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Garmaa G, Bunduc S, Kói T, Hegyi P, Csupor D, Ganbat D, Dembrovszky F, Meznerics FA, Nasirzadeh A, Barbagallo C, Kökény G. A Systematic Review and Meta-Analysis of microRNA Profiling Studies in Chronic Kidney Diseases. Noncoding RNA 2024; 10:30. [PMID: 38804362 PMCID: PMC11130806 DOI: 10.3390/ncrna10030030] [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: 04/08/2024] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024] Open
Abstract
Chronic kidney disease (CKD) represents an increasing health burden. Evidence suggests the importance of miRNA in diagnosing CKD, yet the reports are inconsistent. This study aimed to determine novel miRNA biomarkers and potential therapeutic targets from hypothesis-free miRNA profiling studies in human and murine CKDs. Comprehensive literature searches were conducted on five databases. Subgroup analyses of kidney diseases, sample types, disease stages, and species were conducted. A total of 38 human and 12 murine eligible studies were analyzed using Robust Rank Aggregation (RRA) and vote-counting analyses. Gene set enrichment analyses of miRNA signatures in each kidney disease were conducted using DIANA-miRPath v4.0 and MIENTURNET. As a result, top target genes, Gene Ontology terms, the interaction network between miRNA and target genes, and molecular pathways in each kidney disease were identified. According to vote-counting analysis, 145 miRNAs were dysregulated in human kidney diseases, and 32 were dysregulated in murine CKD models. By RRA, miR-26a-5p was significantly reduced in the kidney tissue of Lupus nephritis (LN), while miR-107 was decreased in LN patients' blood samples. In both species, epithelial-mesenchymal transition, Notch, mTOR signaling, apoptosis, G2/M checkpoint, and hypoxia were the most enriched pathways. These miRNA signatures and their target genes must be validated in large patient cohort studies.
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Affiliation(s)
- Gantsetseg Garmaa
- Institute of Translational Medicine, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary; (G.G.); (A.N.)
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Department of Pathology, School of Medicine, Mongolian National University of Medical Sciences, Ulan-Bator 14210, Mongolia;
| | - Stefania Bunduc
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Dionisie Lupu Street 37, 020021 Bucharest, Romania
- Fundeni Clinical Institute, Fundeni Street 258, 022328 Bucharest, Romania
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Baross út 22-24, 1085 Budapest, Hungary
| | - Tamás Kói
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Department of Stochastics, Institute of Mathematics, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Péter Hegyi
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Baross út 22-24, 1085 Budapest, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Dezső Csupor
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Institute for Translational Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary
- Institute of Clinical Pharmacy, University of Szeged, Szikra utca 8, 6725 Szeged, Hungary
| | - Dariimaa Ganbat
- Department of Pathology, School of Medicine, Mongolian National University of Medical Sciences, Ulan-Bator 14210, Mongolia;
- Department of Public Health, Graduate School of Medicine, International University of Health and Welfare, Tokyo 107-840, Japan
| | - Fanni Dembrovszky
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Baross út 22-24, 1085 Budapest, Hungary
| | - Fanni Adél Meznerics
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Mária utca 41, 1085 Budapest, Hungary
| | - Ailar Nasirzadeh
- Institute of Translational Medicine, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary; (G.G.); (A.N.)
| | - Cristina Barbagallo
- Section of Biology and Genetics “G. Sichel”, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy;
| | - Gábor Kökény
- Institute of Translational Medicine, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary; (G.G.); (A.N.)
- International Nephrology Research and Training Center, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary
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Non-Invasive Nasal Discharge Fluid and Other Body Fluid Biomarkers in Alzheimer’s Disease. Pharmaceutics 2022; 14:pharmaceutics14081532. [PMID: 35893788 PMCID: PMC9330777 DOI: 10.3390/pharmaceutics14081532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
The key to current Alzheimer’s disease (AD) therapy is the early diagnosis for prompt intervention, since available treatments only slow the disease progression. Therefore, this lack of promising therapies has called for diagnostic screening tests to identify those likely to develop full-blown AD. Recent AD diagnosis guidelines incorporated core biomarker analyses into criteria, including amyloid-β (Aβ), total-tau (T-tau), and phosphorylated tau (P-tau). Though effective, the accessibility of screening tests involving conventional cerebrospinal fluid (CSF)- and blood-based analyses is often hindered by the invasiveness and high cost. In an attempt to overcome these shortcomings, biomarker profiling research using non-invasive body fluid has shown the potential to capture the pathological changes in the patients’ bodies. These novel non-invasive body fluid biomarkers for AD have emerged as diagnostic and pathological targets. Here, we review the potential peripheral biomarkers, including non-invasive peripheral body fluids of nasal discharge, tear, saliva, and urine for AD.
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Abstract
The current unidimensional paradigm of kidney disease detection is incompatible with the complexity and heterogeneity of renal pathology. The diagnosis of kidney disease has largely focused on glomerular filtration, while assessment of kidney tubular health has notably been absent. Following insult, the kidney tubular cells undergo a cascade of cellular responses that result in the production and accumulation of low-molecular-weight proteins in the urine and systemic circulation. Modern advancements in molecular analysis and proteomics have allowed the identification and quantification of these proteins as biomarkers for assessing and characterizing kidney diseases. In this review, we highlight promising biomarkers of kidney tubular health that have strong underpinnings in the pathophysiology of kidney disease. These biomarkers have been applied to various specific clinical settings from the spectrum of acute to chronic kidney diseases, demonstrating the potential to improve patient care.
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Affiliation(s)
- William R Zhang
- Kidney Health Research Collaborative, University of California San Francisco School of Medicine, San Francisco, California 94121, USA
| | - Chirag R Parikh
- Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA;
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Yasmin H, Rahman MS, Shibata T. Facile and Selective Determination of Dipeptides Using 3-Methylcatechol as a Novel Fluorogenic Reagent. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-018-9703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lin L, Yu Q, Zheng J, Cai Z, Tian R. Fast quantitative urinary proteomic profiling workflow for biomarker discovery in kidney cancer. Clin Proteomics 2018; 15:42. [PMID: 30607141 PMCID: PMC6303996 DOI: 10.1186/s12014-018-9220-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/14/2018] [Indexed: 12/31/2022] Open
Abstract
Background Urine has evolved as a promising body fluids in clinical proteomics because it can be easily and noninvasively obtained and can reflect physiological and pathological status of the human body. Many efforts have been made to characterize more urinary proteins in recent years, but few have focused on the analysis throughput and detection reproducibility. Increasing the urine proteomic profiling throughput and reproducibility is urgently needed for discovering potential biomarker in large cohorts. Methods In this study, we developed a fast and robust workflow for streamlined urinary proteome analysis. The workflow integrate highly efficient sample preparation technique and urinary specific data-independent acquisition (DIA) approach. The performance of the workflow was systematically evaluated and the workflow was subsequently applied in a proof-of-concept urine proteome study of 21 kidney cancer (KC) patients and 22 healthy controls. Results With this workflow, the entire sample preparation process takes less than 3 h and allows multiplexing on standard centrifuges. Without pre-fractionation, our newly developed DIA method allows quantitative analysis of ~ 1000 proteins within 80 min of MS time (~ 15 samples/day). The quantitation accuracy of the whole workflow was excellent with median CV of 9.1%. The preliminary study on KC identified 125 significantly changed proteins. Conclusions The result suggested the feasibility of applying the high throughput workflow in extensive urinary proteome profiling and clinical relevant biomarker discovery. Electronic supplementary material The online version of this article (10.1186/s12014-018-9220-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lin Lin
- Materials Characterization and Preparation Center, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Quan Yu
- 2Division of Advanced Manufacturing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055 China
| | - Jiaxin Zheng
- 3Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361003 China
| | - Zonglong Cai
- 3Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361003 China
| | - Ruijun Tian
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055 China
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Urine: Waste product or biologically active tissue? Neurourol Urodyn 2018; 37:1162-1168. [PMID: 29464759 DOI: 10.1002/nau.23414] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/18/2017] [Indexed: 01/01/2023]
Abstract
AIMS Historically, urine has been viewed primarily as a waste product with little biological role in the overall health of an individual. Increasingly, data suggest that urine plays a role in human health beyond waste excretion. For example, urine might act as an irritant and contribute to symptoms through interaction with-and potential compromise of-the urothelium. METHODS To explore the concept that urine may be a vehicle for agents with potential or occult bioactivity and to discuss existing evidence and novel research questions that may yield insight into such a role, the National Institute of Diabetes and Digestive and Kidney Disease invited experts in the fields of comparative evolutionary physiology, basic science, nephrology, urology, pediatrics, metabolomics, and proteomics (among others) to a Urinology Think Tank meeting on February 9, 2015. RESULTS This report reflects ideas that evolved from this meeting and current literature, including the concept of urine quality, the biological, chemical, and physical characteristics of urine, including the microbiota, cells, exosomes, pH, metabolites, proteins, and specific gravity (among others). Additionally, the manuscript presents speculative, and hopefully testable, ideas about the functional roles of urine constituents in health and disease. CONCLUSION Moving forward, there are several questions that need further understanding and pursuit. There were suggestions to consider actively using various animal models and their biological specimens to elaborate on basic mechanistic information regarding human bladder dysfunction.
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Abstract
The urinary proteome is the focus of many studies due to the ease of urine collection and the relative proteome stability. Systems biology allows the combination of multiple omics studies, forming a link between proteomics, metabolomics, genomics and transcriptomics. In-depth data interpretation is achieved by bioinformatics analysis of -omics data sets. It is expected that the contribution of systems biology to the study of the urinary proteome will offer novel insights. The main focus of this review is on technical aspects of proteomics studies, available tools for systems biology analysis and the application of urinary proteomics in clinical studies and systems biology.
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Pontillo C, Filip S, Borràs DM, Mullen W, Vlahou A, Mischak H. CE-MS-based proteomics in biomarker discovery and clinical application. Proteomics Clin Appl 2015; 9:322-34. [DOI: 10.1002/prca.201400115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/10/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Claudia Pontillo
- Department of R&D; Mosaiques Diagnostics GmbH; Hanover Germany
- Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Szymon Filip
- Charité-Universitätsmedizin Berlin; Berlin Germany
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
| | - Daniel M. Borràs
- Department of R&D; ServiceXS; Leiden The Netherlands
- Institut National de la Santé et de la Recherche Médicale (INSERM); Institute of Cardiovascular and Metabolic Disease; Toulouse France
- Université Toulouse III Paul-Sabatier; Toulouse France
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
| | - Antonia Vlahou
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
- School of Biomedical and Healthcare Sciences; Plymouth University; Plymouth UK
| | - Harald Mischak
- Department of R&D; Mosaiques Diagnostics GmbH; Hanover Germany
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
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Dallas DC, Guerrero A, Parker EA, Robinson RC, Gan J, German JB, Barile D, Lebrilla CB. Current peptidomics: applications, purification, identification, quantification, and functional analysis. Proteomics 2015; 15:1026-38. [PMID: 25429922 PMCID: PMC4371869 DOI: 10.1002/pmic.201400310] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/24/2014] [Indexed: 12/28/2022]
Abstract
Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.
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Affiliation(s)
- David C. Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Evan A. Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Randall C. Robinson
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Junai Gan
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
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Lygirou V, Makridakis M, Vlahou A. Biological sample collection for clinical proteomics: existing SOPs. Methods Mol Biol 2015; 1243:3-27. [PMID: 25384737 DOI: 10.1007/978-1-4939-1872-0_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proteomic study of clinical samples aims at the better understanding of physiological and pathological conditions, as well as the discovery of diagnostic and prognostic markers for the latter. Quantitative and/or qualitative variations of body fluid proteome may reflect health- or disease-associated events connected to the adjacent or distant body regions of the fluid production/secretion/excretion and/or systemic reactions to the presence of disease. Sample collection and preparation is a critical step in order to obtain useful and valid information in clinical proteomics analysis. In this chapter, we present the current protocols and guidelines for human body fluid collection and storage, prior to proteomic analysis. A variety of body fluids that are currently being used in proteomic analysis and have potential interest in clinical practice are presented including blood plasma and serum, urine, cerebrospinal fluid, cerumen, nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma. With no doubt these body fluids differ in the extent of their application in clinical proteomics investigations, hence in some cases the presented SOPs are established following more extensive testing (e.g., plasma, serum, urine, CSF) than others (nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma). However, even in these latter cases, the presented protocols were reported by at least two independent groups according to the literature. We hope they can thus serve as a reliable guide for sample collection based on our current knowledge in the field and excellent starting points for proteomics investigators. It should also be pointed that variations to these protocols exist and their further refinement in the future is foreseen following the evolution of the proteomics technologies.
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Affiliation(s)
- Vasiliki Lygirou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece
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Soggiu A, Piras C, Bonizzi L, Hussein HA, Pisanu S, Roncada P. A discovery-phase urine proteomics investigation in type 1 diabetes. Acta Diabetol 2012; 49:453-64. [PMID: 22678621 DOI: 10.1007/s00592-012-0407-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/22/2012] [Indexed: 01/15/2023]
Abstract
Diabetes is a chronic metabolic disease which can lead to serious health problems particularly in and to the development of cardiovascular and renal complications. The aim of this study is to possibly identify distinctive molecular features in urine samples which might correlate to the progression and complications of type 1 diabetes. Diabetic patients with normo- and micro-albuminuria have been analyzed and compared to a group of control subjects. Urine proteins of control and type 1 diabetes subjects were investigated in their proteome profiles, using high-resolution two-dimensional gel electrophoresis separation and protein identifications by MALDI-TOF-MS and LC-MS/MS analysis. Proteomics analysis highlighted differential expression of several proteins between control and type 1 diabetes subjects. In particular, five proteins were found to be down-regulated and four proteins up-regulated. Lower protein representations in diabetic subjects were associated with Tamm-Horsfall urinary glycoprotein, apolipoprotein A-I, apolipoprotein E, α2-thiol proteinase inhibitor, and human complement regulatory protein CD59, while higher protein representations were found for α-1-microglobulin, zinc-α2 glycoprotein, α-1B glycoprotein, and retinol-binding protein 4. These differences were maintained comparing control subjects with type 1 diabetes normo-albuminuric and micro-albuminuric subjects. Furthermore, these proteins are correlated to glycosylated hemoglobin and microalbuminuria, confirming their role in diabetic pathology. This study gives new insights on potential molecular mechanisms associated with the complications of type 1 diabetic disease providing evidences of urine proteins potentially exploitable as putative prognostic biomarkers.
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Affiliation(s)
- A Soggiu
- Dipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria, Facoltà di Medicina Veterinaria, Università Degli Studi di Milano, Milan, Italy
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Mischak H, Ioannidis JPA, Argiles A, Attwood TK, Bongcam-Rudloff E, Broenstrup M, Charonis A, Chrousos GP, Delles C, Dominiczak A, Dylag T, Ehrich J, Egido J, Findeisen P, Jankowski J, Johnson RW, Julien BA, Lankisch T, Leung HY, Maahs D, Magni F, Manns MP, Manolis E, Mayer G, Navis G, Novak J, Ortiz A, Persson F, Peter K, Riese HH, Rossing P, Sattar N, Spasovski G, Thongboonkerd V, Vanholder R, Schanstra JP, Vlahou A. Implementation of proteomic biomarkers: making it work. Eur J Clin Invest 2012; 42:1027-36. [PMID: 22519700 PMCID: PMC3464367 DOI: 10.1111/j.1365-2362.2012.02674.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
While large numbers of proteomic biomarkers have been described, they are generally not implemented in medical practice. We have investigated the reasons for this shortcoming, focusing on hurdles downstream of biomarker verification, and describe major obstacles and possible solutions to ease valid biomarker implementation. Some of the problems lie in suboptimal biomarker discovery and validation, especially lack of validated platforms with well-described performance characteristics to support biomarker qualification. These issues have been acknowledged and are being addressed, raising the hope that valid biomarkers may start accumulating in the foreseeable future. However, successful biomarker discovery and qualification alone does not suffice for successful implementation. Additional challenges include, among others, limited access to appropriate specimens and insufficient funding, the need to validate new biomarker utility in interventional trials, and large communication gaps between the parties involved in implementation. To address this problem, we propose an implementation roadmap. The implementation effort needs to involve a wide variety of stakeholders (clinicians, statisticians, health economists, and representatives of patient groups, health insurance, pharmaceutical companies, biobanks, and regulatory agencies). Knowledgeable panels with adequate representation of all these stakeholders may facilitate biomarker evaluation and guide implementation for the specific context of use. This approach may avoid unwarranted delays or failure to implement potentially useful biomarkers, and may expedite meaningful contributions of the biomarker community to healthcare.
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Affiliation(s)
- Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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Abstract
PURPOSE OF REVIEW Urinary proteomics has emerged as an approach that could deliver relevant clinical information. In this review, we aim at highlighting the recent developments, especially with respect to clinical implementation. We review several of the recent publications reporting on larger cohorts, focusing on those that aim at qualification and/or validation of urinary proteomics biomarkers. RECENT FINDINGS Several components of the urinary proteome, especially its low molecular weight fraction (sometimes referred to as the 'peptidome'), have been significantly associated with chronic kidney disease (CKD). Independent studies, encompassing sometimes close to 1000 independent samples, indicate that specific peptides from extracellular matrix (ECM) proteins encompass a major component of the urinary proteome. Highly significant changes in the abundance of some of these peptides are associated with CKD indicating that alterations in ECM, reflected via the urinary proteome, may represent an early stage in CKD pathology. These peptides may serve as specific early biomarkers, and interference with pathological ECM accumulation may be a valuable new therapeutic approach in CKD. SUMMARY Urinary proteomic biomarkers have emerged as clinically relevant variables. First studies involving several hundred individuals indicate a potential added benefit of urinary proteomic biomarkers. First large clinical trials are being initiated to employ urinary proteomics in clinical decision making.
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“Cheek-to-cheek” urinary proteome profiling via combinatorial peptide ligand libraries: A novel, unexpected elution system. J Proteomics 2012; 75:796-805. [DOI: 10.1016/j.jprot.2011.09.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/15/2011] [Accepted: 09/23/2011] [Indexed: 11/24/2022]
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