ArticleProteomics. Clinical applications2012
Application of systems biology principles to protein biomarker discovery: urinary exosomal proteome in renal transplantation.
Article in Proteomics. Clinical applications, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 56 citations in OpenAlex.
- Urinary Extracellular Vesicles Are a Novel Tool to Monitor Allograft Function in Kidney Transplantation: A Systematic Review.International journal of molecular sciences · 2021Pooled it
- Molecular immune monitoring in kidney transplant rejection: a state-of-the-art review.Frontiers in immunology · 2023Review
- Proteomics for Biomarker Discovery for Diagnosis and Prognosis of Kidney Transplantation Rejection.Proteomes · 2022Review
- Exosomal proteomics in kidney disease: From technical approaches to clinical applications.Journal of food and drug analysis · 2022Review
- Exosome Carrier Effects; Resistance to Digestion in Phagolysosomes May Assist Transfers to Targeted Cells; II Transfers of miRNAs Are Better Analyzed via Systems Approach as They Do Not Fit Conventional Reductionist Stoichiometric Concepts.International journal of molecular sciences · 2022Review
- Extracellular Vesicles in Transplantation.Frontiers in immunology · 2022Review
- Experimental and Biological Insights from Proteomic Analyses of Extracellular Vesicle Cargos in Normalcy and Disease.Advanced biosystems · 2020Review
- Exosomes in Nephropathies: A Rich Source of Novel Biomarkers.Disease markers · 2020Review
- An Update on Isolation Methods for Proteomic Studies of Extracellular Vesicles in Biofluids.Molecules (Basel, Switzerland) · 2019Review
- Exosomes and microvesicles in normal physiology, pathophysiology, and renal diseases.Pediatric nephrology (Berlin, Germany) · 2019Review
- GCN5L1 interacts with αTAT1 and RanBP2 to regulate hepatic α-tubulin acetylation and lysosome trafficking.Journal of cell science · 2018Article
- Extracellular vesicles in renal disease.Nature reviews. Nephrology · 2017Review
- Renal extracellular vesicles: from physiology to clinical application.The Journal of physiology · 2016Review
- Proteomics of Urinary Vesicles Links Plakins and Complement to Polycystic Kidney Disease.Journal of the American Society of Nephrology : JASN · 2016Article
- Proteomics for rejection diagnosis in renal transplant patients: Where are we now?World journal of transplantation · 2016Review
- Extracellular Vesicles in Renal Diseases: More than Novel Biomarkers?Journal of the American Society of Nephrology : JASN · 2016Review
- Proteomics of ovarian cancer: functional insights and clinical applications.Cancer metastasis reviews · 2015Review
- A modified precipitation method to isolate urinary exosomes.Journal of visualized experiments : JoVE · 2015Article
- Proteomic analysis of proteins surrounding occludin and claudin-4 reveals their proximity to signaling and trafficking networks.PloS one · 2015Article
- Biotin ligase tagging identifies proteins proximal to E-cadherin, including lipoma preferred partner, a regulator of epithelial cell-cell and cell-substrate adhesion.Journal of cell science · 2014Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
purposeIn mass spectrometry (MS)-based studies to discover urinary protein biomarkers, an important question is how to analyze the data to find the most promising potential biomarkers to be advanced to large-scale validation studies. Here, we describe a "systems biology-based" approach to address this question. EXPERIMENTAL
designWe analyzed large-scale liquid chromatography-tandem mass spectrometry (LC-MS/MS) data of urinary exosomes from renal allograft recipients with biopsy-proven evidence of immunological rejection or tubular injury (TI). We asked whether bioinformatic analysis of urinary exosomal proteins can identify biological-process based protein groups that correlate with biopsy findings and whether the protein groups fit with general knowledge of the pathophysiological mechanisms involved.
resultsLC-MS/MS analysis of urinary exosomal proteomes identified more than 1000 proteins in each pathologic group. These protein lists were analyzed computationally to identify the Biological Process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway terms that are significantly associated with each pathological group. Among the most informative terms for each group were: "sodium ion transport" for TI; "immune response" for all rejection; "epithelial cell differentiation" for cell-mediated rejection; and "acute inflammatory response" for antibody-mediated rejection. Based on these terms, candidate biomarkers were identified using a novel strategy to allow a dichotomous classification between different pathologic categories. CONCLUSIONS AND CLINICAL RELEVANCE: The terms and candidate biomarkers identified make rational connections to pathophysiological mechanisms, suggesting that the described bioinformatic approach will be useful in advancing large-scale biomarker identification studies toward a validation phase.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.