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Frantzi M, Bhat A, Latosinska A. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med 2014; 3:7. [PMID: 24679154 PMCID: PMC3994249 DOI: 10.1186/2001-1326-3-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/06/2014] [Indexed: 12/11/2022] Open
Abstract
Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
| | - Akshay Bhat
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
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König S. Urine molecular profiling distinguishes health and disease: new methods in diagnostics? Focus on UPLC–MS. Expert Rev Mol Diagn 2014; 11:383-91. [DOI: 10.1586/erm.11.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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53
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Clinical applications of capillary electrophoresis coupled to mass spectrometry in biomarker discovery: Focus on bladder cancer. Proteomics Clin Appl 2013; 7:779-93. [DOI: 10.1002/prca.201300038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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54
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Stalmach A, Albalat A, Mullen W, Mischak H. Recent advances in capillary electrophoresis coupled to mass spectrometry for clinical proteomic applications. Electrophoresis 2013; 34:1452-64. [DOI: 10.1002/elps.201200708] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Angelique Stalmach
- Department of Proteomics and Systems Medicine; BHF Glasgow Cardiovascular Research Centre; Institute of Cardiovascular and Medical Sciences; College of Medical Veterinary and Life Sciences; University of Glasgow; Glasgow; UK
| | - Amaya Albalat
- Department of Proteomics and Systems Medicine; BHF Glasgow Cardiovascular Research Centre; Institute of Cardiovascular and Medical Sciences; College of Medical Veterinary and Life Sciences; University of Glasgow; Glasgow; UK
| | - William Mullen
- Department of Proteomics and Systems Medicine; 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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Roscioni SS, de Zeeuw D, Hellemons ME, Mischak H, Zürbig P, Bakker SJL, Gansevoort RT, Reinhard H, Persson F, Lajer M, Rossing P, Lambers Heerspink HJ. A urinary peptide biomarker set predicts worsening of albuminuria in type 2 diabetes mellitus. Diabetologia 2013; 56:259-67. [PMID: 23086559 DOI: 10.1007/s00125-012-2755-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/26/2012] [Indexed: 12/24/2022]
Abstract
AIMS/HYPOTHESIS Microalbuminuria is considered the first clinical sign of kidney dysfunction and is associated with a poor renal and cardiovascular prognosis in type 2 diabetes. Detection of patients who are prone to develop micro- or macroalbuminuria may represent an effective strategy to start or optimise therapeutic intervention. Here we assessed the value of a urinary proteomic-based risk score (classifier) in predicting the development and progression of microalbuminuria. METHODS We conducted a prospective case-control study. Cases (n = 44) and controls (n = 44) were selected from the PREVEND (Prevention of Renal and Vascular End-stage Disease) study and from the Steno Diabetes Center (Gentofte, Denmark). Cases were defined by transition from normo- to microalbuminuria or from micro- to macroalbuminuria over a follow-up of 3 years. Controls with no transitions in albuminuria were pair-matched for age, sex and albuminuria status. A model for the progression of albuminuria was built using a proteomic classifier based on 273 urinary peptides. RESULTS The proteomic classifier was independently associated with transition to micro- or macroalbuminuria (OR 1.35 [95% CI 1.02, 1.79], p = 0.035). The classifier predicted the development and progression of albuminuria on top of albuminuria and estimated GFR (eGFR, area under the receiver operating characteristic [ROC] curve increase of 0.03, p = 0.002; integrated discrimination index [IDI]: 0.105, p = 0.002). Fragments of collagen and α-2-HS-glycoprotein showed significantly different expression between cases and controls. CONCLUSIONS/INTERPRETATION Although limited by the relatively small sample size, these results suggest that analysis of a urinary biomarker set enables early renal risk assessment in patients with diabetes. Further work is required to confirm the role of urinary proteomics in the prevention of renal failure in diabetes.
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Affiliation(s)
- S S Roscioni
- Department of Clinical Pharmacology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, the Netherlands.
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Siwy J, Zoja C, Klein J, Benigni A, Mullen W, Mayer B, Mischak H, Jankowski J, Stevens R, Vlahou A, Kossida S, Perco P, Bahlmann FH. Evaluation of the Zucker diabetic fatty (ZDF) rat as a model for human disease based on urinary peptidomic profiles. PLoS One 2012; 7:e51334. [PMID: 23236474 PMCID: PMC3517416 DOI: 10.1371/journal.pone.0051334] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 11/07/2012] [Indexed: 01/31/2023] Open
Abstract
Representative animal models for diabetes-associated vascular complications are extremely relevant in assessing potential therapeutic drugs. While several rodent models for type 2 diabetes (T2D) are available, their relevance in recapitulating renal and cardiovascular features of diabetes in man is not entirely clear. Here we evaluate at the molecular level the similarity between Zucker diabetic fatty (ZDF) rats, as a model of T2D-associated vascular complications, and human disease by urinary proteome analysis. Urine analysis of ZDF rats at early and late stages of disease compared to age- matched LEAN rats identified 180 peptides as potentially associated with diabetes complications. Overlaps with human chronic kidney disease (CKD) and cardiovascular disease (CVD) biomarkers were observed, corresponding to proteins marking kidney damage (eg albumin, alpha-1 antitrypsin) or related to disease development (collagen). Concordance in regulation of these peptides in rats versus humans was more pronounced in the CVD compared to the CKD panels. In addition, disease-associated predicted protease activities in ZDF rats showed higher similarities to the predicted activities in human CVD. Based on urinary peptidomic analysis, the ZDF rat model displays similarity to human CVD but might not be the most appropriate model to display human CKD on a molecular level.
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Affiliation(s)
- Justyna Siwy
- Mosaiques Diagnostics, Hannover, Germany
- Charite- Universitaetsmedizin Berlin, Germany
| | - Carlamaria Zoja
- Mario Negri Institute for Pharmacological Research, Centro Anna Maria Astori, Bergamo, Italy
| | - Julie Klein
- School of Computer Science, University of Manchester, United Kingdom
| | - Ariela Benigni
- Mario Negri Institute for Pharmacological Research, Centro Anna Maria Astori, Bergamo, Italy
| | - Wiliam Mullen
- e BHF Glasgow Cardiovascular Research Centre, University of Glasgow, United Kingdom
| | - Bernd Mayer
- Emergentec Biodevelopment GmbH, Vienna, Austria
| | - Harald Mischak
- Mosaiques Diagnostics, Hannover, Germany
- e BHF Glasgow Cardiovascular Research Centre, University of Glasgow, United Kingdom
| | | | - Robert Stevens
- School of Computer Science, University of Manchester, United Kingdom
| | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens, Greece
| | - Sophia Kossida
- Biomedical Research Foundation, Academy of Athens, Greece
| | - Paul Perco
- Emergentec Biodevelopment GmbH, Vienna, Austria
| | - Ferdinand H. Bahlmann
- Department of Internal Medicine, Saarland University Hospital, Homburg, Germany
- * E-mail:
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Haselberg R, de Jong GJ, Somsen GW. CE-MS for the analysis of intact proteins 2010-2012. Electrophoresis 2012; 34:99-112. [DOI: 10.1002/elps.201200439] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/08/2012] [Accepted: 10/09/2012] [Indexed: 12/18/2022]
Affiliation(s)
- Rob Haselberg
- Biomolecular Analysis; Utrecht University; CG Utrecht; The Netherlands
| | | | - Govert W. Somsen
- Biomolecular Analysis; Utrecht University; CG Utrecht; The Netherlands
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Zürbig P, Jerums G, Hovind P, Macisaac RJ, Mischak H, Nielsen SE, Panagiotopoulos S, Persson F, Rossing P. Urinary proteomics for early diagnosis in diabetic nephropathy. Diabetes 2012; 61:3304-13. [PMID: 22872235 PMCID: PMC3501878 DOI: 10.2337/db12-0348] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diabetic nephropathy (DN) is a progressive kidney disease, a well-known complication of long-standing diabetes. DN is the most frequent reason for dialysis in many Western countries. Early detection may enable development of specific drugs and early initiation of therapy, thereby postponing/preventing the need for renal replacement therapy. We evaluated urinary proteome analysis as a tool for prediction of DN. Capillary electrophoresis-coupled mass spectrometry was used to profile the low-molecular weight proteome in urine. We examined urine samples from a longitudinal cohort of type 1 and 2 diabetic patients (n = 35) using a previously generated chronic kidney disease (CKD) biomarker classifier to assess peptides of collected urines for signs of DN. The application of this classifier to samples of normoalbuminuric subjects up to 5 years prior to development of macroalbuminuria enabled early detection of subsequent progression to macroalbuminuria (area under the curve [AUC] 0.93) compared with urinary albumin routinely used to determine the diagnosis (AUC 0.67). Statistical analysis of each urinary CKD biomarker depicted its regulation with respect to diagnosis of DN over time. Collagen fragments were prominent biomarkers 3-5 years before onset of macroalbuminuria. Before albumin excretion starts to increase, there is a decrease in collagen fragments. Urinary proteomics enables noninvasive assessment of DN risk at an early stage via determination of specific collagen fragments.
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Wei SY, Wang LF, Yang YH, Yeh HH, Chen YC, Chen SH. Sample stacking by field-amplified sample injection and sweeping for simultaneous analysis of acidic and basic components in clinic application. Electrophoresis 2012; 33:1571-81. [DOI: 10.1002/elps.201100716] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shao-Yun Wei
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung; Taiwan
| | - Li-Fang Wang
- Department of Medicinal and Applied Chemistry; Kaohsiung Medical University; Kaohsiung; Taiwan
| | - Yuan-Han Yang
- Department of Neurology; Kaohsiung Medical University Hospital; Kaohsiung; Taiwan
| | - Hsin-Hua Yeh
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung; Taiwan
| | - Yi-Chin Chen
- School of Nursing; College of Nursing; Kaohsiung Medical University; Kaohsiung; Taiwan
| | - Su-Hwei Chen
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung; Taiwan
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Shevalye H, Lupachyk S, Watcho P, Stavniichuk R, Khazim K, Abboud HE, Obrosova IG. Prediabetic nephropathy as an early consequence of the high-calorie/high-fat diet: relation to oxidative stress. Endocrinology 2012; 153:1152-61. [PMID: 22234462 PMCID: PMC3281531 DOI: 10.1210/en.2011-1997] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study evaluated early renal functional, structural, and biochemical changes in high-calorie/high-fat diet fed mice, a model of prediabetes and alimentary obesity. Male C57BL6/J mice were fed normal (11 kcal% fat) or high-fat (58 kcal% fat) diets for 16 wk. Renal changes were evaluated by histochemistry and immunohistochemistry, Western blot analysis, ELISA, enzymatic assays, and chemiluminometry. High-fat diet consumption led to increased body and kidney weights, impaired glucose tolerance, hyperinsulinemia, polyuria, a 2.7-fold increase in 24-h urinary albumin excretion, 20% increase in renal glomerular volume, 18% increase in renal collagen deposition, and 8% drop of glomerular podocytes. It also resulted in a 5.3-fold increase in urinary 8-isoprostane excretion and a 38% increase in renal cortex 4-hydroxynonenal adduct accumulation. 4-hydroxynonenal adduct level and immunoreactivity or Sirtuin 1 expression in renal medulla were not affected. Studies of potential mechanisms of the high-fat diet induced renal cortex oxidative injury revealed that whereas nicotinamide adenine dinucleotide phosphate reduced form oxidase activity only tended to increase, 12/15-lipoxygenase was significantly up-regulated, with approximately 12% increase in the enzyme protein expression and approximately 2-fold accumulation of 12(S)-hydroxyeicosatetraenoic acid, a marker of 12/15-lipoxygenase activity. Accumulation of periodic acid-Schiff -positive material, concentrations of TGF-β, sorbitol pathway intermediates, and expression of nephrin, CAAT/enhancer-binding protein homologous protein, phosphoeukaryotic initiation factor-α, and total eukaryotic initiation factor-α in the renal cortex were indistinguishable between experimental groups. Vascular endothelial growth factor concentrations were reduced in high-fat diet fed mice. In conclusion, systemic and renal cortex oxidative stress associated with 12/15-lipoxygenase overexpression and activation is an early phenomenon caused by high-calorie/high-fat diet consumption and a likely contributor to kidney disease associated with prediabetes and alimentary obesity.
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Affiliation(s)
- Hanna Shevalye
- Pennington Biomedical Research Center, Louisiana State University, 6400 Perkins Road, Baton Rouge, Louisiana 70808, USA
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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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Zürbig P, Dihazi H, Metzger J, Thongboonkerd V, Vlahou A. Urine proteomics in kidney and urogenital diseases: Moving towards clinical applications. Proteomics Clin Appl 2011; 5:256-68. [PMID: 21591267 DOI: 10.1002/prca.201000133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 03/04/2011] [Accepted: 03/09/2011] [Indexed: 12/14/2022]
Abstract
To date, multiple biomarker discovery studies in urine have been conducted. Nevertheless, the rate of progression of these biomarkers to qualification and even more clinical application is extremely low. The scope of this article is to provide an overview of main clinically relevant proteomic findings from urine focusing on kidney diseases, bladder and prostate cancers. In addition, approaches for promoting the use of urine in clinical proteomics including potential means to facilitate the validation of existing promising findings (biomarker candidates identified from previous studies) and to increase the chances for success for the identification of new biomarkers are discussed.
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Spasovski G, Ortiz A, Vanholder R, El Nahas M. Proteomics in chronic kidney disease: The issues clinical nephrologists need an answer for. Proteomics Clin Appl 2011; 5:233-40. [PMID: 21538916 DOI: 10.1002/prca.201000150] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 01/07/2011] [Accepted: 01/18/2011] [Indexed: 11/05/2022]
Abstract
A growing number of patients are recognised to have chronic kidney disease (CKD). However, only a minority will progress to end-stage renal disease requiring dialysis or transplantation. Currently available diagnostic and staging tools frequently fail to identify those at higher risk of progression or death. Furthermore within specific disease entities there are shortcomings in the prediction of the need for therapeutic interventions or the response to different forms of therapy. Kidney and urine proteomic biomarkers are considered as promising diagnostic tools to predict CKD progression early in diabetic nephropathy, facilitating timely and selective intervention that may reduce the related health-care expenditures. However, independent groups have not validated these findings and the technique is not currently available for routine clinical care. Furthermore, there are gaps in our understanding of predictors of progression or need for therapy in non-diabetic CKD. Presumably, a combination of tissue and urine biomarkers will be more informative than individual markers. This review identifies clinical questions in need of an answer, summarises current information on proteomic biomarkers and CKD, and describes the European Kidney and Urine Proteomics initiative that has been launched to carry out a clinical study aimed at identifying urinary proteomic biomarkers distinguishing between fast and slow progressors among patients with biopsy-proven primary glomerulopathies.
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Clinical proteomics: Current techniques and potential applications in the elderly. Maturitas 2011; 68:233-44. [DOI: 10.1016/j.maturitas.2010.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 10/29/2010] [Accepted: 11/01/2010] [Indexed: 02/01/2023]
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