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Srialluri N, Surapaneni A, Schlosser P, Chen TK, Schmidt IM, Rhee EP, Coresh J, Grams ME. Circulating Proteins and Mortality in CKD: A Proteomics Study of the AASK and ARIC Cohorts. Kidney Med 2023; 5:100714. [PMID: 37711886 PMCID: PMC10498294 DOI: 10.1016/j.xkme.2023.100714] [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: 09/16/2023] Open
Abstract
Rationale & Objective Proteomics could provide pathophysiologic insight into the increased risk of mortality in patients with chronic kidney disease (CKD). This study aimed to investigate associations between the circulating proteome and all-cause mortality among patients with CKD. Study Design Observational cohort study. Setting & Participants Primary analysis in 703 participants in the African American Study of Kidney Disease and Hypertension (AASK) and validation in 1,628 participants with CKD in the Atherosclerosis Risk in Communities (ARIC) study who attended visit 5. Exposure Circulating proteins. Outcome All-cause mortality. Analytical Approach Among AASK participants, we evaluated the associations of 6,790 circulating proteins with all-cause mortality using multivariable Cox proportional hazards models. Proteins with significant associations were further studied in ARIC Visit 5 participants with CKD. Results In the AASK cohort, the mean age was 54.5 years, 271 (38.5%) were women, and the mean measured glomerular filtration rate (GFR) was 46 mL/min/1.73 m2. The median follow-up was 9.6 years, and 7 distinct proteins were associated with all-cause mortality at the Bonferroni-level threshold (P < 0.05 of the 6,790) after adjustment for demographics and clinical factors, including baseline measured estimated GFR and proteinuria. In the ARIC visit 5 cohort, the mean age was 77.2 years, 903 (55.5%) were women, the mean estimated GFR was 54 mL/min/1.73 m2 and median follow-up was 6.9 years. Of the 7 proteins found in AASK, 3 (β2-microglobulin, spondin-1, and N-terminal pro-brain natriuretic peptide) were available in the ARIC data, with all 3 significantly associated with death in ARIC. Limitations Possibility of unmeasured confounding. Cause of death was not known. Conclusions Using large-scale proteomic analysis, proteins were reproducibly associated with mortality in 2 cohorts of participants with CKD. Plain-Language Summary Patients with chronic kidney disease (CKD) have a high risk of premature death, with various pathophysiological processes contributing to this increased risk of mortality. This observational cohort study aimed to investigate the associations between circulating proteins and all-cause mortality in patients with CKD using large-scale proteomic analysis. The study analyzed data from the African American Study of Kidney Disease and Hypertension (AASK) study and validated the findings in the Atherosclerosis Risk in Communities (ARIC) Study. A total of 6,790 circulating proteins were evaluated in AASK, and 7 proteins were significantly associated with all-cause mortality. Three of these proteins (β2-microglobulin, spondin-1, and N-terminal pro-brain natriuretic peptide (BNP)) were also measured in ARIC and were significantly associated with death. Additional studies assessing biomarkers associated with mortality among patients with CKD are needed to evaluate their use in clinical practice.
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Affiliation(s)
- Nityasree Srialluri
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Aditya Surapaneni
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, New York University, New York, New York
| | - Pascal Schlosser
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Teresa K. Chen
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
- Kidney Health Research Collaborative; Division of Nephrology, Department of Medicine, University of California San Francisco and San Francisco VA Health Care System, San Francisco, California
| | - Insa M. Schmidt
- Department of Medicine, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts
| | - Eugene P. Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Josef Coresh
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Morgan E. Grams
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, New York University, New York, New York
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Okamura K, Lu S, He Z, Altmann C, Montford JR, Li AS, Lucia MS, Orlicky DJ, Weiser-Evans M, Faubel S. IL-6 mediates the hepatic acute phase response after prerenal azotemia in a clinically defined murine model. Am J Physiol Renal Physiol 2023; 325:F328-F344. [PMID: 37471421 PMCID: PMC10511171 DOI: 10.1152/ajprenal.00267.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
Prerenal azotemia (PRA) is a major cause of acute kidney injury and uncommonly studied in preclinical models. We sought to develop and characterize a novel model of PRA that meets the clinical definition: acute loss of glomerular filtration rate (GFR) that returns to baseline with resuscitation. Adult male C57BL/6J wild-type (WT) and IL-6-/- mice were studied. Intraperitoneal furosemide (4 mg) or vehicle was administered at time = 0 and 3 h to induce PRA from volume loss. Resuscitation began at 6 h with 1 mL intraperitoneal saline for four times for 36 h. Six hours after furosemide administration, measured glomerular filtration rate was 25% of baseline and returned to baseline after saline resuscitation at 48 h. After 6 h of PRA, plasma interleukin (IL)-6 was significantly increased, kidney and liver histology were normal, kidney and liver lactate were normal, and kidney injury molecule-1 immunofluorescence was negative. There were 327 differentially regulated genes upregulated in the liver, and the acute phase response was the most significantly upregulated pathway; 84 of the upregulated genes (25%) were suppressed in IL-6-/- mice, and the acute phase response was the most significantly suppressed pathway. Significantly upregulated genes and their proteins were also investigated and included serum amyloid A2, serum amyloid A1, lipocalin 2, chemokine (C-X-C motif) ligand 1, and haptoglobin; hepatic gene expression and plasma protein levels were all increased in wild-type PRA and were all reduced in IL-6-/- PRA. This work demonstrates previously unknown systemic effects of PRA that includes IL-6-mediated upregulation of the hepatic acute phase response.NEW & NOTEWORTHY Prerenal azotemia (PRA) accounts for a third of acute kidney injury (AKI) cases yet is rarely studied in preclinical models. We developed a clinically defined murine model of prerenal azotemia characterized by a 75% decrease in measured glomerular filtration rate (GFR), return of measured glomerular filtration rate to baseline with resuscitation, and absent tubular injury. Numerous systemic effects were observed, such as increased plasma interleukin-6 (IL-6) and upregulation of the hepatic acute phase response.
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Affiliation(s)
- Kayo Okamura
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Sizhao Lu
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Zhibin He
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Chris Altmann
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - John R Montford
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- Renal Section, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, United States
| | - Amy S Li
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - M Scott Lucia
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - David J Orlicky
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Mary Weiser-Evans
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Sarah Faubel
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
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3
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Li Y, Tam WW, Yu Y, Zhuo Z, Xue Z, Tsang C, Qiao X, Wang X, Wang W, Li Y, Tu Y, Gao Y. The application of Aptamer in biomarker discovery. Biomark Res 2023; 11:70. [PMID: 37468977 DOI: 10.1186/s40364-023-00510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Biomarkers are detectable molecules that can reflect specific physiological states of cells, organs, and organisms and therefore be regarded as indicators for specific diseases. And the discovery of biomarkers plays an essential role in cancer management from the initial diagnosis to the final treatment regime. Practically, reliable clinical biomarkers are still limited, restricted by the suboptimal methods in biomarker discovery. Nucleic acid aptamers nowadays could be used as a powerful tool in the discovery of protein biomarkers. Nucleic acid aptamers are single-strand oligonucleotides that can specifically bind to various targets with high affinity. As artificial ssDNA or RNA, aptamers possess unique advantages compared to conventional antibodies. They can be flexible in design, low immunogenicity, relative chemical/thermos stability, as well as modifying convenience. Several SELEX (Systematic Evolution of Ligands by Exponential Enrichment) based methods have been generated recently to construct aptamers for discovering new biomarkers in different cell locations. Secretome SELEX-based aptamers selection can facilitate the identification of secreted protein biomarkers. The aptamers developed by cell-SELEX can be used to unveil those biomarkers presented on the cell surface. The aptamers from tissue-SELEX could target intracellular biomarkers. And as a multiplexed protein biomarker detection technology, aptamer-based SOMAScan can analyze thousands of proteins in a single run. In this review, we will introduce the principle and workflow of variations of SELEX-based methods, including secretome SELEX, ADAPT, Cell-SELEX and tissue SELEX. Another powerful proteome analyzing tool, SOMAScan, will also be covered. In the second half of this review, how these methods accelerate biomarker discovery in various diseases, including cardiovascular diseases, cancer and neurodegenerative diseases, will be discussed.
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Affiliation(s)
- Yongshu Li
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China.
| | - Winnie Wailing Tam
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhenjian Zhuo
- State Key Laboratory of Chemical Oncogenomic, Peking University Shenzhen Graduate School, Shenzhen, China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhichao Xue
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China
| | - Chiman Tsang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoting Qiao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiaokang Wang
- Department of Pharmacy, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Weijing Wang
- Shantou University Medical College, Shantou, China
| | - Yongyi Li
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yanyang Tu
- Research Center, Huizhou Central People's Hospital, Guangdong Medical University, Huizhou City, China.
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China.
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4
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Paranjpe I, Jayaraman P, Su CY, Zhou S, Chen S, Thompson R, Del Valle DM, Kenigsberg E, Zhao S, Jaladanki S, Chaudhary K, Ascolillo S, Vaid A, Gonzalez-Kozlova E, Kauffman J, Kumar A, Paranjpe M, Hagan RO, Kamat S, Gulamali FF, Xie H, Harris J, Patel M, Argueta K, Batchelor C, Nie K, Dellepiane S, Scott L, Levin MA, He JC, Suarez-Farinas M, Coca SG, Chan L, Azeloglu EU, Schadt E, Beckmann N, Gnjatic S, Merad M, Kim-Schulze S, Richards B, Glicksberg BS, Charney AW, Nadkarni GN. Proteomic characterization of acute kidney injury in patients hospitalized with SARS-CoV2 infection. COMMUNICATIONS MEDICINE 2023; 3:81. [PMID: 37308534 PMCID: PMC10258469 DOI: 10.1038/s43856-023-00307-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/18/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. METHODS Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N = 437), we identified 413 higher plasma abundances of protein targets and 30 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p < 0.05). Of these, 62 proteins were validated in an external cohort (p < 0.05, N = 261). RESULTS We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p < 0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury. CONCLUSIONS Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.
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Affiliation(s)
- Ishan Paranjpe
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Pushkala Jayaraman
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Computer Science, Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Steven Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane Marie Del Valle
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shan Zhao
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Suraj Jaladanki
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumardeep Chaudhary
- Clinical Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Steven Ascolillo
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akhil Vaid
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Justin Kauffman
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arvind Kumar
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manish Paranjpe
- Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Ross O Hagan
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samir Kamat
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Faris F Gulamali
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joceyln Harris
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Craig Batchelor
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergio Dellepiane
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leisha Scott
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew A Levin
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Cijiang He
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Department of Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven G Coca
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lili Chan
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evren U Azeloglu
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam Beckmann
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miram Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Computer Science, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Twin Research, King's College London, London, GB, UK
| | | | - Alexander W Charney
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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5
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Dubin RF, Deo R, Ren Y, Lee H, Shou H, Feldman H, Kimmel P, Waikar SS, Rhee EP, Tin A, Chen J, Coresh J, Go AS, Kelly T, Rao PS, Chen TK, Segal MR, Ganz P. Analytical and Biological Variability of a Commercial Modified Aptamer Assay in Plasma Samples of Patients with Chronic Kidney Disease. J Appl Lab Med 2023; 8:491-503. [PMID: 36705086 PMCID: PMC11658805 DOI: 10.1093/jalm/jfac145] [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: 09/09/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND We carried out a study of the aptamer proteomic assay, SomaScan V4, to evaluate the analytical and biological variability of the assay in plasma samples of patients with moderate to severe chronic kidney disease (CKD). METHODS Plasma samples were selected from 2 sources: (a) 24 participants from the Chronic Renal Insufficiency Cohort (CRIC) and (b) 49 patients from the Brigham and Women's Hospital-Kidney/Renal Clinic. We calculated intra-assay variability from both sources and examined short-term biological variability in samples from the Brigham clinic. We also measured correlations of aptamer measurements with traditional biomarker assays. RESULTS A total of 4656 unique proteins (4849 total aptamer measures) were analyzed in all samples. Median (interquartile range [IQR] intra-assay CV) was 3.7% (2.8-5.3) in CRIC and 5.0% (3.8-7.0) in Brigham samples. Median (IQR) biological CV among Brigham samples drawn from one individual on 2 occasions separated by median (IQR) 7 (4-14) days was 8.7% (6.2-14). CVs were independent of CKD stage, diabetes, or albuminuria but were higher in patients with systemic lupus erythematosus. Rho correlations between aptamer and traditional assays for biomarkers of interest were cystatin C = 0.942, kidney injury model-1 = 0.905, fibroblast growth factor-23 = 0.541, tumor necrosis factor receptors 1 = 0.781 and 2 = 0.843, P < 10-100 for all. CONCLUSIONS Intra-assay and within-subject variability for SomaScan in the CKD setting was low and similar to assay variability reported from individuals without CKD. Intra-assay precision was excellent whether samples were collected in an optimal research protocol, as were CRIC samples, or in the clinical setting, as were the Brigham samples.
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Affiliation(s)
- Ruth F. Dubin
- Division of Nephrology, University of Texas Southwestern Medical Center, San Francisco, CA, USA
| | - Rajat Deo
- Division of Cardiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yue Ren
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hongzhe Lee
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Haochang Shou
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Harold Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Washington, DC, USA
| | - Sushrut S. Waikar
- Division of Nephrology, Boston University School of Medicine, Boston, MA, USA
| | - Eugene P. Rhee
- Division of Nephrology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Adrienne Tin
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jingsha Chen
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joseph Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | - Alan S. Go
- Division of Research, Kaiser Permanente Northern California Division of Research, Oakland, CA, USA
| | - Tanika Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Paduranga S. Rao
- Department of Medicine, University of Michigan Ann Arbor, Ann Arbor, MI, USA
| | - Teresa K. Chen
- Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mark R. Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter Ganz
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
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6
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Chen Z, Wang Y. Interleukin-6 levels can be used to estimate cardiovascular and all-cause mortality risk in dialysis patients: A meta-analysis and a systematic review. Immun Inflamm Dis 2023; 11:e818. [PMID: 37102647 PMCID: PMC10132186 DOI: 10.1002/iid3.818] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Although previous studies have explored the correlation of interleukin (IL)-6 with mortality risk in dialysis patients, the findings have been conflicting. Hence, this meta-analysis aimed to comprehensively assess the use of IL-6 measurement for estimating cardiovascular mortality and all-cause mortality in dialysis patients. METHODS The Embase, PubMed, Web of Science, and MEDLINE databases were searched to identify relevant studies. After screening out the eligible studies, the data were extracted. RESULTS Twenty-eight eligible studies with 8370 dialysis patients were included. Pooled analyses revealed that higher IL-6 levels were related to increased cardiovascular mortality risk (hazard ratio [HR] = 1.55, 95% confidence interval [CI]: 1.20-1.90) and all-cause mortality risk (HR = 1.11, 95% CI: 1.05-1.17) in dialysis patients. Further subgroup analyses suggested that higher IL-6 levels were associated with elevated cardiovascular mortality in hemodialysis patients (HR = 1.59, 95% CI: 1.36-1.81) but not in peritoneal dialysis patients (HR = 1.56, 95% CI: 0.46-2.67). Moreover, sensitivity analyses indicated that the results were robust. Egger's test revealed potential publication bias among studies exploring the correlation of IL-6 levels with cardiovascular mortality (p = .004) and all-cause mortality (p < .001); however, publication bias was not observed when using Begg's test (both p > .05). CONCLUSIONS This meta-analysis reveals that higher IL-6 levels could indicate higher risks of cardiovascular mortality and all-cause mortality in dialysis patients. These findings suggest that monitoring IL-6 cytokine may help to enhance dialysis management and improve the general prognosis of patients.
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Affiliation(s)
- Zeyu Chen
- Department of CardiologyThe First People's Hospital of ZiyangZiyangChina
| | - Yan Wang
- Department of NephrologyThe First People's Hospital of ZiyangZiyangChina
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Nadkami G, Paranjpe I, Jayaraman P, Su CY, Zhou S, Chen S, Valle DD, Thompson R, Kenigsberg E, Zhao S, Jaladanki S, Chaudhary K, Ascolillo S, Vaid A, Gonzalez-Kozlova E, Kumar A, Paranjpe M, O'Hagan R, Kamat S, Gulamali F, Kauffman J, Xie H, Harris J, Patel M, Argueta K, Batchelor C, Nie K, Dellepiane S, Scott L, Levin M, He J, Suárez-Fariñas M, Coca S, Chan L, Azeloglu E, Schadt E, Beckmann N, Gnjatic S, Merad M, Kim-Schulze S, Richards JB, Glicksberg B, Charney A. Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection. RESEARCH SQUARE 2023:rs.3.rs-2379226. [PMID: 36993735 PMCID: PMC10055503 DOI: 10.21203/rs.3.rs-2379226/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Background Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). Results We demonstrate that COVID-AKI is associated with increased markers of tubular injury ( NGAL ) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2 , trefoil factor 3 , transmembrane emp24 domain-containing protein 10 , and cystatin-C indicating tubular dysfunction and injury. Conclusions Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.
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Affiliation(s)
| | - Ishan Paranjpe
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | | | | | | | | | | | | | - Shan Zhao
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | | | | | | | | | | | | | - Hui Xie
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | - Kai Nie
- Icahn School of Medicine at Mount Sinai
| | | | | | | | - John He
- Mount Sinai School of Medicine
| | | | | | - Lili Chan
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | | | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital
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8
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Paranjpe I, Jayaraman P, Su CY, Zhou S, Chen S, Thompson R, Del Valle DM, Kenigsberg E, Zhao S, Jaladanki S, Chaudhary K, Ascolillo S, Vaid A, Kumar A, Kozlova E, Paranjpe M, O’Hagan R, Kamat S, Gulamali FF, Kauffman J, Xie H, Harris J, Patel M, Argueta K, Batchelor C, Nie K, Dellepiane S, Scott L, Levin MA, He JC, Suarez-Farinas M, Coca SG, Chan L, Azeloglu EU, Schadt E, Beckmann N, Gnjatic S, Merad M, Kim-Schulze S, Richards B, Glicksberg BS, Charney AW, Nadkarni GN. Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.12.09.21267548. [PMID: 36093350 PMCID: PMC9460972 DOI: 10.1101/2021.12.09.21267548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Using measurements of ∼4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury. Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.
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Affiliation(s)
- Ishan Paranjpe
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Stanford University, San Francisco, California, United States of America
| | - Pushkala Jayaraman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Steven Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane Marie Del Valle
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shan Zhao
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Suraj Jaladanki
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumardeep Chaudhary
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Ascolillo
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akhil Vaid
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arvind Kumar
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Kozlova
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manish Paranjpe
- Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Ross O’Hagan
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samir Kamat
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Faris F. Gulamali
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Justin Kauffman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Stanford University, San Francisco, California, United States of America
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joceyln Harris
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Craig Batchelor
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergio Dellepiane
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Leisha Scott
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew A Levin
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - John Cijiang He
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mayte Suarez-Farinas
- Department of Biostatistics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Steven G Coca
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Lili Chan
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Evren U Azeloglu
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam Beckmann
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miram Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
| | - Benjamin S Glicksberg
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Girish N Nadkarni
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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Nucleic Acid Nanotechnology for Diagnostics and Therapeutics in Acute Kidney Injury. Int J Mol Sci 2022; 23:ijms23063093. [PMID: 35328515 PMCID: PMC8953740 DOI: 10.3390/ijms23063093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
Acute kidney injury (AKI) has impacted a heavy burden on global healthcare system with a high morbidity and mortality in both hospitalized and critically ill patients. However, there are still some shortcomings in clinical approaches for the disease to date, appealing for an earlier recognition and specific intervention to improve long-term outcomes. In the past decades, owing to the predictable base-pairing rule and highly modifiable characteristics, nucleic acids have already become significant biomaterials for nanostructure and nanodevice fabrication, which is known as nucleic acid nanotechnology. In particular, its excellent programmability and biocompatibility have further promoted its intersection with medical challenges. Lately, there have been an influx of research connecting nucleic acid nanotechnology with the clinical needs for renal diseases, especially AKI. In this review, we begin with the diagnostics of AKI based on nucleic acid nanotechnology with a highlight on aptamer- and probe-functionalized detection. Then, recently developed nanoscale nucleic acid therapeutics towards AKI will be fully elucidated. Furthermore, the strengths and limitations will be summarized, envisioning a wiser and wider application of nucleic acid nanotechnology in the future of AKI.
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10
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Diagnostic and Prognostic Protein Biomarkers of β-Cell Function in Type 2 Diabetes and Their Modulation with Glucose Normalization. Metabolites 2022; 12:metabo12030196. [PMID: 35323639 PMCID: PMC8950787 DOI: 10.3390/metabo12030196] [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: 01/17/2022] [Revised: 01/29/2022] [Accepted: 02/12/2022] [Indexed: 12/04/2022] Open
Abstract
Development of type-2 diabetes(T2D) is preceded by β-cell dysfunction and loss. However, accurate measurement of β-cell function remains elusive. Biomarkers have been reported to predict β-cell functional decline but require validation. Therefore, we determined whether reported protein biomarkers could distinguish patients with T2D (onset < 10-years) from controls. A prospective, parallel study in T2D (n = 23) and controls (n = 23) was undertaken. In T2D subjects, insulin-induced blood glucose normalization from baseline 7.6 ± 0.4 mmol/L (136.8 ± 7.2 mg/dL) to 4.5 ± 0.07 mmol/L (81 ± 1.2 mg/dL) was maintained for 1-h. Controls were maintained at 4.9 ± 0.1 mmol/L (88.2 ± 1.8 mg/dL). Slow Off-rate Modified Aptamer (SOMA) -scan plasma protein measurement determined a 43-protein panel reported as diagnostic and/or prognostic for T2D. At baseline, 9 proteins were altered in T2D. Three of 13 prognostic/diagnostic proteins were lower in T2D: Adiponectin (p < 0.0001), Endocan (p < 0.05) and Mast/stem cell growth factor receptor-Kit (KIT) (p < 0.01). Two of 14 prognostic proteins [Cathepsin-D (p < 0.05) and Cadherin-E (p < 0.005)], and four of 16 diagnostic proteins [Kallikrein-4 (p = 0.001), Aminoacylase-1 (p = 0.001), Insulin-like growth factor-binding protein-4 (IGFBP4) (p < 0.05) and Reticulon-4 receptor (RTN4R) (p < 0.001)] were higher in T2D. Protein levels were unchanged following glucose normalization in T2D. Our results suggest that a focused biomarker panel may be useful for assessing β-cell dysfunction and may complement clinical decision-making on insulin therapy. Unchanged post-glucose normalization levels indicate these are not acute-phase proteins or affected by glucose variability.
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11
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Serum metabolite profiles predict outcomes in critically ill patients receiving renal replacement therapy. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1187:123024. [PMID: 34815179 DOI: 10.1016/j.jchromb.2021.123024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/16/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022]
Abstract
Acute kidney injury (AKI) requiring renal replacement therapy (RRT) is associated with increased incidence of dialysis dependence and portends high mortality in critically ill patients. At the early stage of RRT, serum metabolic biomarkers might differntiate patients with a high risk of mortality or permanent kidney injury from those who can recover. Serum samples from participants enrolled in the Veteran's Affairs/National Institutes of Health Acute Renal Failure Trial Network study were collected on day 1 (n = 97) and day 8 (n = 105) of randomized RRT. The samples were further evaluated using LC/MS-based metabolic profiling. A model predicting mortality by day 8 was built from samples collected on day 1 and based on four metabolites with an area under the curve (AUC) of 0.641. A model most predictive of mortality by day 28 was built from the levels of 11 serum metabolites from day 8 with an AUC of 0.789. Both day 1 and day 8 samples had lower serum levels of 1-arachidonoyl-lysoPC and 1-eicosatetraenoyl-lysoPC (involved in anti-inflammatory processes) in the critically ill patients who died by day 8 or day 28. Higher levels of amino acids and amino acid metabolites in the day 8 model predicting < day 28 mortality may be indicative of muscle wasting. A kidney recovery biomarker panel based on the serum levels of three metabolites from day 8 samples with an AUC of 0.70 was devised. Serum metabolic profiling of AKI critically ill patients requiring RRT revealed predictive models of mortality based on observed differences in four serum metabolites at day 1 and 11 metabolites at day 8 which were predictive of mortality. Significant changes in the levels of these metabolites suggest links to inflammatory processes and/or muscle wasting.
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12
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Daniels JR, Ma JZ, Cao Z, Beger RD, Sun J, Schnackenberg L, Pence L, Choudhury D, Palevsky PM, Portilla D, Yu LR. Discovery of Novel Proteomic Biomarkers for the Prediction of Kidney Recovery from Dialysis-Dependent AKI Patients. KIDNEY360 2021; 2:1716-1727. [PMID: 34913041 PMCID: PMC8670726 DOI: 10.34067/kid.0002642021] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND AKI requiring dialysis (AKI-D) is associated with prolonged hospitalization, mortality, and progressive CKD among survivors. Previous studies have examined only select urine or serum biomarkers for predicting kidney recovery from AKI. METHODS Serum samples collected on day 8 of randomized RRT from 72 patients enrolled in the Veteran's Affairs/National Institutes of Health Acute Renal Failure Trial Network study were analyzed by the SOMAscan proteomic platform to profile 1305 proteins in each sample. Of these patients, 38 recovered kidney function and dialysis was discontinued, whereas another 34 patients remained on dialysis by day 28. RESULTS Differential serum levels of 119 proteins, with 53 higher and 66 lower, were detected in samples from patients who discontinued dialysis, compared with patients who remained on dialysis by day 28. Patients were classified into tertiles on the basis of SOMAscan protein measurements for the 25 proteins most differentially expressed. The association of serum levels of each protein with kidney recovery was further evaluated using logistic regression analysis. Higher serum levels of CXCL11, CXCL2/CXCL3, CD86, Wnt-7a, BTK, c-Myc, TIMP-3, CCL5, ghrelin, PDGF-C, survivin, CA2, IL-9, EGF, and neuregulin-1, and lower levels of soluble CXCL16, IL1RL1, stanniocalcin-1, IL-6, and FGF23 when classified in tertiles were significantly associated with better kidney recovery. This significant association persisted for each of these proteins after adjusting for potential confounding risk factors including age, sex, cardiovascular SOFA score, congestive heart failure, diabetes, modality of intensive dialysis treatment, cause of AKI, baseline serum creatinine, day 8 urine volume, and estimated 60-day mortality risk. CONCLUSIONS These results suggest concerted changes between survival-related proteins and immune-regulatory chemokines in regulating angiogenesis, endothelial and epithelial remodeling, and kidney cell regeneration, illustrating potential mechanisms of kidney recovery. Thus, this study identifies potential novel predictive biomarkers of kidney recovery in patients with AKI-D.
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Affiliation(s)
- Jaclyn R. Daniels
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Jennie Z. Ma
- Division of Biostatistics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia,Division of Nephrology, Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, Charlottesville, Virginia
| | - Zhijun Cao
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Richard D. Beger
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Laura Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Lisa Pence
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Devasmita Choudhury
- Division of Nephrology, Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, Charlottesville, Virginia,Salem Veterans Affairs Medical Center, Salem, Virginia
| | - Paul M. Palevsky
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania,Renal-Electrolye Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Didier Portilla
- Division of Nephrology, Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, Charlottesville, Virginia
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
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Huang J, Chen X, Fu X, Li Z, Huang Y, Liang C. Advances in Aptamer-Based Biomarker Discovery. Front Cell Dev Biol 2021; 9:659760. [PMID: 33796540 PMCID: PMC8007916 DOI: 10.3389/fcell.2021.659760] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The discovery and identification of biomarkers promote the rational and fast development of medical diagnosis and therapeutics. Clinically, the application of ideal biomarkers still is limited due to the suboptimal technology in biomarker discovery. Aptamers are single-stranded deoxyribonucleic acid or ribonucleic acid molecules and can selectively bind to varied targets with high affinity and specificity. Compared with antibody, aptamers have desirable advantages, such as flexible design, easy synthesis and convenient modification with different functional groups. Currently, different aptamer-based technologies have been developed to facilitate biomarker discovery, especially CELL-SELEX and SOMAScan technology. CELL-SELEX technology is mainly used to identify cell membrane surface biomarkers of various cells. SOMAScan technology is an unbiased biomarker detection method that can analyze numerous and even thousands of proteins in complex biological samples at the same time. It has now become a large-scale multi-protein biomarker discovery platform. In this review, we introduce the aptamer-based biomarker discovery technologies, and summarize and highlight the discovered emerging biomarkers recently in several diseases.
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Affiliation(s)
- Jie Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xinxin Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xuekun Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zheng Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Yuhong Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chao Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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Abstract
The rapid rise in circulating fibroblast growth factor 23 (FGF23) associated with kidney injury results in calcitriol deficiency, altered calcium homeostasis, and secondary hyperparathyroidism, and may contribute to cardiovascular complications and death. However, the mechanisms of increased FGF23 in states of kidney injury remain unclear. In this issue of the JCI, Simic et al. screened plasma taken from the renal vein of patients undergoing cardiac catheterization and identified glycerol-3-phosphate (G-3-P) as the most significant correlate of simultaneous arterial FGF23 levels. When G-3-P was administered to mice, FGF23 production increased in bone. In a series of elegant mouse studies, the authors discovered a pathway linking increased G-3-P to increased FGF23 via increases in lysophosphatidic acid (LPA), which activates the LPA receptor 1 in FGF23-secreting cells in the bone and bone marrow. Although the authors present human data that broadly support the results from the mouse models, further research is needed to determine whether targeting the G-3-P/FGF23 pathway has the potential to modify FGF23-related complications in the clinic.
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Affiliation(s)
| | - Myles Wolf
- Division of Nephrology, Department of Medicine, and.,Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
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15
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McConnell EM, Cozma I, Morrison D, Li Y. Biosensors Made of Synthetic Functional Nucleic Acids Toward Better Human Health. Anal Chem 2019; 92:327-344. [PMID: 31656066 DOI: 10.1021/acs.analchem.9b04868] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Ioana Cozma
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1.,Department of Surgery, Division of General Surgery , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Devon Morrison
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
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16
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Daniels JR, Cao Z, Maisha M, Schnackenberg LK, Sun J, Pence L, Schmitt TC, Kamlage B, Rogstad S, Beger RD, Yu LR. Stability of the Human Plasma Proteome to Pre-analytical Variability as Assessed by an Aptamer-Based Approach. J Proteome Res 2019; 18:3661-3670. [PMID: 31442052 DOI: 10.1021/acs.jproteome.9b00320] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Variable processing and storage of whole blood and/or plasma are potential confounders in biomarker development and clinical assays. The goal of the study was to investigate how pre-analytical variables impact the human plasma proteome. Whole blood obtained from 16 apparently healthy individuals was collected in six EDTA tubes and processed randomly under six pre-analytical variable conditions including blood storage at 0 °C or RT for 6 h (B6h0C or B6hRT) before processing to plasma, plasma storage at 4 °C or RT for 24 h (P24h4C or P24hRT), low centrifugal force at 1300 × g, (Low×g), and immediate processing to plasma under 2500 × g (control) followed by plasma storage at -80 °C. An aptamer-based proteomic assay was performed to identify significantly changed proteins (fold change ≥1.2, P < 0.05, and false discovery rate < 0.05) relative to the control from a total of 1305 proteins assayed. Pre-analytical conditions Low×g and B6h0C resulted in the most plasma proteome changes with 200 and 148 proteins significantly changed, respectively. Only 36 proteins were changed under B6hRT. Conditions P24h4C and P24hRT yielded changes of 28 and 75 proteins, respectively. The complement system was activated in vitro under the conditions B6hRT, P24h4C, and P24hRT. The results suggest that particular pre-analytical variables should be controlled for clinical measurement of specific biomarkers.
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Affiliation(s)
- Jaclyn R Daniels
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
| | - Zhijun Cao
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
| | - Mackean Maisha
- Division of Bioinformatics & Biostatistics , NCTR, FDA , Jefferson , Arkansas 72079 , United States
| | - Laura K Schnackenberg
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
| | - Jinchun Sun
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
| | - Lisa Pence
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
| | - Thomas C Schmitt
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
| | | | - Sarah Rogstad
- Center for Drug Evaluation and Research , FDA , Silver Spring , Maryland 20993 , United States
| | - Richard D Beger
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
| | - Li-Rong Yu
- Division of Systems Biology , National Center for Toxicological Research (NCTR) , U.S. Food and Drug Administration (FDA), Jefferson , Arkansas 72079 , United States
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17
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Ahmadi S, Rabiee N, Rabiee M. Application of Aptamer-based Hybrid Molecules in Early Diagnosis and Treatment of Diabetes Mellitus: From the Concepts Towards the Future. Curr Diabetes Rev 2019; 15:309-313. [PMID: 29875005 DOI: 10.2174/1573399814666180607075550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/23/2018] [Accepted: 06/03/2018] [Indexed: 02/07/2023]
Abstract
Aptamers have several positive advantages that made them eminent as a potential factor in diagnosing and treating diseases such as their application in prevention and treatment of diabetes. In this opinion-based mini-review article, we aimed to investigate the DNA and RNA-based hybrid molecules specifically aptamers and had a logical conclusion as a promising future perspective in early diagnosis and treatment of diabetes.
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Affiliation(s)
- Sepideh Ahmadi
- Department of Biology, Faculty of Basic Sciences, University of Zabol, Zabol, Iran
| | - Navid Rabiee
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Rabiee
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
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18
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Coca SG. "Scanning" into the Future: The Promise of SOMAScan Technology for Kidney Disease. Kidney Int Rep 2018; 3:1020-1022. [PMID: 30197965 PMCID: PMC6127447 DOI: 10.1016/j.ekir.2018.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Steven G. Coca
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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