy to identify patients with kidney disease at high cardiovascular risk.
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Affiliation(s)
- Markus P. Schneider
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Schmid
- Department of Medical Biometry, Informatics, and Epidemiology (IMBIE), University Hospital Bonn, Bonn, Germany
| | - Jennifer Nadal
- Department of Medical Biometry, Informatics, and Epidemiology (IMBIE), University Hospital Bonn, Bonn, Germany
| | - Vera Krane
- Department of Medicine 1, Division of Nephrology, University Hospital Würzburg, Würzburg, Germany
| | - Turgay Saritas
- Department of Nephrology and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Martin Busch
- Department of Internal Medicine III, University Hospital Jena, Friedrich-Schiller Universität, Jena, Germany
| | - Ulla T. Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center and Department of Medicine IV – Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Jürgen Floege
- Department of Nephrology and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Austria
| | - Christoph Wanner
- Department of Medicine 1, Division of Nephrology, University Hospital Würzburg, Würzburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Germany
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Kim DK. Metabolomics profiling: a potential tool for predicting immunoglobulin A nephropathy progression. Kidney Res Clin Pract 2023; 42:539-540. [PMID: 37813521 PMCID: PMC10565451 DOI: 10.23876/j.krcp.23.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Kidney Research Institute, Seoul National University, Seoul, Republic of Korea
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Kim Y, Lee J, Kang MS, Song J, Kim SG, Cho S, Huh H, Lee S, Park S, Jo HA, Yang SH, Paek JH, Park WY, Han SS, Lee H, Lee JP, Joo KW, Lim CS, Hwang GS, Kim DK. Urinary Metabolite Profile Predicting the Progression of CKD. KIDNEY360 2023; 4:1048-1057. [PMID: 37291728 PMCID: PMC10476680 DOI: 10.34067/kid.0000000000000158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
Key Points As a biomarker, urinary metabolites could bridge the gap between genetic abnormalities and phenotypes of diseases. We found that levels of betaine, choline, fumarate, citrate, and glucose were significantly correlated with kidney function and could predict kidney outcomes, providing prognostic biomarkers in CKD. Background Because CKD is caused by genetic and environmental factors, biomarker development through metabolomic analysis, which reflects gene-derived downstream effects and host adaptation to the environment, is warranted. Methods We measured the metabolites in urine samples collected from 789 patients at the time of kidney biopsy and from urine samples from 147 healthy participants using nuclear magnetic resonance. The composite outcome was defined as a 30% decline in eGFR, doubling of serum creatinine levels, or end-stage kidney disease. Results Among the 28 candidate metabolites, we identified seven metabolites showing (1 ) good discrimination between healthy controls and patients with stage 1 CKD and (2 ) a consistent change in pattern from controls to patients with advanced-stage CKD. Among the seven metabolites, betaine, choline, glucose, fumarate, and citrate showed significant associations with the composite outcome after adjustment for age, sex, eGFR, the urine protein–creatinine ratio, and diabetes. Furthermore, adding choline, glucose, or fumarate to traditional biomarkers, including eGFR and proteinuria, significantly improved the ability of the net reclassification improvement (P < 0.05) and integrated discrimination improvement (P < 0.05) to predict the composite outcome. Conclusion Urinary metabolites, including betaine, choline, fumarate, citrate, and glucose, were found to be significant predictors of the progression of CKD. As a signature of kidney injury–related metabolites, it would be warranted to monitor to predict the renal outcome.
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Affiliation(s)
- Yaerim Kim
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Mi Sun Kang
- Integrated Metabolomics Research Group, Western Seoul center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Jeongin Song
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Seong Geun Kim
- Department of Internal Medicine, Inje University Sanggye Paik Hospital, Seoul, Korea
| | - Semin Cho
- Department of Internal Medicine, Chungang University Gwangmyeong hospital, Gyeonggi-do, Korea
| | - Hyuk Huh
- Department of Internal Medicine, Inje University Busan Paik Hospital, Busan, Korea
| | - Soojin Lee
- Department of Internal Medicine, Uijeongbu Eulji University Medical Center, Gyeonggi-do, Korea
| | - Sehoon Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Hyung Ah Jo
- Department of Internal Medicine, Inje University Ilsan Paik Hospital, Ilsan, Korea
| | - Seung Hee Yang
- Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Jin Hyuk Paek
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Woo Yeong Park
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Seung Seok Han
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jung Pyo Lee
- Department of Internal Medicine, SMG-SNU Boramae Medical Center, Seoul, Korea
- Departement of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kwon Wook Joo
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Departement of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Chun Soo Lim
- Department of Internal Medicine, SMG-SNU Boramae Medical Center, Seoul, Korea
- Departement of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul center, Korea Basic Science Institute, Seoul, Republic of Korea
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Departement of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
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Bienaimé F, Muorah M, Metzger M, Broeuilh M, Houiller P, Flamant M, Haymann JP, Vonderscher J, Mizrahi J, Friedlander G, Stengel B, Terzi F. Combining robust urine biomarkers to assess chronic kidney disease progression. EBioMedicine 2023; 93:104635. [PMID: 37285616 DOI: 10.1016/j.ebiom.2023.104635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/21/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Urinary biomarkers may improve the prediction of chronic kidney disease (CKD) progression. Yet, data reporting the applicability of most commercial biomarker assays to the detection of their target analyte in urine together with an evaluation of their predictive performance are scarce. METHODS 30 commercial assays (ELISA) were tested for their ability to quantify the target analyte in urine using strict (FDA-approved) validation criteria. In an exploratory analysis, LASSO (Least Absolute Shrinkage and Selection Operator) logistic regression analysis was used to identify potentially complementary biomarkers predicting fast CKD progression, determined as the 51CrEDTA clearance-based measured glomerular filtration rate (mGFR) decline (>10% per year) in a subsample of 229 CKD patients (mean age, 61 years; 66% men; baseline mGFR, 38 mL/min) from the NephroTest prospective cohort. FINDINGS Among the 30 assays, directed against 24 candidate biomarkers, encompassing different pathophysiological mechanisms of CKD progression, 16 assays fulfilled the FDA-approved criteria. LASSO logistic regressions identified a combination of five biomarkers including CCL2, EGF, KIM1, NGAL, and TGF-α that improved the prediction of fast mGFR decline compared to the kidney failure risk equation variables alone: age, gender, mGFR, and albuminuria. Mean area under the curves (AUC) estimated from 100 re-samples was higher in the model with than without these biomarkers, 0.722 (95% confidence interval 0.652-0.795) vs. 0.682 (0.614-0.748), respectively. Fully-adjusted odds-ratios (95% confidence interval) for fast progression were 1.87 (1.22, 2.98), 1.86 (1.23, 2.89), 0.43 (0.25, 0.70), 1.10 (0.71, 1.83), 0.55 (0.33, 0.89), and 2.99 (1.89, 5.01) for albumin, CCL2, EGF, KIM1, NGAL, and TGF-α, respectively. INTERPRETATION This study provides a rigorous validation of multiple assays for relevant urinary biomarkers of CKD progression which combination may improve the prediction of CKD progression. FUNDING This work was supported by Institut National de la Santé et de la Recherche Médicale, Université de Paris, Assistance Publique Hôpitaux de Paris, Agence Nationale de la Recherche, MSDAVENIR, Pharma Research and Early Development Roche Laboratories (Basel, Switzerland), and Institut Roche de Recherche et Médecine Translationnelle (Paris, France).
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Affiliation(s)
- Frank Bienaimé
- Département « Croissance et Signalisation », Institut Necker Enfants Malades, INSERM U1151, CNRS UMR 8253, Université de Paris Cité, Paris, France; Service d'Explorations Fonctionnelles, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.
| | - Mordi Muorah
- Département « Croissance et Signalisation », Institut Necker Enfants Malades, INSERM U1151, CNRS UMR 8253, Université de Paris Cité, Paris, France
| | - Marie Metzger
- CESP, Centre de Recherche en Epidémiologie et Santé des Populations, INSERM U1018, Université Paris-Saclay, Villejuif, France
| | - Melanie Broeuilh
- Département « Croissance et Signalisation », Institut Necker Enfants Malades, INSERM U1151, CNRS UMR 8253, Université de Paris Cité, Paris, France
| | - Pascal Houiller
- Service d'Explorations Fonctionnelles, Hôpital Européen George Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Martin Flamant
- Service d'Explorations Fonctionnelles, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jean-Philippe Haymann
- Service d'Explorations Fonctionnelles, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jacky Vonderscher
- Pharma Research and Early Development, Hoffmann-La-Roche Ltd, Basel, France
| | - Jacques Mizrahi
- Pharma Research and Early Development, Hoffmann-La-Roche Ltd, Basel, France
| | - Gérard Friedlander
- Département « Croissance et Signalisation », Institut Necker Enfants Malades, INSERM U1151, CNRS UMR 8253, Université de Paris Cité, Paris, France
| | - Bénédicte Stengel
- CESP, Centre de Recherche en Epidémiologie et Santé des Populations, INSERM U1018, Université Paris-Saclay, Villejuif, France
| | - Fabiola Terzi
- Département « Croissance et Signalisation », Institut Necker Enfants Malades, INSERM U1151, CNRS UMR 8253, Université de Paris Cité, Paris, France.
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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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Sandokji I, Xu Y, Denburg M, Furth S, Abraham AG, Greenberg JH. Current and Novel Biomarkers of Progression Risk in Children with Chronic Kidney Disease. Nephron Clin Pract 2023; 148:1-10. [PMID: 37232009 PMCID: PMC10840447 DOI: 10.1159/000530918] [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: 09/15/2022] [Accepted: 02/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Due to the complexity of chronic kidney disease (CKD) pathophysiology, biomarkers representing different mechanistic pathways have been targeted for the study and development of novel biomarkers. The discovery of clinically useful CKD biomarkers would allow for the identification of those children at the highest risk of kidney function decline for timely interventions and enrollment in clinical trials. SUMMARY Glomerular filtration rate and proteinuria are traditional biomarkers to classify and prognosticate CKD progression in clinical practice but have several limitations. Over the recent decades, novel biomarkers have been identified from blood or urine with metabolomic screening studies, proteomic screening studies, and an improved knowledge of CKD pathophysiology. This review highlights promising biomarkers associated with the progression of CKD that could potentially serve as future prognostic markers in children with CKD. KEY MESSAGES Further studies are needed in children with CKD to validate putative biomarkers, particularly candidate proteins and metabolites, for improving clinical management.
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Affiliation(s)
- Ibrahim Sandokji
- Department of Pediatrics, Taibah University College of Medicine, Medina, Saudi Arabia,
| | - Yunwen Xu
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michelle Denburg
- Division of Nephrology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susan Furth
- Division of Nephrology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alison G Abraham
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jason H Greenberg
- Department of Pediatrics, Section of Nephrology, Clinical and Translational Research Accelerator, Yale School of Medicine, New Haven, Connecticut, USA
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9
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Rhee EP. Kidney-specific metabolomic profiling in machine perfusate. Kidney Int 2023; 103:661-663. [PMID: 36948766 DOI: 10.1016/j.kint.2022.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/21/2022] [Indexed: 03/24/2023]
Abstract
Given their accessibility and relevance to established clinical workflows, blood and urine have been the major focus of investigation in metabolomics studies of human kidney disease. In this issue, Liu et al. describe the application of metabolomics to perfusate from donor kidneys subjected to hypothermic machine perfusion. In addition to providing an elegant model for investigating kidney metabolism, this study highlights the limitations of allograft quality assessment and identifies metabolites of interest in kidney ischemia.
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Affiliation(s)
- Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.
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10
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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11
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Zhou XJ, Zhong XH, Duan LX. Integration of artificial intelligence and multi-omics in kidney diseases. FUNDAMENTAL RESEARCH 2023; 3:126-148. [PMID: 38933564 PMCID: PMC11197676 DOI: 10.1016/j.fmre.2022.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 10/18/2022] Open
Abstract
Kidney disease is a leading cause of death worldwide. Currently, the diagnosis of kidney diseases and the grading of their severity are mainly based on clinical features, which do not reveal the underlying molecular pathways. More recent surge of ∼omics studies has greatly catalyzed disease research. The advent of artificial intelligence (AI) has opened the avenue for the efficient integration and interpretation of big datasets for discovering clinically actionable knowledge. This review discusses how AI and multi-omics can be applied and integrated, to offer opportunities to develop novel diagnostic and therapeutic means in kidney diseases. The combination of new technology and novel analysis pipelines can lead to breakthroughs in expanding our understanding of disease pathogenesis, shedding new light on biomarkers and disease classification, as well as providing possibilities of precise treatment.
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Affiliation(s)
- Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Beijing 100034, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing 100034, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing 100034, China
| | - Xu-Hui Zhong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Li-Xin Duan
- The Big Data Research Center, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
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12
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Kurano M, Jubishi D, Okamoto K, Hashimoto H, Sakai E, Morita Y, Saigusa D, Kano K, Aoki J, Harada S, Okugawa S, Doi K, Moriya K, Yatomi Y. Dynamic modulations of urinary sphingolipid and glycerophospholipid levels in COVID-19 and correlations with COVID-19-associated kidney injuries. J Biomed Sci 2022; 29:94. [PMCID: PMC9647768 DOI: 10.1186/s12929-022-00880-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Among various complications of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), renal complications, namely COVID-19-associated kidney injuries, are related to the mortality of COVID-19. Methods In this retrospective cross-sectional study, we measured the sphingolipids and glycerophospholipids, which have been shown to possess potent biological properties, using liquid chromatography-mass spectrometry in 272 urine samples collected longitudinally from 91 COVID-19 subjects and 95 control subjects without infectious diseases, to elucidate the pathogenesis of COVID-19-associated kidney injuries. Results The urinary levels of C18:0, C18:1, C22:0, and C24:0 ceramides, sphingosine, dihydrosphingosine, phosphatidylcholine, lysophosphatidylcholine, lysophosphatidic acid, and phosphatidylglycerol decreased, while those of phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, and lysophosphatidylethanolamine increased in patients with mild COVID-19, especially during the early phase (day 1–3), suggesting that these modulations might reflect the direct effects of infection with SARS-CoV-2. Generally, the urinary levels of sphingomyelin, ceramides, sphingosine, dihydrosphingosine, dihydrosphingosine l-phosphate, phosphatidylcholine, lysophosphatidic acid, phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, lysophosphatidylglycerol, phosphatidylinositol, and lysophosphatidylinositol increased, especially in patients with severe COVID-19 during the later phase, suggesting that their modulations might result from kidney injuries accompanying severe COVID-19. Conclusions Considering the biological properties of sphingolipids and glycerophospholipids, an understanding of their urinary modulations in COVID-19 will help us to understand the mechanisms causing COVID-19-associated kidney injuries as well as general acute kidney injuries and may prompt researchers to develop laboratory tests for predicting maximum severity and/or novel reagents to suppress the renal complications of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00880-5.
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Affiliation(s)
- Makoto Kurano
- grid.26999.3d0000 0001 2151 536XDepartment of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan ,grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Daisuke Jubishi
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koh Okamoto
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Hashimoto
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Sakai
- grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoshifumi Morita
- grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Daisuke Saigusa
- grid.264706.10000 0000 9239 9995Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Kuniyuki Kano
- grid.26999.3d0000 0001 2151 536XDepartment of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- grid.26999.3d0000 0001 2151 536XDepartment of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sohei Harada
- grid.26999.3d0000 0001 2151 536XDepartment of Infection Control and Prevention, The University of Tokyo, Tokyo, Japan
| | - Shu Okugawa
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kent Doi
- grid.412708.80000 0004 1764 7572Department of Emergency and Critical Care Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Kyoji Moriya
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Infection Control and Prevention, The University of Tokyo, Tokyo, Japan
| | - Yutaka Yatomi
- grid.26999.3d0000 0001 2151 536XDepartment of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan ,grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
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13
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Wen D, Zheng Z, Surapaneni A, Yu B, Zhou L, Zhou W, Xie D, Shou H, Avila-Pacheco J, Kalim S, He J, Hsu CY, Parsa A, Rao P, Sondheimer J, Townsend R, Waikar SS, Rebholz CM, Denburg MR, Kimmel PL, Vasan RS, Clish CB, Coresh J, Feldman HI, Grams ME, Rhee EP. Metabolite profiling of CKD progression in the chronic renal insufficiency cohort study. JCI Insight 2022; 7:e161696. [PMID: 36048534 PMCID: PMC9714776 DOI: 10.1172/jci.insight.161696] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDMetabolomic profiling in individuals with chronic kidney disease (CKD) has the potential to identify novel biomarkers and provide insight into disease pathogenesis.METHODSWe examined the association between blood metabolites and CKD progression, defined as the subsequent development of end-stage renal disease (ESRD) or estimated glomerular filtrate rate (eGFR) halving, in 1,773 participants of the Chronic Renal Insufficiency Cohort (CRIC) study, 962 participants of the African-American Study of Kidney Disease and Hypertension (AASK), and 5,305 participants of the Atherosclerosis Risk in Communities (ARIC) study.RESULTSIn CRIC, more than half of the measured metabolites were associated with CKD progression in minimally adjusted Cox proportional hazards models, but the number and strength of associations were markedly attenuated by serial adjustment for covariates, particularly eGFR. Ten metabolites were significantly associated with CKD progression in fully adjusted models in CRIC; 3 of these metabolites were also significant in fully adjusted models in AASK and ARIC, highlighting potential markers of glomerular filtration (pseudouridine), histamine metabolism (methylimidazoleacetate), and azotemia (homocitrulline). Our findings also highlight N-acetylserine as a potential marker of kidney tubular function, with significant associations with CKD progression observed in CRIC and ARIC.CONCLUSIONOur findings demonstrate the application of metabolomics to identify potential biomarkers and causal pathways in CKD progression.FUNDINGThis study was supported by the NIH (U01 DK106981, U01 DK106982, U01 DK085689, R01 DK108803, and R01 DK124399).
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Affiliation(s)
- Donghai Wen
- Nephrology Division and
- Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics & Environmental Sciences, University of Texas Health Sciences Center at Houston School of Public Health, Houston, Texas, USA
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Wen Zhou
- Nephrology Division and
- Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Dawei Xie
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Haochang Shou
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
| | - Chi-Yuan Hsu
- Division of Nephrology, University of California San Francisco School of Medicine, San Francisco, California, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), Bethesda, Maryland, USA
| | - Panduranga Rao
- Division of Nephrology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - James Sondheimer
- Division of Nephrology and Hypertension, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Raymond Townsend
- Renal-Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sushrut S. Waikar
- Section of Nephrology, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts, USA
| | - Casey M. Rebholz
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michelle R. Denburg
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Pediatric Nephrology, Children’s Hospital of Philadelphia, and
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul L. Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), Bethesda, Maryland, USA
| | - Ramachandran S. Vasan
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
- Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- 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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14
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Schneider MP, Schmid M, Nadal J, Wanner C, Krane V, Floege J, Saritas T, Busch M, Sitter T, Friedrich N, Stockmann H, Meiselbach H, Nauck M, Kronenberg F, Eckardt KU. Heart-Type Fatty Acid Binding Protein, Cardiovascular Outcomes, and Death: Findings From the German CKD Cohort Study. Am J Kidney Dis 2022; 80:483-494.e1. [PMID: 35288215 DOI: 10.1053/j.ajkd.2022.01.424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/05/2022] [Indexed: 02/02/2023]
Abstract
RATIONALE & OBJECTIVE Heart-type fatty acid binding protein (H-FABP) is a biomarker that has been shown to provide long-term prognostic information in patients with coronary artery disease independently of high-sensitivity troponin T (hs-TNT). We examined the independent associations of H-FABP with cardiovascular outcomes in patients with chronic kidney disease (CKD). STUDY DESIGN Prospective cohort study. SETTING & PARTICIPANTS 4,951 patients enrolled in the German Chronic Kidney Disease (GCKD) study with an estimated glomerular filtration rate of 30-60 mL/min/1.73 m2 or overt proteinuria (urinary albumin-creatinine ratio > 300 mg/g or equivalent). EXPOSURE Serum levels of H-FABP and hs-TNT were measured at study entry. OUTCOME Noncardiovascular (non-CV) death, CV death, combined major adverse CV events (MACE), and hospitalization for congestive heart failure (CHF). ANALYTICAL APPROACH Hazard ratios (HRs) for associations of H-FABP and hs-TNT with outcomes were estimated using Cox regression analyses adjusted for established risk factors. RESULTS During a maximum follow-up of 6.5 years, 579 non-CV deaths, 190 CV deaths, 522 MACE, and 381 CHF hospitalizations were observed. In Cox regression analyses adjusted for established risk factors, H-FABP was associated with all 4 outcomes, albeit with lower HRs than those found for hs-TNT. After further adjustment for hs-TNT levels, H-FABP was found to be associated with non-CV death (HR, 1.57 [95% CI, 1.14-2.18]) and MACE (HR, 1.40 [95% CI, 1.02-1.92]) but with neither CV death (HR, 1.64 [95% CI, 0.90-2.99]) nor CHF hospitalizations (HR, 1.02 [95% CI, 0.70-1.49]). LIMITATIONS Single-point measurements of H-FABP and hs-TNT. Uncertain generalizability to non-European populations. CONCLUSIONS In this large cohort of patients with CKD, H-FABP was associated with non-CV death and MACE, even after adjustment for hs-TNT. Whether measurement of H-FABP improves cardiovascular disease risk prediction in these patients warrants further studies.
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Affiliation(s)
- Markus P Schneider
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Matthias Schmid
- Department of Medical Biometry, Informatics, and Epidemiology (IMBIE), University Hospital Bonn, Bonn, Germany
| | - Jennifer Nadal
- Department of Medical Biometry, Informatics, and Epidemiology (IMBIE), University Hospital Bonn, Bonn, Germany
| | - Christoph Wanner
- Department of Medicine 1, Division of Nephrology, University Hospital Würzburg, Würzburg, Germany
| | - Vera Krane
- Department of Medicine 1, Division of Nephrology, University Hospital Würzburg, Würzburg, Germany
| | - Jürgen Floege
- Department of Nephrology and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Turgay Saritas
- Department of Nephrology and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Martin Busch
- Department of Internal Medicine III, University Hospital Jena, Friedrich-Schiller Universität, Jena, Germany
| | - Thomas Sitter
- Department of Nephrology, University Hospital, Ludwig-Maximilians-Universität München, München, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Helena Stockmann
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
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15
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Rinaldi A, Lazareth H, Poindessous V, Nemazanyy I, Sampaio JL, Malpetti D, Bignon Y, Naesens M, Rabant M, Anglicheau D, Cippà PE, Pallet N. Impaired fatty acid metabolism perpetuates lipotoxicity along the transition to chronic kidney injury. JCI Insight 2022; 7:161783. [PMID: 35998043 DOI: 10.1172/jci.insight.161783] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Energy metabolism failure in proximal tubule cells (PTC) is a hallmark of chronic kidney injury. We combined transcriptomic, metabolomic and lipidomic approaches in experimental models and patient cohorts to investigate the molecular bases of the progression to chronic kidney allograft injury initiated by ischemia-reperfusion injury (IRI). The urinary metabolome of kidney transplant recipients with chronic allograft injury and who experienced severe IRI was significantly enriched with long chain fatty acids (FA). We identified a renal FA-related gene signature with low levels of Cpt2 and Acsm5 and high levels of Acsl4 and Acsm5 associated with IRI, transition to chronic injury, and established CKD in mouse models and kidney transplant recipients. The findings were consistent with the presence of Cpt2-, Acsl4+, Acsl5+, Acsm5- PTC failing to recover from IRI as identified by snRNAseq. In vitro experiments indicated that endoplasmic reticulum (ER) stress contributes to CPT2 repression, which, in turn, promotes lipids accumulation, drives profibrogenic epithelial phenotypic changes, and activates the unfolded protein response. ER stress through CPT2 inhibition and lipid accumulation, engages an auto-amplification loop leading to lipotoxicity and self-sustained cellular stress. Thus, IRI imprints a persistent FA metabolism disturbance in the proximal tubule sustaining the progression to chronic kidney allograft injury.
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Affiliation(s)
- Anna Rinaldi
- Department of Medicine, Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Hélène Lazareth
- Centre de Recherche des Cordeliers, INSERM U1138, Paris, France
| | | | - Ivan Nemazanyy
- PMM: The Metabolism-Metabolome Platform, Necker Federative Research Structu, INSERM US24/CNRS, UMS3633, Paris, France
| | - Julio L Sampaio
- CurieCoreTech Metabolomics and Lipidomics Technology Platform, Paris, France
| | - Daniele Malpetti
- Instituto Dalle Molle di Studi sull'Intelligenza Artificiale, Lugano, Switzerland
| | - Yohan Bignon
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marion Rabant
- Department of Pathology, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Dany Anglicheau
- Department of Kidney Transplantation, Necker Hospital, Paris, France
| | - Pietro E Cippà
- Department of Medicine, Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Nicolas Pallet
- Centre de Recherche des Cordeliers, INSERM U1138, Paris, France
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16
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Characteristics of Normalization Methods in Quantitative Urinary Metabolomics—Implications for Epidemiological Applications and Interpretations. Biomolecules 2022; 12:biom12070903. [PMID: 35883459 PMCID: PMC9313036 DOI: 10.3390/biom12070903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
A systematic comparison is presented for the effects of seven different normalization schemes in quantitative urinary metabolomics. Morning spot urine samples were analyzed with nuclear magnetic resonance (NMR) spectroscopy from a population-based group of 994 individuals. Forty-four metabolites were quantified and the metabolite–metabolite associations and the associations of metabolite concentrations with two representative clinical measures, body mass index and mean arterial pressure, were analyzed. Distinct differences were observed when comparing the effects of normalization for the intra-urine metabolite associations with those for the clinical associations. The metabolite–metabolite associations show quite complex patterns of similarities and dissimilarities between the different normalization methods, while the epidemiological association patterns are consistent, leading to the same overall biological interpretations. The results indicate that, in general, the normalization method appears to have only minor influences on standard epidemiological regression analyses with clinical/physiological measures. Multimetabolite normalization schemes showed consistent results with the customary creatinine reference. Nevertheless, interpretations of intra-urine metabolite associations and nuanced understanding of the epidemiological associations call for comparisons with different normalizations and accounting for the physiology, metabolism and kidney function related to the normalization schemes.
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17
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Minakata S, Manabe S, Inai Y, Ikezaki M, Nishitsuji K, Ito Y, Ihara Y. Protein C-Mannosylation and C-Mannosyl Tryptophan in Chemical Biology and Medicine. Molecules 2021; 26:molecules26175258. [PMID: 34500691 PMCID: PMC8433626 DOI: 10.3390/molecules26175258] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022] Open
Abstract
C-Mannosylation is a post-translational modification of proteins in the endoplasmic reticulum. Monomeric α-mannose is attached to specific Trp residues at the first Trp in the Trp-x-x-Trp/Cys (W-x-x-W/C) motif of substrate proteins, by the action of C-mannosyltransferases, DPY19-related gene products. The acceptor substrate proteins are included in the thrombospondin type I repeat (TSR) superfamily, cytokine receptor type I family, and others. Previous studies demonstrated that C-mannosylation plays critical roles in the folding, sorting, and/or secretion of substrate proteins. A C-mannosylation-defective gene mutation was identified in humans as the disease-associated variant affecting a C-mannosylation motif of W-x-x-W of ADAMTSL1, which suggests the involvement of defects in protein C-mannosylation in human diseases such as developmental glaucoma, myopia, and/or retinal defects. On the other hand, monomeric C-mannosyl Trp (C-Man-Trp), a deduced degradation product of C-mannosylated proteins, occurs in cells and extracellular fluids. Several studies showed that the level of C-Man-Trp is upregulated in blood of patients with renal dysfunction, suggesting that the metabolism of C-Man-Trp may be involved in human kidney diseases. Together, protein C-mannosylation is considered to play important roles in the biosynthesis and functions of substrate proteins, and the altered regulation of protein C-manosylation may be involved in the pathophysiology of human diseases. In this review, we consider the biochemical and biomedical knowledge of protein C-mannosylation and C-Man-Trp, and introduce recent studies concerning their significance in biology and medicine.
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Affiliation(s)
- Shiho Minakata
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Shino Manabe
- Pharmaceutical Department, The Institute of Medicinal Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan;
- Research Center for Pharmaceutical Development, Graduate School of Pharmaceutical Science & Faculty of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Sendai, Miyagi 980-8578, Japan
| | - Yoko Inai
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Midori Ikezaki
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Kazuchika Nishitsuji
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Yukishige Ito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan;
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshito Ihara
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
- Correspondence: ; Tel.: +81-73-441-0628
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18
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Kidney Allograft Function Is a Confounder of Urine Metabolite Profiles in Kidney Allograft Recipients. Metabolites 2021; 11:metabo11080533. [PMID: 34436474 PMCID: PMC8399888 DOI: 10.3390/metabo11080533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/24/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
Noninvasive biomarkers of kidney allograft status can help minimize the need for standard of care kidney allograft biopsies. Metabolites that are measured in the urine may inform about kidney function and health status, and potentially identify rejection events. To test these hypotheses, we conducted a metabolomics study of biopsy-matched urine cell-free supernatants from kidney allograft recipients who were diagnosed with two major types of acute rejections and no-rejection controls. Non-targeted metabolomics data for 674 metabolites and 577 unidentified molecules, for 192 biopsy-matched urine samples, were analyzed. Univariate and multivariate analyses identified metabolite signatures for kidney allograft rejection. The replicability of a previously developed urine metabolite signature was examined. Our study showed that metabolite profiles can serve as biomarkers for discriminating rejection biopsies from biopsies without rejection features, but also revealed a role of estimated Glomerular Filtration Rate (eGFR) as a major confounder of the metabolite signal.
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19
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Schultheiss UT, Sekula P. The Promise of Metabolomics in Decelerating CKD Progression in Children. Clin J Am Soc Nephrol 2021; 16:1152-1154. [PMID: 34362783 PMCID: PMC8455046 DOI: 10.2215/cjn.07400521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 02/04/2023]
Affiliation(s)
- Ulla T. Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany,Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
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20
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Schultheiss UT, Kosch R, Kotsis F, Altenbuchinger M, Zacharias HU. Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses. Metabolites 2021; 11:460. [PMID: 34357354 PMCID: PMC8304377 DOI: 10.3390/metabo11070460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Kidney diseases still pose one of the biggest challenges for global health, and their heterogeneity and often high comorbidity load seriously hinders the unraveling of their underlying pathomechanisms and the delivery of optimal patient care. Metabolomics, the quantitative study of small organic compounds, called metabolites, in a biological specimen, is gaining more and more importance in nephrology research. Conducting a metabolomics study in human kidney disease cohorts, however, requires thorough knowledge about the key workflow steps: study planning, sample collection, metabolomics data acquisition and preprocessing, statistical/bioinformatics data analysis, and results interpretation within a biomedical context. This review provides a guide for future metabolomics studies in human kidney disease cohorts. We will offer an overview of important a priori considerations for metabolomics cohort studies, available analytical as well as statistical/bioinformatics data analysis techniques, and subsequent interpretation of metabolic findings. We will further point out potential research questions for metabolomics studies in the context of kidney diseases and summarize the main results and data availability of important studies already conducted in this field.
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Affiliation(s)
- Ulla T. Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany; (U.T.S.); (F.K.)
- Department of Medicine IV—Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Robin Kosch
- Computational Biology, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany; (U.T.S.); (F.K.)
- Department of Medicine IV—Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Michael Altenbuchinger
- Institute of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany;
| | - Helena U. Zacharias
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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